Anatrack Ranges Support - User contributions [en]

Modelling Analysis

2014-12-11T19:08:35Z

RobertKenward: /* Kaplan-Meier Survival */

When Ranges 4 was launched in 1990, individual-based modelling of animal populations was in its infancy. However, it was becoming clear that not only was such modelling powerful for predicting population beyond the envelope of conditions in which individuals were measured, but also that radio-tracking could provide the linkages of habitats and sociality with persistence or dispersal, and survival and productivity, that would be needed for modelling. So the provision of a toolkit for modelling was a long-term aspiration for this type of software [[Bibliography|(Kenward 1992)]].

== Introduction ==

The initial contribution to modelling is a new approach to analysing resources, such as habitats, which can estimate minimal requirements of individual animals and hence enable individual-based modelling. There is also a method for estimating survival or dispersal rates that is convenient for data from radio-tagging. There are illustrated explanations of both methods in ([[Bibliography|Kenward 2001]]). Further components of a toolkit for modelling will be added to this tab in due course, with the ultimate aspiration of linking these in order to automate population modelling from location data and maps.

== Resource Area Dependence Analysis ==

The principle that underlies this analysis is that if an animal requires a particular amount of a resource, such as a particular tree or area of habitat, then it will extend its home-range to an extent necessary to contain than amount of resource. If the resource is rarer, range outlines will be larger. In this case, there will be a negative relationship between range area and resource content. For strong resource dependence, the relationship tends to become negative exponential ([[Bibliography|Kenward 1982]]), but is linear with negative correlation if the logarithm of resource content is plotted against the logarithm of range area. Moreover, the range area at a point where the resource proportion is 1 is an estimate of the minimum area of resource required.

Another important consideration is that a single patch of habitat enclosed within range outlines of varying size will show a negative relationship of proportion with area by chance. To avoid misinterpretation of random events, the significance of observed correlations should be compared with random range placement in the same areas. In the case of a single resource, its occurrence significantly more frequently in observed ranges than in random placements may be the best indication of its importance.

This analysis requires an edge file and a habitat file. Suitable example files are in the folder squirrel, as described for [[Habitat#sources|habitat analysis]].

=== analysis options ===

For a rapid examination of whether the prevalence of any of the habitats in a set correlate negatively with range size, analysis of observed values only is appropriate. The statistics available from such are run are the observed value of r, the slope b for the regression of (log) habitat prevalence on (log) range area, the standard error of b, the (log) area intercept c for 100% habitat, the percentage of ranges with no habitat at all in the core, and the percentage with none of the habitat in a particular row. On the graph, the green regression line is for the observed values.

To investigate significance, randomisations are available with 99, 199 and 999 iterations. During randomisation, outlines of all the observed ranges are randomly rotated and displaced within an envelope. By default, that envelope is the minimum convex polygon round all observed outlines for the largest core size among a set of core sizes. N outlines are chosen at random with replacement from the N observed outlines, and an r, b and c calculated in each case.

Statistics from randomisations include the mean and median values for r by randomisation, z for the difference of this r from the observedr, with associated 95% confidence limits, on the assumption that r is distributed normally. The next value is a more robust test statistic, which is the number of random r values more extremely negative than the observed value. In a two-tailed test, with 999 iterations, a value less than 25 indicates P<0.05, with 5 or less for P<=0.01 and 0 for P<=0.02. There are then mean values for b, its SE and c by randomisation, which are used to plot the yellow line on the graph, and finally the proportion of random placements of the range outlines that lack the relevant habitat. Percentages below the observed percentage of ranges without the habitat indicate non-random placement of observed range outlines with respect to that habitat.

=== zero handling ===

Animals may differ in their use of resources. Some may specialise in a quite different resource to the majority, either through choice or exclusion, so that it does not occur in their range. Excluded animals may have above average range size, in which case addition of a value below other values (which is done automatically for the replace zeros option), will tend to maintain negative correlations. However, if resource strategy is divergent, inclusion of missing (or very low) proportions of the resource may conceal a major effect. At present, a choice of excluding missing values is possible, with two options; resample zeros to obtain resource within all outlines is appropriate if it is suspected that large ranges are more likely to include habitat by chance; otherwise the ignore zeros option will give very similar results but will be faster and will estimate the proportion of randomly-placed outlines that lack the resource. When there are very low values of resource in some observed ranges, it may in future be possible to exclude these objectively as statistical outliers and then examine these ranges for different resource area dependence relationships.

=== exclude habitats ===

As in analyses of habitat preference, disproportionate use of one relatively abundant resource can conceal a dependence also on one or more uncommon resources. This effect can be avoided by removing the area of the first resource from the range and then re-analysing for the second, in a step-wise approach. Resource exclusion of this type is supported in Ranges 9. The Ctrl key can be held to select multiple habitats to exclude, and is also required to remove previous selections.

=== envelope ===

The default envelope, mcp around max edge file core may allow very little rotation and displacement of large ranges in a small area, which can greatly slow analyses. If resources have a wide distribution, a larger user defined envelope may be used to speed the randomisation, at least for a first quick test, by loading the envelope separately. This is also useful if analysis is focussed in small cores (say, 50% cluster cores), but a polygon around all the locations is being used to standardise the envelope.

== Kaplan-Meier Survival ==

The Kaplan-Meier approach ([[Bibliography|Kaplan & Meier 1958]]), as described for radio-tracking by [[Bibliography|Pollock et al. (1989)]], is provided as a first survival estimation technique. Its interval-based estimation procedure adapts well to the asynchronous (staggered) entries and departures for unknown reasons that are typical for groups of radio-tagged animals.

Example data are in the folder goshawk from 205 first year goshawks that were tagged in or near their natal nests (Juv_Male.srv and Juv_Female.srv.

=== analysis options ===

Choice of one set will run an analysis on one survival file, with a plot that includes error bars for 95% confidence limits based on [[Bibliography|Cox-Oakes (1984)]] variance estimation. The statistics include, for each time interval in the analysis, the number of animals with active tags at the beginning and end of the interval, the number that died, had lost signals for unexplained reasons, were known to have lived through expiry of tag (e.g. due to battery exhaustion) or were added through tag attachment. There is then an estimate of the survival with two types of 95% confidence limits, and the survival decrease since the last period. The numbers in each category are summed at the bottom of the table, with a count of the total number of active tag-days. If the statistics file is saved, it can be opening in Excel or other spreadsheet for .csv files. The .kms graphics file can be opened at a later date in the graphics window.

Choice of two sets for comparison will run two plots as above, but also estimate statistics for the comparison between the survival rates. These are log-rank chi-square statistics with one degree of freedom, estimated in progressively more conservative ways, on the penultimate row of the table, and a comparison (see [[Bibliography|Pollock et al. (1989)]] and [[Bibliography|Kenward (2001)]] for further details. The two-sets option enables re-entry of the same file as for the first set, using a second '''[[Selections|Make Selections]]''' button and box to choose a different category of animal (e.g. adult rather than juvenile) within the file.

=== time interval ===

The length of time intervals for analysis should be great enough to provide opportunity for a number of deaths, but not too long to detect seasonal differences in timing of mortality. A choice of days rather than one month will bring up a box in which the number of days for each interval can be entered. Typically, monthly intervals are selected unless the period to be analysed is less than about 3 months.

=== set 1 start date ===

Although the default is the first animal start date, this often starts the analysis with too few animals in the first time interval; there should ideally be at least 20, because otherwise the confidence limits will be very large, with a tendency for differences between categories to lack significance. Even when many animals are marked within a short time, there may be a need to delay the start of analysis to exclude animals with possible adversely affects of capture or considered more vulnerable while adjusting to tags. Selecting specified date will bring up a calendar to assist the choice of date.

=== set 1 end date ===

The default of last animal end date will often result in very few individuals in the last sample interval, and hence undesirably large confidence limits. It is therefore possible either to set a specified date with a calendar, or to give a duration in days for the analysis.
=== set 2 start date and end date ===

For a comparison run, two further option boxes appear. For cases where the time period for comparison is the same in both files, or categories within the same file, it is convenient to be able to choose set 1 start date and set 1 end date, as well as having other options similar to those for the first set of data.

=== treat lost as dead ===

When carcases are found, the category of died is not hard to assign in survival files. Likewise, when tracking is stopped at a particular date, or tag cell is due to expire the fate category lived can be assigned. However, a problem arises when tracking animals for which deaths are frequently associated with destruction of the radio (e.g. through trauma) or severe loss of signal range or transport of the carcase away from a monitored area. In this case, survival is overestimated by the default of treating the lost signals as tag failure. For conservative estimates of survival during population modelling, it may be most appropriate to treat signals lost before the likely end of tag cell life as if they represent deaths, by ticking this box. The difference in survival estimated by merely censoring the radios will not be large if radios are highly reliable. Correction for“lost” animals that are subsequently retrapped or resighted after the study period can involve reclassifying their fate as lived; more sophisticated correction from such data ([[Bibliography|Kenward 2001]]) will be added in due course.

Tutorial

2014-12-11T19:06:35Z

RobertKenward: /* Kaplan Meier Survival Analysis */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:Location analysis7.png|thumb|right|upright=1.6|Cluster analysis with objective cores.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

 
 
 
 
 
 

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:Modelling_analysis1.png|thumb|right|upright=1.6|Plotting observed data only.]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:Modelling_analysis2.png|thumb|right|upright=1.6|Comparing observed and random data.]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

==== Plotting survival for a single data set ====

[[File:Modelling_analysis3.png|thumb|right|upright=1.6|Plotting survival for a single data set.]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''kaplan meier survival''.

* Under '''Analysis Options''' ensure ''one set'' is selected

* Under '''Input files''' press '''browse''' and find, for the ''set 1 survival file'' the file ''<RangesFolder>\samples\goshawk\Juv_Male.srv''.

* Press the '''Run Analysis''' button.

Looking at the statistics window, the sample size was not adequate until the start of the second month, and became less than 30 animals due to moulting of tail-mounted radio tags after 30 April. Run the analysis again, selecting as '''set 1 start date''' the ''specified date'' and use the calendar to select 1 July 1980 (around the fledging date), then in '''set 1 end date''' again select ''specified date'' and set 31 March 1981. This estimates juvenile male survival to the start of the next egg-laying period, as used in [[Bibliography|Kenward et al. (1999)]].

==== Comparing two sets of survival data ====

[[File:Modelling_analysis4.png|thumb|right|upright=1.6|Comparing two sets of survival data .]]

* Under '''Analysis Options''' select ''two sets for comparison''

* Under '''Input files''' check that the ''set 1 survival file'' is still ''<RangesFolder>\samples\goshawk\Juv_Male.srv''.

* Check that '''set 1 start date''' has ''specified date'' selected, of 1 July 1980.

* Check that '''set 1 end date''' has ''specified date'' selected, of 31 March 1981.

* Press '''browse''' for the ''set 2 survival file'' and find ''<RangesFolder>\samples\goshawk\Juv_Female.srv''.

* For the '''set 2 start date''', use the ''set 1 start date'' option.

* For the '''set 2 end date''', use the ''set 2 end date'' option.

* Press the '''Run Analysis''' button.

The survival is poorer for juvenile males than for juvenile females due mainly to differences from October (month 4) onwards. The ''z'' values of 2.07 to 2.13 are higher than the value of 1.96 for alpha = 0.05, so ''P'' < 0.05.

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward (2001), Kenward et al. (2001)]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls & Kenward 1995, 1998, 2001]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission. Goshawk survival data were collected on the Swedish island of Gotland ([[Bibliography|Kenward et al. 1993, 1999]]); the natal year of all fledged cohorts has been set to 1980 in the example files.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel, buzzard and goshawk data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology), in the last case in cooperation with Uppsala University and the Swedish Hunters' Association. The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-12-11T17:54:56Z

RobertKenward: /* Kaplan Meier Survival Analysis */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

==== Plotting survival for a single data set ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''kaplan meier survival''.

* Under '''Analysis Options''' ensure ''one set'' is selected

* Under '''Input files''' press '''browse''' and find, for the ''set 1 survival file'' the file ''<RangesFolder>\samples\goshawk\GoshawkJuvMale.srv''.

* Press the '''Run Analysis''' button.

Looking at the statistics window, the sample size was not adequate until the start of the second month, and became less than 30 animals due to moulting of tail-mounted radio tags after 30 April. Run the analysis again, selecting as '''set 1 start date''' the ''specified date'' and use the calendar to select 1 July 1980 (around the fledging date), then in '''set 1 end date''' again select ''specified date'' and set 31 March 1981. This estimates juvenile male survival to the start of the next egg-laying period, as used in [[Bibliography|Kenward et al. (1999)]].

==== Comparing two sets of survival data ====

[[File:To be added]]

* Under '''Analysis Options''' select ''two sets for comparison''

* Under '''Input files''' check that the ''set 1 survival file'' is still ''<RangesFolder>\samples\goshawk\GoshawkJuvMale.srv''.

* Check that '''set 1 start date''' has ''specified date'' selected, of 1 July 1980.

* Check that '''set 1 end date''' has ''specified date'' selected, of 31 March 1981.

* Press '''browse''' for the ''set 2 survival file'' and find ''<RangesFolder>\samples\goshawk\GoshawkJuvFem.srv''.

* For the '''set 2 start date''', use the ''set 1 start date'' option.

* For the '''set 2 end date''', use the ''set 2 end date'' option.

* Press the '''Run Analysis''' button.

The survival is poorer for juvenile males than for juvenile females due mainly to differences from October (month 4) onwards. The ''z'' values of 2.07 to 2.13 are higher than the value of 1.96 for alpha = 0.05, so ''P'' < 0.05.

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward (2001), Kenward et al. (2001)]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls & Kenward 1995, 1998, 2001]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission. Goshawk survival data were collected on the Swedish island of Gotland ([[Bibliography|Kenward et al. 1993, 1999]]); the natal year of all fledged cohorts has been set to 1980 in the example files.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel, buzzard and goshawk data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology), in the last case in cooperation with Uppsala University and the Swedish Hunters' Association. The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Modelling Analysis

2014-12-11T13:25:19Z

RobertKenward: /* Kaplan-Meier Survival */

When Ranges 4 was launched in 1990, individual-based modelling of animal populations was in its infancy. However, it was becoming clear that not only was such modelling powerful for predicting population beyond the envelope of conditions in which individuals were measured, but also that radio-tracking could provide the linkages of habitats and sociality with persistence or dispersal, and survival and productivity, that would be needed for modelling. So the provision of a toolkit for modelling was a long-term aspiration for this type of software [[Bibliography|(Kenward 1992)]].

== Introduction ==

The initial contribution to modelling is a new approach to analysing resources, such as habitats, which can estimate minimal requirements of individual animals and hence enable individual-based modelling. There is also a method for estimating survival or dispersal rates that is convenient for data from radio-tagging. There are illustrated explanations of both methods in ([[Bibliography|Kenward 2001]]). Further components of a toolkit for modelling will be added to this tab in due course, with the ultimate aspiration of linking these in order to automate population modelling from location data and maps.

== Resource Area Dependence Analysis ==

The principle that underlies this analysis is that if an animal requires a particular amount of a resource, such as a particular tree or area of habitat, then it will extend its home-range to an extent necessary to contain than amount of resource. If the resource is rarer, range outlines will be larger. In this case, there will be a negative relationship between range area and resource content. For strong resource dependence, the relationship tends to become negative exponential ([[Bibliography|Kenward 1982]]), but is linear with negative correlation if the logarithm of resource content is plotted against the logarithm of range area. Moreover, the range area at a point where the resource proportion is 1 is an estimate of the minimum area of resource required.

Another important consideration is that a single patch of habitat enclosed within range outlines of varying size will show a negative relationship of proportion with area by chance. To avoid misinterpretation of random events, the significance of observed correlations should be compared with random range placement in the same areas. In the case of a single resource, its occurrence significantly more frequently in observed ranges than in random placements may be the best indication of its importance.

This analysis requires an edge file and a habitat file. Suitable example files are in the folder squirrel, as described for [[Habitat#sources|habitat analysis]].

=== analysis options ===

For a rapid examination of whether the prevalence of any of the habitats in a set correlate negatively with range size, analysis of observed values only is appropriate. The statistics available from such are run are the observed value of r, the slope b for the regression of (log) habitat prevalence on (log) range area, the standard error of b, the (log) area intercept c for 100% habitat, the percentage of ranges with no habitat at all in the core, and the percentage with none of the habitat in a particular row. On the graph, the green regression line is for the observed values.

To investigate significance, randomisations are available with 99, 199 and 999 iterations. During randomisation, outlines of all the observed ranges are randomly rotated and displaced within an envelope. By default, that envelope is the minimum convex polygon round all observed outlines for the largest core size among a set of core sizes. N outlines are chosen at random with replacement from the N observed outlines, and an r, b and c calculated in each case.

Statistics from randomisations include the mean and median values for r by randomisation, z for the difference of this r from the observedr, with associated 95% confidence limits, on the assumption that r is distributed normally. The next value is a more robust test statistic, which is the number of random r values more extremely negative than the observed value. In a two-tailed test, with 999 iterations, a value less than 25 indicates P<0.05, with 5 or less for P<=0.01 and 0 for P<=0.02. There are then mean values for b, its SE and c by randomisation, which are used to plot the yellow line on the graph, and finally the proportion of random placements of the range outlines that lack the relevant habitat. Percentages below the observed percentage of ranges without the habitat indicate non-random placement of observed range outlines with respect to that habitat.

=== zero handling ===

Animals may differ in their use of resources. Some may specialise in a quite different resource to the majority, either through choice or exclusion, so that it does not occur in their range. Excluded animals may have above average range size, in which case addition of a value below other values (which is done automatically for the replace zeros option), will tend to maintain negative correlations. However, if resource strategy is divergent, inclusion of missing (or very low) proportions of the resource may conceal a major effect. At present, a choice of excluding missing values is possible, with two options; resample zeros to obtain resource within all outlines is appropriate if it is suspected that large ranges are more likely to include habitat by chance; otherwise the ignore zeros option will give very similar results but will be faster and will estimate the proportion of randomly-placed outlines that lack the resource. When there are very low values of resource in some observed ranges, it may in future be possible to exclude these objectively as statistical outliers and then examine these ranges for different resource area dependence relationships.

=== exclude habitats ===

As in analyses of habitat preference, disproportionate use of one relatively abundant resource can conceal a dependence also on one or more uncommon resources. This effect can be avoided by removing the area of the first resource from the range and then re-analysing for the second, in a step-wise approach. Resource exclusion of this type is supported in Ranges 9. The Ctrl key can be held to select multiple habitats to exclude, and is also required to remove previous selections.

=== envelope ===

The default envelope, mcp around max edge file core may allow very little rotation and displacement of large ranges in a small area, which can greatly slow analyses. If resources have a wide distribution, a larger user defined envelope may be used to speed the randomisation, at least for a first quick test, by loading the envelope separately. This is also useful if analysis is focussed in small cores (say, 50% cluster cores), but a polygon around all the locations is being used to standardise the envelope.

== Kaplan-Meier Survival ==

The Kaplan-Meier approach ([[Bibliography|Kaplan & Meier 1958]]), as described for radio-tracking by [[Bibliography|Pollock et al. (1989)]], is provided as a first survival estimation technique. Its interval-based estimation procedure adapts well to the asynchronous (staggered) entries and departures for unknown reasons that are typical for groups of radio-tagged animals.

Example data are in the folder raptors) from 205 first year goshawks that were tagged in or near their natal nests (GoshawkJuvMale.srv and GoshawkJuvFem.srv.

=== analysis options ===

Choice of one set will run an analysis on one survival file, with a plot that includes error bars for 95% confidence limits based on [[Bibliography|Cox-Oakes (1984)]] variance estimation. The statistics include, for each time interval in the analysis, the number of animals with active tags at the beginning and end of the interval, the number that died, had lost signals for unexplained reasons, were known to have lived through expiry of tag (e.g. due to battery exhaustion) or were added through tag attachment. There is then an estimate of the survival with two types of 95% confidence limits, and the survival decrease since the last period. The numbers in each category are summed at the bottom of the table, with a count of the total number of active tag-days. If the statistics file is saved, it can be opening in Excel or other spreadsheet for .csv files. The .kms graphics file can be opened at a later date in the graphics window.

Choice of two sets for comparison will run two plots as above, but also estimate statistics for the comparison between the survival rates. These are log-rank chi-square statistics with one degree of freedom, estimated in progressively more conservative ways, on the penultimate row of the table, and a comparison (see [[Bibliography|Pollock et al. (1989)]] and [[Bibliography|Kenward (2001)]] for further details. The two-sets option enables re-entry of the same file as for the first set, using a second '''[[Selections|Make Selections]]''' button and box to choose a different category of animal (e.g. adult rather than juvenile) within the file.

=== time interval ===

The length of time intervals for analysis should be great enough to provide opportunity for a number of deaths, but not too long to detect seasonal differences in timing of mortality. A choice of days rather than one month will bring up a box in which the number of days for each interval can be entered. Typically, monthly intervals are selected unless the period to be analysed is less than about 3 months.

=== set 1 start date ===

Although the default is the first animal start date, this often starts the analysis with too few animals in the first time interval; there should ideally be at least 20, because otherwise the confidence limits will be very large, with a tendency for differences between categories to lack significance. Even when many animals are marked within a short time, there may be a need to delay the start of analysis to exclude animals with possible adversely affects of capture or considered more vulnerable while adjusting to tags. Selecting specified date will bring up a calendar to assist the choice of date.

=== set 1 end date ===

The default of last animal end date will often result in very few individuals in the last sample interval, and hence undesirably large confidence limits. It is therefore possible either to set a specified date with a calendar, or to give a duration in days for the analysis.
=== set 2 start date and end date ===

For a comparison run, two further option boxes appear. For cases where the time period for comparison is the same in both files, or categories within the same file, it is convenient to be able to choose set 1 start date and set 1 end date, as well as having other options similar to those for the first set of data.

=== treat lost as dead ===

When carcases are found, the category of died is not hard to assign in survival files. Likewise, when tracking is stopped at a particular date, or tag cell is due to expire the fate category lived can be assigned. However, a problem arises when tracking animals for which deaths are frequently associated with destruction of the radio (e.g. through trauma) or severe loss of signal range or transport of the carcase away from a monitored area. In this case, survival is overestimated by the default of treating the lost signals as tag failure. For conservative estimates of survival during population modelling, it may be most appropriate to treat signals lost before the likely end of tag cell life as if they represent deaths, by ticking this box. The difference in survival estimated by merely censoring the radios will not be large if radios are highly reliable. Correction for“lost” animals that are subsequently retrapped or resighted after the study period can involve reclassifying their fate as lived; more sophisticated correction from such data ([[Bibliography|Kenward 2001]]) will be added in due course.

Output Files

2014-12-11T13:01:33Z

RobertKenward: /* Statistics files */

== Introduction ==

Output files options are offered in the fourth column of the user interface for [[Location Analysis|Location Analysis]], [[Overlap Analysis|Overlap]], [[Interaction Analysis|Interaction]], [[Habitat Analysis|Habitat]] and [[Modelling Analysis|Modelling]]. The options that are offered are dependent upon the analysis being conducted.

If an output file tick box is visible, selecting this tick box will cause the creation of a permanent file with a default filename created by taking the name (and folder) of the input file and adding a code identifying the analysis used to create it. If the tickbox is not selected the output file is given a temporary name and will be overwritten by subsequent analyses. To choose a different filename from the default, select the tickbox and type in the text box or press browse to search your files. If you choose an existing file you will be asked whether you want to overwrite that file, if you choose '''Yes''' the existing file will be renamed to overwrite.bak in the Ranges directory, and the new file will be created after the '''Run Analysis''' button is pressed.

All data files in Ranges contain text, and can therefore be viewed in text editors, except for raster maps (''.rst'') and image files (''.ima'') which are byte arrays. Coverage of the following output files can be seen in File Types.

==== Statistics files ====

These are files with column headers saved in comma-separated variable (''.csv'') format that can be opened in the Statistics window, double-clicked to open in Microsoft Excel or imported to an alternative spreadsheet.

==== Ranges files ====

Other files are mainly to be used as inputs for other Ranges analyses and for display as maps and as plots. They can also be viewed in a spreadsheet but the data are arranged to save space rather than for ease of interpretation.

== Output filename codes for location analyses ==

The following codes are added to default output filenames, enabling the analysis that created them to be identified. Codes are highlighted in bold.

ConveX polygons

Peel centre:

: focal site 
: harmonic mean 
: kernel centre 
: arithmetic mean centre 
: recalculated arithmetic mean 

ConcaVe polygons

Edge restriction:

: 01 to 09 for 0.1 to 0.9, or in metres : 10m

Ellipses

Clusters

concaVe or conveX 
Joining priority:
: nearest neighbour, centroid 
objective cores : 
: outlier exclusion:
: truncation of distance distribution, iterative at 0.1,0.5,1% : i01, i05, i10 
for convex: 
: separate polygons 
: inclusive polygon 
for concave: 
: edge restrictions : 001 to 10 for 0.01 to 1.0 

Kernels or Harmonic mean contours

Contours:
: density, location inclusive (fitted to locations) 
Harmonic mean options: 
: Locations centred, unmodified 
Kernel type: 
: fixed, tail weighted, core weighted 
Kernel smoothing: 
: multiplier 01 to 20, lscv Inflection, lscv Local min., lscv Global min 
Matrix: 
: number of cells : e.g. n40, size of cells e.g. s10

Cores

e.g.: 
: selected cores : _50%75%95% 
: 5% intervals : _25to100%

Input & Graphics

2014-12-11T12:58:59Z

RobertKenward: /* Survival file data tables */

== Introduction ==

The main Ranges panel allows you to [[#Open|open]] and visualize existing Ranges files, create [[#New|new]] files, [[#Import|import]] text files, [[#Modify|modify]] file contents, [[#Export|export]] and [[#Save|save]] files. The [[#Data Tables|data tables]] for files are editable (with the exception of edge files), and the [[#Map Display|map display]] is mouse sensitive allowing selection and creation of locations and vector points as well as zooming.

== Open ==

Use this to open existing Ranges format files, allowing you to visualize the data, edit data points, modify file attributes and export to text files.

On pressing the open button, the file filter will show files of any Ranges type. List specific Ranges file types using the '''Files of type''' drop down. Location files contain the locations of animals whereas the Vector files and Raster files are two different ways of storing maps. Location files contain location data in groups which may represent individuals or ranges, and have the potential to store associated information on both the locations and the groups. Vector files store point information which may define points, lines or shapes. Raster files contain grid based data, where each cell in the grid is represented by a value, usually representing a habitat. Edge files store the coordinates of home-range shapes generated in [[Location Analysis|location analyses]] they cannot be edited but may be exported. For edge files, if you hold the pointer over the filename a description of the analysis used to create the analysis will be displayed. [[File Types#Utilisation Files|Utilisation files]] are created in location analyses and contain the areas of range cores at 5% intervals (e.g. for [[Convex Polygons|convex polygons]]), if you select Utilisation files (providing there is a ''.uti'' and ''.edg'' file with the same prefix), a [[#Utilisation plots||utilisation plot]] will be displayed. [[File Types#Incremental Files |Incremental files]] are also created in location analyses and contain the areas of ranges created from sub-samples of locations, starting from the first three and finishing with the entire set (e.g. for [[Clusters|clusters]]). Opening them here will display the location file and corresponding [[#Utilisation plots||Incremental plots]]. Ranges Image files are images aligned for display with other map files. RADA files contain the output of a resource area dependency analysis. Survival files contain dates and fate data for use with Kaplan Meier analysis; this analysis outputs Kaplan Meier Survival graph files.

See [[File Types|File Types]] for more details on the difference between these.

On clicking '''Open''', the file will be opened in the panel. Depending on the type, the left-hand column tables will populated with data, a map will be shown and a chart will be displayed in a new window.

== New ==

Use '''New''' to create new Location, Vector or Raster map or Survival files, either by entering data directly from the keyboard or by copying and pasting from another application such as a spreadsheet or word processor. Vector files can be added to using the right mouse button for [[#On-screen digitising||on-screen digitising]]. Before entering the data itself, you will have to enter attribute information that will be used in the creation of the file.

=== Location file ===

You will be prompted to enter location file parameters. This allows you to determine the attributes of the file to be created, including the age and sex labels, the number of location-qualifying variables (LQVs), map scale and tracking resolution and UTM (Universal Transverse Mercator coordinate system) ellipsoid and zone data to place the data in a latitude-longitude system. Location file attributes are explained [[File Types#File attribute variables|here]]. After OK is pressed, a file with a single range and no locations is created. Refer to [[#Data Tables|data tables]] for details on how to add data to this minimal file.

=== Vector file ===

You will be prompted to set vector file attributes (more details [[File Types#Vector Files|here]]). This determines the attributes of the file to be created, including whether it is a point, line or shape file, UTM data, the scale and the number, name and colour of vector map categories. After OK is pressed, an empty file is created, you may add to this using on-screen digitising or other methods outlined in [[#Data Tables|data tables]].

=== Raster file ===

You will be prompted to set raster file attributes (more details [[File Types#Raster Files|here]]). This determines the attributes of the file to be created, including its size, edge coordinates, habitat names and colours. After OK is pressed, an empty file is created. Refer to [[#Data Tables|data tables]] for details on how to add data to the file.

=== Survival file ===

[[File Types#Survival Files|Survival files]] do not contain any map data. You will only be prompted to choose age and sex labels.

== Import ==

On pressing the import button, you will be prompted to choose between the following import file types:

[[#Location file from column text file|Location file from column text file]] 
[[#Vector map from column text file|Vector map from column text file]] 
[[#Vector map from ArcView shapefile|Vector map from ArcView shapefile]] 
[[#Location file from ArcView points shapefile|Location file from ArcView points shapefile]] 
[[#Raster map from ArcInfo ASCII Grid format|Raster map from ArcInfo ASCII Grid format]] 
[[#Raster map from Idrisi ASCII format|Raster map from Idrisi ASCII format]] 
[[#Image file from JPEG/GIF/PNG/BMP|Image file from JPEG/GIF/PNG/BMP]] 
[[#Survival file from Ranges location file|Survival file from Ranges location file]]

=== Location file from column text file ===

Use this to import a text column file, as exported from a spreadsheet, into a Ranges [[File Types#Location Files|location file]]. The minimum requirement is a file with two columns, one containing coordinate eastings and the other containing coordinate northings. Files may also contain columns specifying range attribute variables such as ID, age, sex, month, year and focal site coordinates (such as a nest) and up to 50 location-qualifying variables (LQVs). So a typical file to be imported could start like this:

{|
| style="width: 60px;" | ID || style="width: 60px;" | Age || style="width: 60px;" | Sex || style="width: 60px;" | Month || style="width: 60px;" | Year || style="width: 60px;" | FocalE || style="width: 60px;" | FocalN || style="width: 60px;" | E || style="width: 60px;" | N || style="width: 60px;" | lqv1 || style="width: 60px;" | lqv2
|-
|A456 ||2 ||1 ||7 ||02 ||1003 ||586 ||1000 ||500 ||2 ||5
|-
|A456 ||2 ||1 ||7 ||02 ||1003 ||586 ||1052 ||510 ||3 ||10
|-
|A456 ||2 ||1 ||7 ||02 ||1003 ||586 ||1068 ||513 ||2 ||6
|-
|A456 ||2 ||1 ||7 ||02 ||1003 ||586 ||1009 ||525 ||0 ||5
|-
|B563-2 ||1 ||2 ||7 ||02 ||987 ||556 ||972 ||583 ||3 ||15
|-
|B563-2 ||1 ||2 ||7 ||02 ||987 ||556 ||988 ||532 ||4 ||2
|-
|B563-2 ||1 ||2 ||7 ||02 ||987 ||556 ||955 ||551 ||9 ||7
|-
|B563-2 ||1 ||2 ||7 ||02 ||987 ||556 ||997 ||533 ||2 ||5
|}

Try [[#Export|exporting]] and re-importing a location file to see how the data is assessed. You can look at the exported file in a text editor or spreadsheet such as notepad or excel.

The first prompt is to choose a file for importing. Initially, only files with a .txt extension will be displayed; however, you can alter the ''Files of Type'' choice box at the bottom of the dialog to display all files.

Once you have chosen a file, providing that it is in an appropriate format, an [[Location Import|import screen]] will appear. This will display the first 10 lines of the file to be imported, so that you can select which data are in which columns and set other attributes of the location file to be created. If the first row of data is the table header information, check the '''Header Row''' checkbox so that ranges does not attempt to import this as data. The '''Input Data Summary''' will reflect this,

Ranges is unable to use non-Cartesian coordinate systems. If the location data are latitude/longitude coordinates, you can convert these to metres in the UTM coordinate system by selecting ''latitude-longitude to utm'' in the '''Coordinate System Conversion''' list then selecting a '''Reference Ellipsoid''', usually ''WGS84'' but it will depend on your coordinate capturing device.

Set the '''Scale of Coordinates''' which is the number of metres a coordinate value of 1 represents and the '''Tracking Resolution''' which is important for drawing boundary strips around calculated ranges. A value of 10 is an appropriate resolution in most situations.

Setting '''Include Nest/Focal Site In Locations''' means that the coordinates for the range defined by FocalE and FocalN will be used in the analyses.

Click OK to import the data. You will be prompted for a folder and file name for the new Ranges location file. Once saved, the data will be displayed in the [[#Data Tables|data tables]] and on the [[#Map Display|map display]].

=== Vector map from column text file ===

Use this to import a text column file, as from a spreadsheet, into a Ranges [[File Types#Vector Files|vector file]]. The minimum requirement is a file with two columns, one containing coordinate eastings and the other containing coordinate northings. Files may also contain columns specifying ID, label and colour information.

Each ID can only have one label and colour, the one associated with the first coordinates with a particular ‘No.’ will be used.

Holes and other secondary polygons (for shapes) should be separated from the primary polygon by a blank row (blank rows are not needed between the primary polygons themselves). Holes should have an ID which is the negative of that of the primary polygon (and secondary polygons should have the same ID as the primary polygon).

The file below would import as one shape with a hole and another shape that fills the hole:

{|
| style="width: 60px;" | E || style="width: 60px;" | N || style="width: 60px;" | Id || style="width: 60px;" | Label
|-
|0 || 4 || 7 || habitat1
|-
|4 || 4 || 7 || habitat1
|-
|4 || 0 || 7 || habitat1
|-
|0 || 4 || 7 || habitat1
|-
|  ||  ||  || 
|-
|2 || 3 || -7 || habitat1
|-
|3 || 3 || -7 || habitat1
|-
|3 || 2 || -7 || habitat1
|-
|2 || 3 || -7 || habitat1
|-
|2 || 3 || 10 || habitat2
|-
|3 || 3 || 10 || habitat2
|-
|3 || 2 || 10 || habitat2
|-
|2 || 3 || 10 || habitat2
|}

For shapes the polygons should close by repeating the first coordinate as above.

The first prompt is to choose a file for importing. Initially only files with a ''.txt'' extension will be displayed. However, you can alter the '''Files of Type''' choice box at the bottom of the dialog to display all files.

Once you have chosen a file, providing that it is in an appropriate format an import screen will appear. This will display the first 10 lines of the file to be imported, so that you can select which data are in which columns and set other attributes of the vector file to be created.

==== Input Data Summary ====

The table at the top of the import vector window displays the first 10 lines of the file. If it detects that the first value in the first column is not a number it assumes that the first row is a header row and uses it to add titles to each column. The header row can be switched on and off using the tick box at the top right. The data in this table is not editable, but allows you to check what values are in which columns.

==== Attribute Mapping ====

On the middle left of the window there are 5 choice boxes with titles E, N, ID, Label, Colour. The selections you make in these boxes will determine which columns in the input file the vector data will be obtained from. If the file has a header row, the choice boxes will contain the column titles, if not they will contain the column numbers. Using an input file with a header row reduces the risk of importing the wrong columns.

All of the choice boxes, with the exception of E and N, have ''absent'' as the last option. This is used to indicate that the file does not contain any data for that attribute. The ''absent'' option is not available for E and N as it would be meaningless to create a vector file lacking one or both coordinates.

The ID determines which point group, line or shape that row of data will be read into. Data with the same ID need not be adjacent.

Category label and colour are variables associated with a particular point group, line or shape. The program assigns the label and colour obtained from the first coordinate of each ID. It does NOT check whether the label and colour assigned for subsequent coordinates with the same ID are the same as the first.

Finally choose the vector file type, point, line or shape, from the list and set the '''Scale of Coordinates''' which is the number of metres a coordinate value of 1 represents.

Click OK to import the data. You will be prompted for a folder and file name for the new Ranges location file. Once saved, the data will be displayed in the [[#Data Tables|data tables]] and on the Map Display. The file is not saved in Ranges format until the [[#Save|'''save'''] button is pressed.

=== Vector map from ArcView shapefile ===

Use this to import an ArcView shapefile to a Ranges [[File Types#Vector Files|vector file]]. Note: to reverse the process see [[#Export|export]], but note that the data format will be changed such that whilst the location and areas of shapes will remain the same the shapefile produced will not be identical to the original.

The following shapefile types are supported: point, polyline, polygon and multipoint. Point and multipoint files are imported as Ranges vector points, polyline files as vector lines and polygon files as vector shapes. The [[#Modify|'''modify''']] button can be used to convert between these formats after import.

==== Choose category column ====

ArcView shapefiles consist of 3 files with the suffixes ''.shp'', ''.shx'' and ''.dbf''. If the ''.dbf'' file is not present the points will be imported with no attribute information. If the .dbf file is present you will be presented with a choice box, allowing you to choose which column to get the habitat labels from (note that if the attribute fields in the shapefile contain spaces these are replaced by '_' ). You probably want to choose the field/column that contains the habitat information; in shapefiles that are exported from Ranges this field is called ''Label''. If you choose ID as the category column each shape will be put into a separate category.

==== Polygon and polyline details ====

In polygon and polyline shapefiles, multiple parts (shapes or lines) can be stored in a single record. In contrast, Ranges [[File Types#Vector Files|vector files]] contain a single shape or line for each record; this conversion takes place during the import process.

=== Location file from ArcView points shapefile ===

Use this to import an ArcView point or multipoint shapefile to a Ranges location file.

The coordinates from the ''.shp'' file, and any attribute information from the ''.dbf'' file are displayed in an [[Import Locations|import locations]] window, allowing you to choose which fields to import.

=== Raster map from ArcInfo ASCII Grid format ===

Use this to import a gridascii file into a Ranges raster file. A gridascii file is a text file that can be exported from ArcView and other GIS packages. Alternatively it can be created in a spreadsheet or text editor.

To export a gridascii file from ArcView, choose '''File...Export data source'''. When you '''Select export file type''' to be ''ASCII Raster'' and you will be prompted to choose a Grid file. You can first convert an ArcView shapefile to a Grid file by choosing '''Theme...Convert to Grid'''.

A gridascii file needs to have a header in the following format :

{|
| style="width: 60px;" | ncols || style="width: 60px;" | 200
|-
|ncols || 200
|-
|nrows || 200
|-
|xllcorner || 392000
|-
|yllcorner || 89000
|-
|cellsize || 25
|-
|NODATA_value || -9999
|}

''ncols'' and ''nrows'' specify the number of columns and rows. ''xllcorner'' and ''yllcorner'' specify the minimum eastings and northings. ''cellsize'' specifies the number of coordinate units per cell. ''NODATA_value'' specifies the value that indicates there is no data for that cell.

This can easily be seen by exporting buzzard\buzmap.rst and looking at the exported file in a text editor. However, please be aware that viewing text files in some text editors may add hidden characters to the file which may make the file unsuitable for re-importing.

Following the header, the cell data needs to be in rows separated by line feeds. Within rows, values should be separated by spaces.

Once you have chosen a gridascii file, Ranges will read the data and display with a screen offering options to set raster file attributes. This is the same screen that you will see when creating a raster file from scratch using '''new''' or modifying an existing raster file using '''modify'''. Large raster files, in excess of a million cells, will take a while to import, for more details see [[File Types#Raster Files|raster files]].

=== Raster map from Idrisi ASCII format ===

Export a raster map from idrisi choosing the ascii option and it will create two files one .rst and the other .rdc or .doc (depending which version of Idrisi you have). To import to Ranges select the .rst file and Ranges will automatically look for the associated file. Be careful that Idrisi and Ranges raster files have the same extension (''.rst'') but are not in the same format, so make sure that you don’t overwrite one with the other.

Once you have chosen an Idrisi raster file, Ranges will read the data and present you with a screen offering options to set raster file attributes. This is the same screen that you will see when creating a raster file from scratch using '''new''' or modifying an existing raster file using '''modify'''.

=== Image file from JPEG/GIF/PNG/BMP ===

Images can be loaded as backgrounds in Ranges with other file type data displayed in the foreground. In order for the image to aligned properly, a Ranges image file, ''.ima'', containing the alignment data needs to be created by importing a JPEG, GIF, PNG or bitmap file.

To import the image, select the file; it will be loaded in to the alignment tool. As for the main map display, yuo can pan and zoom around the image using the controls in the top right, you can zoom to an area by right click and dragging to create the area and you can zoom in and out of a point in the image using the mouse wheel or equivalent.

Alignment requires that four points, A, B, C and D, on image correspond to points in the real world. These points are entered into the grid in the top right. '''Image Coords''' are pixel position with 0,0 being the top left of the image and '''World Coordinates''' are the position in metres of these points in the world (note that in the northern hemispere, eastings will be lower at the bottom of the image. You can type directly into the grid to set these.

The image coordinates are indicated by orange flags on the image. The flags can be dragged around the image as an alternative way of specifying image coordinates. By default the image coordinates, and the flags, are in the four corners of the image.

Once the alignment coordinates are defined, click OK to save the image file and to show it on the Map Display. It is more usefully loaded as the '''Background'''.

=== Survival file from Ranges location file ===

Survival files require more range qualifying variables than lcoation files but do not contain any location data. They can be created from existing location files by simply selecting the .loc file to import from.

If the location file has date definitions as LQVs these dates will be used to define the start date and end date of each range in the survival file. If they do not exist, the start date will use the month and year from the range labels and you will need to fill out the remaining date details.

Survival data also requires a fate code for each animal; this is not imported but must be input manually. Once imported, the data will be displayed in the [[#Data Tables|data tables]].

== Modify ==

You can modify locations, edges, vectors, rasters, images and survival files. Click '''modify''' with the location file loaded to display the file settings for editing. Note that modified files are not saved until the '''save''' button is clicked.

==== Sampling locations and edges ====

Generally it is useful to have all the data in the file, so that any corrections can be made in one place. However, there are times when subsets of the data are being repeatedly run, so rather than make those choices all the time it is better to create a file of just that subset. Additionally, using a subset can reduce analysis time.

To create a subset, click '''Sample''' on the '''modify''' window. This will allow you to select a subsample of your data by its attributes (e.g. age, sex, time, activity), and to save this to a file with a new name. The selection frame allows you to select ranges, cores and locations depending on the file type. When you click OK, you will first be prompted for a new filename; it is important to save the new file under a different name to avoid losing the original data.

==== Random subsampling locations ====

There are also times when you may not want to use an entire location dataset, e.g. to avoid [[Interaction Analysis#Autocorrelation|autocorrelation]] or to investigate how much the analyses are affected by the number of locations. Use the '''Random Subsampling''' section, where you can determine the percentage of locations to select, or specify a particular number of locations to use and specify if you want a minimum time between each location. Press the OK button once the appropriate choices have been entered.

==== Merging location and edge files ====

Merge a second file with the one that is loaded by clicking the '''Merge''' button on the '''modify''' window. Location files can only be merged if they have the same number of age and sex labels, have the same scale, tracking resolution and have the same number of location qualifier variables. Edge files need to have the cores too. When you click OK, you will be prompted for a new filename; it is important to save the new file under a different name to avoid losing the original data.

== Export ==

You can export the active file to a chosen file type by clicking '''export'''.

=== Location files ===

==== Text file ====

Exports the location file to a plain text file in column format. For each location there are seven columns specifying the range attributes, two columns for the location coordinates and as many columns as there are location qualifying variables (LQVs).

The column headings will be as follows :

{|
| style="width: 60px;" | Id || style="width: 60px;" | Age|| style="width: 60px;" | Sex || style="width: 60px;" |Month || style="width: 60px;" | Year || style="width: 60px;" | FocalE || style="width: 60px;" | FocalN || style="width: 60px;" | E || style="width: 60px;" | N || style="width: 60px;" | LQV1 || style="width: 60px;" | LQV2 || style="width: 60px;" | ...
|}

==== ArcView Shapefile ====

Creates the 3 files that make up an ESRI shapefile (''.shp'', ''.shx'' and ''.dbf'').

Coordinates will be multiplied by the [[File Types#Scale|scale]] parameter to convert them to metres.

==== Text file for display in Excel ====

Creates a text file in a format for display in Excel. In the resulting CSV (comma separated variable) file, each range has two columns, for the easting and northing; these columns are headed with a string containing the range labels.

==== KML ====

Creates a KML (Keyhole Markup Language) file containing the location data. KML files can be displayed in third party applications such as Google Earth.

=== Vector files ===

==== Text file ====

This exports the vector file to a plain text file in column format. For each coordinate pair there are five columns.

{|
| style="width: 60px;" | E || style="width: 60px;" | N || style="width: 60px;" | ID || style="width: 60px;" | Label || style="width: 60px;" | Colour
|}

where E and N are the coordinates, ID is the identity of the feature (point group, line or shape) to which the coordinates belong, Label is the habitat label for the feature and Colour is the colour for the feature (in shorthand hexadecimal RGB)

==== ArcView Shapefile ====

This creates the three files that make up an Esri ArcView shapefile (''.shp'', ''.shx'' and ''.dbf'').

Coordinates will be multiplied by the [[File Types#Scale|vector scale]] parameter to convert them to metres.

==== Text file for display in Excel ====

Creates a text file in a format for display in Excel. In the resulting CSV (comma separated variable) file, each shape has two columns, for the easting and northing; these columns are headed with a string containing the shape labels.

=== Raster files ===

This exports raster files in gridascii format (see [[#Raster map from ArcInfo ASCII Grid format|Import Raster]] for details) that can be imported to Esri software.

=== Edge files ===

==== ArcView Shapefile Polyline ====

Creates the three files that make up an Esri ArcView polyline shapefile (''.shp'', ''.shx'' and ''.dbf''). In ArcView polyline files, shapes are displayed as unfilled lines. Coordinates will be multiplied by the scale parameter from the location file that they were derived to convert them to metres.

==== ArcView Shapefile Polyline - 1 per range ====

As in the previous option, but creates one shapefile for each range in your edge file. This can be useful if you want to choose which ranges to display within ArcView. A warning message is generated because this could create a very large number of files if your edge file has lots of ranges. The filenames will be based on the name you choose with _r[range_num] added to each, e.g. if you chose the name fox.shp, the files would be named fox_r0.shp, fox_r1.shp, fox_r2.shp etc. Any existing files with the same names will be overwritten without prompting.

==== ArcView Shapefile Polygon ====

Creates the 3 files that make up an Esri ArcView polygon shapefile (''.shp'', ''.shx'' and ''.dbf''). In ArcView polygon files, shapes are displayed as filled polygons. Coordinates will be multiplied by the scale parameter from the location file that they were derived to convert them to metres.

==== Text file for display in Excel ====

Creates a text file in a format for display in Excel. In the resulting CSV (comma separated variable) file, each edge has two columns, for the easting and northing; these columns are headed with a string containing the edge labels.

==== Separate Ranges Edge files - 1 per range ====

Subdivides your edge file, creating one edge file for each range. (This can be useful for viewing individual ranges against the locations used to produce them within the Input & Graphics display, loading the location file as the primary file, and the individual range edge file as the background file.) A warning message is generated because this could create a very large number of files if your edge file has lots of ranges. The filenames will be based on the name you choose with _r[range_num] added to each, e.g. if you chose the name ''fox.edg'', the files would be named ''fox_r0.edg'', ''fox_r1.edg'', ''fox_r2.edg'' etc. Any existing files with the same names will be overwritten without prompting.

==== Export to KML ====

Creates a KML (Keyhole Markup Language) file containing the edge polygons. KML files can be displayed in third party applications such as Google Earth.

=== Survival files ===

This exports survival file data to a plain text file in column format. For each range pair there are ten columns:

{|
| style="width: 60px;" | Id || style="width: 60px;" | Age || style="width: 60px;" | Sex || style="width: 60px;" |StartDay || style="width: 60px;" |StartMonth || style="width: 60px;" |StartYear || style="width: 60px;" |EndDay || style="width: 60px;" |EndMonth || style="width: 60px;" |EndYear || style="width: 60px;" |FateCode
|}

== Save ==

This saves the active file in Ranges format. You will be prompted with a dialog box allowing you to browse your files, if you enter a filename with no extension then the appropriate file type extension will be added. If you try to overwrite an existing file you will be warned.

== Data Tables ==

The two data tables on the left hand side of the '''Input & Graphics''' panel, display and allow editing of the currently loaded file. The tables differ according to the file type as follows

{| class="wikitable"
! style="text-align:left;width:120px"| File Type
! style="text-align:left;width:120px"| Top Table
! style="text-align:left;width:120px"| Bottom Table
|-
|location || ranges || locations
|-
|vector points || point groups || points
|-
|vector lines || lines || line vertices
|-
|vector shapes || shapes || shape vertices
|-
|raster || map categories || raster cell values
|-
|edge || edge shapes || edge vertices
|-
|utilisation || edge shapes || edge vertices
|-
|incremental || ranges || locations
|-
|image || - || -
|-
|RADA || RADA habitat cores || -
|-
|survival || survival ranges || -
|-
|Kaplan Meier survival graph || - || -
|}

The following features are common to each table:

* column widths can be changed by clicking and dragging in the header row
* white cells are editable grey cells are not
* click 3 times in editable cells to overwrite, twice to add.
* multiple rows can be selected by using Ctrl click, or shift click to select a series

Any editing does not effect the opened file (and is not saved) until the '''save''' button is pressed.

=== Location file data tables and incremental plots ===

==== Viewing ====

Within [[File Types#Location Files|location files]], locations are grouped into ranges. The upper table displays the attributes of each range. The lower table displays the locations and location qualifying variables (LQVs) for the range that is selected in the upper table.

Selecting different rows in the ranges table will cause different sets of locations to be displayed in the locations table. To step through all of the ranges in the file, select the first row in the ranges table and then use the down cursor key to display each range in turn. Locations in the selected range are displayed in blue in the map display.

Selecting a row within the locations table will cause that location to be circled red within the map display.

Clicking with the SHIFT key held down on a blue location within the map display causes the row associated with that location to be selected (if there are multiple locations at the same point then all of the relevant rows will be selected).

==== Editing ====

Data are non-editable if the table cell is grey and editable if the table cell is white. In the ranges table Age, Sex and Month cells have pull down menus with available options, these are activated by a left mouse click.

For other editable cells, use the left button of the mouse to click once or twice within the cell and you will be able to add to or delete from the existing cell contents. Click three times and you can overwrite the cell contents.

In the locations table, you can use CTRL+C to copy and CTRL+V to paste blocks of data between portions of the table or between the table and a spreadsheet such as Microsoft Excel. Please note, if you wish to copy more than one column you have to select them by moving the cursor right or left, even though that does not alter the look of the cell.

In the ranges table use the '''add''' button to add a blank range and the '''delete''' to remove selected ranges.

To add locations, simply type additional locations into the blank cells immediately following the existing locations in the locations table. If data are pasted in the number of rows in the table will increase to accommodate them. Use the '''delete''' button to delete selected locations.

=== Incremental area plots ===

If you have opened an Incremental file (''.inc'', created in [[Convex Polygons#Incremental area analysis|location analysis]]), an incremental plot is displayed in a new window. This allows you to examine how the range area changes as successive locations are added. The plot will display the range that is selected in the upper table; click on rows in the upper table to display other ranges. If the chart window is closed, it can be reopened by clicking on the '''display''' button below the locations table. For more details see [[Range Use Plots#Incremental area plots|Incremental area plots]].

=== Vector file data tables ===

==== Viewing ====

For [[File Types#Vector Files|vector files]], groups of coordinates are stored in a similar way to location files. For points, the upper table displays point groups and the lower table points. For lines, the upper table displays lines and the lower table line vertices. For shapes, the upper table displays shape polygons and the lower table shape vertices.

As for location file data, tables changing the row that is selected in the upper table changes which data are displayed in the lower table. The selected point group, line or shape is displayed in blue in the map display.

Selecting a row in the upper table will highlight the point, line or shape by circling it in black within the map display. Selecting a row within the points, line vertices or shape vertices table will cause that location to be circled red.

Clicking on a blue location within the map display causes the row associated with that point, line vertex or shape vertex to be selected (if there are multiple features at the same point then all of the relevant rows will be selected).

==== Editing ====

The upper table (point groups, lines or shapes) contains ''No.'', ''ID'' and ''Category'' columns. ''No.'' is not editable. ''ID'' is editable but must contain an integer. ''Category'' is editable with a pull down list of available categories. Choose [[#Modify|'''modify''']] to add categories .

Holes can be added to shapes: first select the boundary shape and click '''hole'''. The ID and category of a hole is the same as its shell shape and cannot be edited.

Use the '''add''' button to create a new feature and '''delete''' to remove a feature. The feature will be inserted below the currently selected one. You cannot add a new shape between a hole and its shell.

The lower table (points, line vertices or shape vertices) contains the coordinate data.

In the locations table, you can use CTRL+C to copy and CTRL+V to paste blocks of data between portions of the table or between the table and a spreadsheet such as Microsoft Excel. Please note, if you wish to copy more than one column you have to select them by moving the cursor right or left, even though that does not alter the look of the cell.

Use the '''delete''' button to delete selected coordinates.

==== On-screen digitising ====

You can add points to the selected point group, line or shape by left-clicking on the map with the CTRL key held down (you are in ''draw'' mode when the the cursor over the map becomes a pen. You can remove points from an object, from last to first by right-clicking on the map with the CTRL key held down.

For vector files, using the right or middle mouse buttons when the cursor is within the map display will add the corresponding point to the currently selected shape. You can use this to create new vector files by tracing around an existing file loaded as a [[#Background maps|background]]. This is a good way of creating a vector shape file that can be used in habitat analyses from an image file (perhaps from a scanned map or aerial photograph). For vector shape files, coordinates should always be added in a clockwise direction. To add a shape that fills a hole, simply add another shape and then copy all the coordinates (CTRL+C) from the table for hole into that for the new shape (CTRL+V).

=== Raster file data tables ===

==== Viewing ====

For Raster files, the upper table contains the map categories and the lower table the raster cell values.

Clicking on a cell in the raster cell values table draws a white box at that point in the map display.

==== Editing ====

The map categories table is not editable; press the [[#Modify|'''modify''']] button to edit attributes of the raster map.

The raster cell values table is editable and changes made will be shown in the map display. Use CTRL+C to copy and CTRL+V to paste blocks of data between portions of the table or between the table and a spreadsheet such as Microsoft Excel.

=== Edge file data tables and utilisation plots ===

==== Viewing ====

For Edge files, the upper table contains the edge shapes and the lower table the coordinates specifying the edge vertices. Edge file data is not editable. In the upper table, columns ''ID'', ''Age'', ''Sex'', ''Month'' and ''Year'' are the same as for locations and ''core'' displays the core %.

Note that a core may contain multiple shapes e.g. following cluster analysis or if there is a hole generated by contouring. In this case subsequent shapes will have the same ID and category.

As for location file data tables, changing the row that is selected in the upper table changes which data are displayed in the lower table. The selected edge shape is displayed in blue in the map display.

==== Utilisation plots ====

If you have opened an Utilisation file (''.uti'', created in location analysis), an incremental plot is displayed in a new window. The plot will display the range that is selected in the upper table; click on rows in the upper table to display other ranges. If the chart window is closed, it can be reopened by clicking on the '''display''' button below the locations table. For more details see [[Range Use Plots#Utilisation plots|Utilisation plots]].

Examination of utilisation plots ([[Bibliography|Ford & Krumme 1979]]) provides a method of deciding on the percentage of locations that define a core range. In Ranges, utilisation plots display the area of estimated home range cores at 5% intervals from 20-100%. If there are a few locations far from the range centre, the slope of the plot is initially steep, but becomes shallower when only the core locations remain. This slope discontinuity, if present, is a useful indicator of how many locations constitute the core range. For more details see Range Use Plots.

==== Editing ====

Edge files are not editable in Input & Graphics.

=== RADA file data tables ===

==== Viewing ====

RADA files contain the output of RADA analyses. There is a row in the top table for each habitat for each core specified in the analysis. See RADA analysis for more details of this table.

Clicking on a row in the table will display the RADA plot for that habitat core. If the plot is hidden, open it again by clicking the '''display''' button below the table.

==== Editing ====

RADA files are not editable.

=== Survival file data tables ===

==== Viewing ====

Survival files contain survival data for Kaplan Meier analysis. There is a row in the top table for each survival record, usually for each animal. As well as ID, Sex and Age labels used to identify the animal there are labels for the tagging Start Date and End Date as well as the Fate Code.

==== Editing ====

The survival data are editable. In the ranges table Age, Sex, the Month cells and Fate Code have pull down menus with available options, these are activated by a left mouse click.

For other editable cells, use the left button of the mouse to click once or twice within the cell and you will be able to add to or delete from the existing cell contents. Click three times and you can overwrite the cell contents.

=== Graphs from location analyses ===

Other location analyses produce graphs, e.g. the distance between locations over time. These are also displayed in a new window. The plot will display the range that is selected in the upper table; click on rows in the upper table to display other ranges. If the chart window is closed, it can be reopened by clicking on the '''display''' button below the locations table. For more details see Incremental area plots.

== Map Display ==

The Map Display is on the right of the window. The size of the window can be changed relative to the Data Tables panel by click on the dividing bar between them and dragging it to the left and right.

The panel displays the contents of the loaded location, vector or raster file and is sensitive to mouse clicks allowing selection of features, zooming and drawing of vector objects.

Display options can be selected from the pull down boxes at the top of the panel.

[[#Background maps|Background files]] can be chosen by clicking '''open''' on the upper right.

Colour options for Location and Edge files can be chosen from the '''range colours''' drop down in the top right.

=== Panning and zooming ===

Controls in the top left of the Map Display control the panning and zooming.

The arrow keys allow panning up down left and right but the easiest way to position the map is to hold down the left mouse button and drag the map.

Buttons in the top left allow zooming in and out and zoom to fit, fitting both foregrounds and background to the Map Display panel. You can also ''zoom to selection'' by holding the right mouse button down and dragging right and down to draw a red rectangle; when you release the mouse button, panel will be filled with the contents of the rectangle. Finally, zoom quickly in and out to the mouse cursor using the mouse scroll wheel or its equivalent.

=== Point selection ===

You can select a point in the map display in two ways:

* select the row in the lower table of the Data Tables panel
* left click the mouse on the map display while holding down the SHIFT key on the keyboard.

This second option will select the closest point to the click in the currently selected range; the point group, line or shape and the row containing it in the lower table will be highlighted. If there are multiple features at the same point then all of the relevant rows will be selected. Note that it is not possible to select coordinates from an un-selected range, point group, line or shape.

=== Focal points and range centres ===

Focal points such as Nests, defined by FocalE and FocalN for the range are indicated by an '''x''' on the map. Ranges centres, calculated during polygon-building location analyses are marked with a '''+'''.

=== Display options ===

For location, vector and edge files, a pull down list at the top of the map display allows you to select whether to display all of the coordinates in the file or just those in the selected group. The options are dependent on the file type.

==== Location Files ====

Display options for location files are as follows:

{| class="wikitable"
! style="text-align:left;width:160px"| Option
! style="text-align:left;"| Function
|-
|''display selected'' || Displays only those features selected in the upper table.
|-
|''display all'' || Displays all ranges or shapes in the file.
|-
|''animate locations by sequence'' || Animates the map for all ranges, animates locations according to their sequence in the file. Additional animation options are made available at the top of the map display panel.
|-
|''animate locations by time'' || Animates the map for all ranges, animates locations according to time variables stored in the location qualifying variables (lqvs). This option is only offered if appropriate time variables are stored in the file. Additional animation options are made available at the top right corner of the user interface.
|-
|''display selected as path'' || Joins the locations within each selected range into a path.
|-
|''display all as paths'' || Joins the locations within each range into a path and displays them all.
|}

==== Edge files ====

Display options for edge files are as follows:

{| class="wikitable"
! style="text-align:left;width:160px"| Option
! style="text-align:left;"| Function
|-
|''display selected'' || Displays only those features selected in the upper table.
|-
|''display 1st selected range'' || Displays all of the cores from the range selected in the upper table. The first selected core% is displayed in blue and others in black. If more than one range is selected, those after the first are displayed in grey.
|-
|''display cores same as 1st selected'' || Displays all the cores for all ranges that have the same value as the first selected one. e.g. if the first selected core is 50%, then the 50% cores for all ranges will be shown.
|-
''display all'' || Displays all ranges or shapes in the file.
|}

==== Vector map files ====

Display options for vector files are as follows:

{| class="wikitable"
! style="text-align:left;width:160px"| Option
! style="text-align:left;"| Function
|-
|''display selected'' || Displays only those features selected in the upper table.
|-
|''display all, selection colours'' || Displays all ranges or shapes in the file. Selected coordinates in red, selected ranges in blue, others in black.
|-
|''display all, range or category colours'' || Displays all the shapes in the colours defined in the file (and can be altered using the '''modify''' button). For location and edge files a single colour is applied for each range from a set colour scheme.
|}

=== Line colour ===

Line colour is only available for location and edge files. Colour options are as follows:

{| class="wikitable"
! style="text-align:left;width:120px"| Option
! style="text-align:left;"| Colour
|-
|selection || red=selected locations, blue=selected ranges or shapes, black=others
|-
|black || all shown in black
|-
|pale || all shown in light grey
|-
|sex || red=F, blue=M, black=?
|-
|pale sex || pink=F, cyan=M, light grey=?
|-
|range || coloured according to range number, 24 potential colours
|-
|age || 12 potential colours
|-
|range month || 12 colours, spring green, summer red, autumn purple, winter blue
|-
|range year || 24 colours
|-
|lqv || the option to colour locations by any of the Location Qualifying Variables in the file. If an LQV is chosen containing HH (hour) data then the colour scheme is set for 24 hours (morning green, midday red, afternoon purple, night blue, midnight nearly black). If not then a colour scheme of 24 colours is used.
|}

=== Animation attributes ===

Two option boxes control the animation, the first determines the number of locations displayed at one time, the second controls the speed of the animation.

=== Background maps ===

Any Ranges spatial file can be used as a background (location, edge, vector, raster or image). Ranges raster maps, vector shape files and images will be displayed in colour, other files will be displayed in grey. Note that a raster map cannot be used as a background for another raster map.

Open the background by clicking the '''open''' button in the '''Background''' panel and selecting a file. The background can be removed with the '''close''' button.

Background maps can be used to compare range edges to the locations they were created from, or for comparing range edges created by different methods.

==== Background opacity ====

This option box allows you to choose how bright a background map should be displayed. There are four options: ''full'' displays the map with its full colours, ''faded'' and ''faint'' display it progressively fainter and ''hide'' hides the background altogether.

==== Background selected only ====

This option is available for edge and location files and allows you to display just those parts of the background file relating to the currently selected range. For example if you open an edge file as the primary file and the location file used to create it as the background, then choose ‘display 1st selected range’, tick ‘selected only in background’, you will be able to scroll down through the range edges, and see just the locations used to create each. Similarly you can load an edge file created by a different method as the background, and look at the differences for each range in turn.

This is the default option following location analyses that create edge files, however it only becomes visible if the two files contain the same number of ranges, so will not be available if you used range selections in the creation of your edge file.

==== Background clipping ====

This option is available for edge files with a raster or vector shape background map. When ticked only those areas of habitat within the ranges are displayed. This is the default option following analysis of ‘habitat in ranges’.

=== Map snapshots ===

The map image can be copied to the clipboard or saved as an image file. To do this, size the Map Display panel to the size you require the image by dragging the main window borders and the central divider into position then click '''Save map''' button (with a picture of a floppy disk). An option window will appear allowing you to select to copy to the clipboard (for pasting into a Word document or elsewhere) or to save to an image file, PNG, JPEG, GIF or bitmap. PNG (portable network graphics) files have the best quality to size ratio. If you chose to save as a file you will be prompted to provide a file name. You can also chose to remove the scale bar from the image (all other Map Display furniture such as the option boxes and zoom/pan controls will be removed from the image).

Glossary

2014-12-11T12:55:16Z

RobertKenward:

'''Accuracy ellipses''' are generated round Locations from bearing data by some packages (e.g. LOCATE II).

'''Activity centre''' is calculated as the Arithmetic mean, Recalculated Arithmetic mean or Harmonic mean centre for a set of Locations (a Range).

'''Arithmetic mean''' is the mean of x and y coordinates for a Range.

'''Autocorrelation analysis''' estimates the degree of spatio-temporal dependence of Locations.

'''ASCII''' is American Standard Code, used to turn bytes into text characters.

'''Bivariate ellipses''' are based on Location distributions along a major and a minor axis.

'''Boundary strips''' round Locations in Polygons have a width of half the Tracking resolution.

'''Byte arrays''' are Ranges storage format for Raster maps; each byte codes for 1 raster.

'''Centroid distance''' in Cluster analysis is from an Arithmetic mean to all the Locations in a Cluster.

'''Cluster analysis''' joins Locations in groups based on the Nearest Neighbour distances between them.

'''Contour analysis''' plots Isolines across a Density Matrix to represent either on a probabilistic or Location-inclusive Utilisation distribution.

'''Core''' denotes one or more areas of high Location density in a set of Locations.

'''CSV files''' are composed of Comma Separated Values (other separators are Break/Space and Tab).

'''Density Matrix''' values are estimated at intersections of an arbitrary grid in Contour analyses.

'''Dispersal detection''' provides an objective estimate of when animals leave an area.

'''Dispersion''' (in contour analyses) the peak density value (at the range centre location) divided by the standard deviation of the density value across all the Locations.

'''Diversity of areas''' in Cluster analysis are Simpson's index for the areas within all the cluster Polygons in a Range.

'''Diversity of locations''' in Cluster analysis are Simpson's index for the numbers of Locations within all the cluster Hulls in a Range.

'''Edge''' denotes an outline estimated round locations as a polygon or by contouring.

'''Ellipses''' include circles.

'''Ellipse asymmetry''' is the ratio of the standard deviations along the major and minor axes.

'''End date''' in a Kaplan Meier Survival analysis is the date to which survival should be estimated; by default the last date for any animal, it may be set earlier to ensure an adequate sample in the last interval or to analyses a particular season; see also Start date.

'''Focal site''' denotes an attraction point in a range, such as a den or nest.

'''ESRI''' is the Environmental Systems Research Institute, which supplies GIS software.

'''Grid cells''' are as wide as the Location resolution.

'''GIS''' is a Geographic Information System.

'''Grid edges''' are the eastmost, westmost, northmost and southmost coordinates in sets of locations.

'''Gridascii''' files are of ASCII values used by ESRI soft for transferring raster map data.

'''Habitat points''' are x,y coordinates associated with habitat codes for different trees, etc.

'''Habitat shapes''' are formed from a clockwise set of x,y values with the same start and end point.

'''Harmonic Mean analyses''' are based on the inverse reciprocal mean of distances to Locations.

'''Harmonic Mean centre''' is the Location in a Range at which the inverse reciprocal mean of distances to all other Locations is minimal.

'''hRef''' is the reference Smoothing parameter in Kernel analyses ( SD / sixth root N )

'''Hull''' is a Polygon with vertices fitted to a set of Locations; a Convex Hull has all external angles greater than 180°.

'''Incremental analysis''' estimates and plots the change in Range area as successive Locations are added.

'''Isolines of equal location density''' are created during Contour analysis and converted to Polygons.

'''Jacob's index''' has values between -1 and +1 to indicate attraction versus avoidance.

'''Kaplan Meier Survival''' plots survival in intervals between Start dates and End dates in .srv files and tests for significance between cohorts.

'''Kernel analyses''' are based on estimating Location density as functions of distance from all the Locations in a Range.

'''Kurtosis''' is an index of spread in the density distribution during Harmonic Mean & Kernel contouring.

'''Location''' denotes x,y coordinates of an observation, often with associated qualifying variables.

'''Location centring''' is computed during Harmonic Mean contouring to remove Location resolution effects.

'''Location resolution''' is the smallest distance that can be recorded between adjacent locations.

'''Location Qualifying Variables''' (LQVs) are time, activity, habitat, values associated with x,y coordinates.

'''Nearest Neighbour distance''' is the minimum distance between spatially separate Locations.

'''Neighbour Linkage analyses''' estimate Polygons round Locations whose individual or summed Nearest Neighbour distances do not exceed a certain value.

'''Nuclei''' are the number of separate Polygons defined by Cluster Analaysis.

'''Objective Cores''' exclude Locations more isolated than a criterion distance based on the distribution of all Nearest Neighbour distances.

'''OREP''' Objective Restrictive Edge Polygons have maximum peripheral edge distances less than a criterion based on the distribution of all Nearest Neighbour distances.

'''Outlier exclusion distances''' (OEDs) are derived from the distribution of all Nearest Neighbour distances as either the distance that excludes the outermost 5% of the distribution, or by iterative exclusion of each distances beyond an alpha level until no locations exceed that level.

'''Outlier locations''' are those more isolated than a criterion distance based on the distribution of all Nearest Neighbour distances.

'''Overlap matrices''' are formed as % overlaps of range A on B and B on A.

'''Partial area''' is the summed area of Clusters divided by a single area encompassing all Clusters.

'''Peeled Polygons''' are formed as Convex Hulls by excluding Locations furthest from an Activity Centre.

'''Polygons''' are formed by lines round a set of vertices, which may be Locations, corners on Vector maps or equal values interpolated on a Density Matrix.

'''RADA''' Resource Area Dependence Analysis uses negative correlations of (log) Range Outline area with (log) resource metric (e.g. habitat proportion in the outline) to detect resources that are important enough for animals to expand the area they cover in order to get an adequate supply.

'''Range''' is an area defined by analysis of a set of animal Locations observed in a particular period.

'''Range Core''' denotes one or more areas of high Location density in a set of Locations.

'''Range variables''' are seven values that code ID, age, sex, month, year and focal site coordinates for a Range.

'''Raster maps''' are composed of equal-size rectangles with different habitat codes.

'''Range outline''' denotes one or more Polygons (including Hulls and Contours) fitted to some or all the Locations in a Range.

'''Recalculated Arithmetic mean''' is the mean x and y coordinates, recalculated after each Location of a Peeled Polygon is excluded.

'''Schoener's index''' increases from 0 with decreasing spatio-temporal dependence between Locations (= mean squared distances between Locations / mean squared distance from each Location to the Arithmetic mean activity centre).

'''Shape files''' are the standard Polygon format in an ESRI GIS.

'''Skew''' in the Location density distribution is estimated during Harmonic Mean and Kernel contouring (the Euclidean distance between the Arithmetic mean centre and the Location with the peak density value, divided by the standard deviation of the density value across all the Locations).

'''Simpson's index''' increases from 1 with increasing diversity between Polygons in Cluster analysis.

'''Smoothing factor''' modulates the density function in Kernel analyses to improve fit of Contours.

'''Span''' of a Range is the maximum diagonal dimension of a Convex Hull enclosing all the Locations.

'''Spread''' of a Range is the grand mean of distances between all the Locations.

'''Start date''' in a Kaplan Meier Survival analysis is the date from which survival should be estimated; by default the first date for any animal, it may be set later to ensure an adequate sample in the first interval or to analyses a particular season; see also End date.

'''Tracking resolution''' is the smallest distance that can be recorded between adjacent Locations.

'''Usual area''' is the single Polygon that encloses all the separate Cluster Polygons on a Range Core.

'''Utilisation plots''' are of Range area against percentages of Location-inclusion or Location-density.

'''UTM''' stands for Universal Transverse Mercator and is a two-dimensional Cartesian coordinate system to give locations on the surface of the Earth.

'''Vector maps''' are composed of lines and closed shapes defined by a sequence of x,y coordinates.

Glossary

2014-12-11T12:53:56Z

RobertKenward:

'''Accuracy ellipses''' are generated round Locations from bearing data by some packages (e.g. LOCATE II).

'''Activity centre''' is is calculated as the Arithmetic mean, Recalculated Arithmetic mean or Harmonic mean centre for a set of Locations (a Range).

'''Arithmetic mean''' is the mean of x and y coordinates for a Range.

'''Autocorrelation analysis''' estimates the degree of spatio-temporal dependence of Locations.

'''ASCII''' is American Standard Code, used to turn bytes into text characters.

'''Bivariate ellipses''' are based on Location distributions along a major and a minor axis.

'''Boundary strips''' round Locations in Polygons have a width of half the Tracking resolution.

'''Byte arrays''' are Ranges storage format for Raster maps; each byte codes for 1 raster.

'''Centroid distance''' in Cluster analysis is from an Arithmetic mean to all the Locations in a Cluster.

'''Cluster analysis''' joins Locations in groups based on the Nearest Neighbour distances between them.

'''Contour analysis''' plots Isolines across a Density Matrix to represent either on a probabilistic or Location-inclusive Utilisation distribution.

'''Core''' denotes one or more areas of high Location density in a set of Locations.

'''CSV files''' are composed of Comma Separated Values (other separators are Break/Space and Tab).

'''Density Matrix''' values are estimated at intersections of an arbitrary grid in Contour analyses.

'''Dispersal detection''' provides an objective estimate of when animals leave an area.

'''Dispersion''' (in contour analyses) the peak density value (at the range centre location) divided by the standard deviation of the density value across all the Locations.

'''Diversity of areas''' in Cluster analysis are Simpson's index for the areas within all the cluster Polygons in a Range.

'''Diversity of locations''' in Cluster analysis are Simpson's index for the numbers of Locations within all the cluster Hulls in a Range.

'''Edge''' denotes an outline estimated round locations as a polygon or by contouring.

'''Ellipses''' include circles.

'''Ellipse asymmetry''' is the ratio of the standard deviations along the major and minor axes.

'''End date''' in a Kaplan Meier Survival analysis is the date to which survival should be estimated; by default the last date for any animal, it may be set earlier to ensure an adequate sample in the last interval or to analyses a particular season; see also Start date.

'''Focal site''' denotes an attraction point in a range, such as a den or nest.

'''ESRI''' is the Environmental Systems Research Institute, which supplies GIS software.

'''Grid cells''' are as wide as the Location resolution.

'''GIS''' is a Geographic Information System.

'''Grid edges''' are the eastmost, westmost, northmost and southmost coordinates in sets of locations.

'''Gridascii''' files are of ASCII values used by ESRI soft for transferring raster map data.

'''Habitat points''' are x,y coordinates associated with habitat codes for different trees, etc.

'''Habitat shapes''' are formed from a clockwise set of x,y values with the same start and end point.

'''Harmonic Mean analyses''' are based on the inverse reciprocal mean of distances to Locations.

'''Harmonic Mean centre''' is the Location in a Range at which the inverse reciprocal mean of distances to all other Locations is minimal.

'''hRef''' is the reference Smoothing parameter in Kernel analyses ( SD / sixth root N )

'''Hull''' is a Polygon with vertices fitted to a set of Locations; a Convex Hull has all external angles greater than 180°.

'''Incremental analysis''' estimates and plots the change in Range area as successive Locations are added.

'''Isolines of equal location density''' are created during Contour analysis and converted to Polygons.

'''Jacob's index''' has values between -1 and +1 to indicate attraction versus avoidance.

'''Kaplan Meier Survival''' plots survival in intervals between Start dates and End dates in .srv files and tests for significance between cohorts.

'''Kernel analyses''' are based on estimating Location density as functions of distance from all the Locations in a Range.

'''Kurtosis''' is an index of spread in the density distribution during Harmonic Mean & Kernel contouring.

'''Location''' denotes x,y coordinates of an observation, often with associated qualifying variables.

'''Location centring''' is computed during Harmonic Mean contouring to remove Location resolution effects.

'''Location resolution''' is the smallest distance that can be recorded between adjacent locations.

'''Location Qualifying Variables''' (LQVs) are time, activity, habitat, values associated with x,y coordinates.

'''Nearest Neighbour distance''' is the minimum distance between spatially separate Locations.

'''Neighbour Linkage analyses''' estimate Polygons round Locations whose individual or summed Nearest Neighbour distances do not exceed a certain value.

'''Nuclei''' are the number of separate Polygons defined by Cluster Analaysis.

'''Objective Cores''' exclude Locations more isolated than a criterion distance based on the distribution of all Nearest Neighbour distances.

'''OREP''' Objective Restrictive Edge Polygons have maximum peripheral edge distances less than a criterion based on the distribution of all Nearest Neighbour distances.

'''Outlier exclusion distances''' (OEDs) are derived from the distribution of all Nearest Neighbour distances as either the distance that excludes the outermost 5% of the distribution, or by iterative exclusion of each distances beyond an alpha level until no locations exceed that level.

'''Outlier locations''' are those more isolated than a criterion distance based on the distribution of all Nearest Neighbour distances.

'''Overlap matrices''' are formed as % overlaps of range A on B and B on A.

'''Partial area''' is the summed area of Clusters divided by a single area encompassing all Clusters.

'''Peeled Polygons''' are formed as Convex Hulls by excluding Locations furthest from an Activity Centre.

'''Polygons''' are formed by lines round a set of vertices, which may be Locations, corners on Vector maps or equal values interpolated on a Density Matrix.

'''RADA''' Resource Area Dependence Analysis uses negative correlations of (log) Range Outline area with (log) resource metric (e.g. habitat proportion in the outline) to detect resources that are important enough for animals to expand the area they cover in order to get an adequate supply.

'''Range''' is an area defined by analysis of a set of animal Locations observed in a particular period.

'''Range Core''' denotes one or more areas of high Location density in a set of Locations.

'''Range variables''' are seven values that code ID, age, sex, month, year and focal site coordinates for a Range.

'''Raster maps''' are composed of equal-size rectangles with different habitat codes.

'''Range outline''' denotes one or more Polygons (including Hulls and Contours) fitted to some or all the Locations in a Range.

'''Recalculated Arithmetic mean''' is the mean x and y coordinates, recalculated after each Location of a Peeled Polygon is excluded.

'''Schoener's index''' increases from 0 with decreasing spatio-temporal dependence between Locations (= mean squared distances between Locations / mean squared distance from each Location to the Arithmetic Mean activity centre).

'''Shape files''' are the standard Polygon format in an ESRI GIS.

'''Skew''' in the Location density distribution is estimated during Harmonic Mean and Kernel contouring (the Euclidean distance between the Arithmetic Mean centre and the Location with the peak density value, divided by the standard deviation of the density value across all the Locations).

'''Simpson's index''' increases from 1 with increasing diversity between Polygons in Cluster analysis.

'''Smoothing factor''' modulates the density function in Kernel analyses to improve fit of Contours.

'''Span''' of a Range is the maximum diagonal dimension of a Convex Hull enclosing all the Locations.

'''Spread''' of a Range is the grand mean of distances between all the Locations.

'''Start date''' in a Kaplan Meier Survival analysis is the date from which survival should be estimated; by default the first date for any animal, it may be set later to ensure an adequate sample in the first interval or to analyses a particular season; see also End date.

'''Tracking resolution''' is the smallest distance that can be recorded between adjacent Locations.

'''Usual area''' is the single Polygon that encloses all the separate Cluster Polygons on a Range Core.

'''Utilisation plots''' are of Range area against percentages of Location-inclusion or Location-density.

'''UTM''' stands for Universal Transverse Mercator and is a two-dimensional Cartesian coordinate system to give locations on the surface of the Earth.

'''Vector maps''' are composed of lines and closed shapes defined by a sequence of x,y coordinates.

Tutorial

2014-12-11T11:32:50Z

RobertKenward: /* Plotting survival for a single data set */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

==== Plotting survival for a single data set ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''kaplan meier survival''.

* Under '''Analysis Options''' ensure ''one set'' is selected

* Under '''Input files''' press '''browse''' and find, for the ''set 1 survival file'' the file ''<RangesFolder>\samples\raptors\GoshawkJuvMale.srv''.

* Press the '''Run Analysis''' button.

Looking at the statistics window, the sample size was not adequate until the start of the second month, and became less than 30 animals due to moulting of tail-mounted radio tags after 30 April. Run the analysis again, selecting as '''set 1 start date''' the ''specified date'' and use the calendar to select 1 July 1980 (around the fledging date), then in '''set 1 end date''' again select ''specified date'' and set 31 March 1981. This estimates juvenile male survival to the start of the next egg-laying period, as used in [[Bibliography|Kenward et al. (1999)]].

==== Comparing two sets of survival data ====

[[File:To be added]]

* Under '''Analysis Options''' select ''two sets for comparison''

* Under '''Input files''' check that the ''set 1 survival file'' is still ''<RangesFolder>\samples\raptors\GoshawkJuvMale.srv''.

* Check that '''set 1 start date''' has ''specified date'' selected, of 1 July 1980.

* Check that '''set 1 end date''' has ''specified date'' selected, of 31 March 1981.

* Press '''browse''' for the ''set 2 survival file'' and find ''<RangesFolder>\samples\raptors\GoshawkJuvFem.srv''.

* For the '''set 2 start date''', use the ''set 1 start date'' option.

* For the '''set 2 end date''', use the ''set 2 end date'' option.

* Press the '''Run Analysis''' button.

The survival is poorer for juvenile males than for juvenile females due mainly to differences from October (month 4) onwards. The ''z'' values of 2.07 to 2.13 are higher than the value of 1.96 for alpha = 0.05, so ''P'' < 0.05.

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward (2001), Kenward et al. (2001)]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls & Kenward 1995, 1998, 2001]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission. Goshawk survival data were collected on the Swedish island of Gotland ([[Bibliography|Kenward et al. 1993, 1999]]); the natal year of all fledged cohorts has been set to 1980 in the example files.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel, buzzard and goshawk data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology), in the last case in cooperation with Uppsala University and the Swedish Hunters' Association. The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-12-11T10:56:38Z

RobertKenward: /* Comparing two sets of survival data */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

==== Plotting survival for a single data set ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''kaplan meier survival''.

* Under '''Analysis Options''' ensure ''one set'' is selected

* Under '''Input files''' press '''browse''' and find, for the ''set 1 survival file'' the file ''<RangesFolder>\samples\raptors\GoshawkJuvMale.srv''.

* Press the '''Run Analysis''' button.

Looking at the statistics window, the sample size was not adequate until the start of the second month, and became less than 30 animals due to moulting of tail-mounted radio tags after 30 April. Run the analysis again, selecting as '''set 1 start date''' the ''specified date'' and use the calendar to select 1 July 1980 (slightly after the fledging date), then in '''set 1 end date''' again select ''specified date'' and set 31 March 1981. This estimates juvenile male survival to the start of the next egg-laying period, as used in [[Bibliography|Kenward et al. (1999)]].

==== Comparing two sets of survival data ====

[[File:To be added]]

* Under '''Analysis Options''' select ''two sets for comparison''

* Under '''Input files''' check that the ''set 1 survival file'' is still ''<RangesFolder>\samples\raptors\GoshawkJuvMale.srv''.

* Check that '''set 1 start date''' has ''specified date'' selected, of 1 July 1980.

* Check that '''set 1 end date''' has ''specified date'' selected, of 31 March 1981.

* Press '''browse''' for the ''set 2 survival file'' and find ''<RangesFolder>\samples\raptors\GoshawkJuvFem.srv''.

* For the '''set 2 start date''', use the ''set 1 start date'' option.

* For the '''set 2 end date''', use the ''set 2 end date'' option.

* Press the '''Run Analysis''' button.

The survival is poorer for juvenile males than for juvenile females due mainly to differences from October (month 4) onwards. The ''z'' values of 2.07 to 2.13 are higher than the value of 1.96 for alpha = 0.05, so ''P'' < 0.05.

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward (2001), Kenward et al. (2001)]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls & Kenward 1995, 1998, 2001]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission. Goshawk survival data were collected on the Swedish island of Gotland ([[Bibliography|Kenward et al. 1993, 1999]]); the natal year of all fledged cohorts has been set to 1980 in the example files.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel, buzzard and goshawk data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology), in the last case in cooperation with Uppsala University and the Swedish Hunters' Association. The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-12-11T10:55:18Z

RobertKenward: /* Comparing two sets of survival data */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

==== Plotting survival for a single data set ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''kaplan meier survival''.

* Under '''Analysis Options''' ensure ''one set'' is selected

* Under '''Input files''' press '''browse''' and find, for the ''set 1 survival file'' the file ''<RangesFolder>\samples\raptors\GoshawkJuvMale.srv''.

* Press the '''Run Analysis''' button.

Looking at the statistics window, the sample size was not adequate until the start of the second month, and became less than 30 animals due to moulting of tail-mounted radio tags after 30 April. Run the analysis again, selecting as '''set 1 start date''' the ''specified date'' and use the calendar to select 1 July 1980 (slightly after the fledging date), then in '''set 1 end date''' again select ''specified date'' and set 31 March 1981. This estimates juvenile male survival to the start of the next egg-laying period, as used in [[Bibliography|Kenward et al. (1999)]].

==== Comparing two sets of survival data ====

[[File:To be added]]

* Under '''Analysis Options''' select ''two sets for comparison''

* Under '''Input files''' check that the ''set 1 survival file'' is still ''<RangesFolder>\samples\raptors\GoshawkJuvMale.srv''.

* Check that '''set 1 start date''' has ''specified date'' selected, of 1 July 1980.

* Check that '''set 1 end date''' has ''specified date'' selected, of 31 March 1981.

* Press '''browse''' for the ''set 2 survival file'' and find ''<RangesFolder>\samples\raptors\GoshawkJuvFem.srv''.

* Set the '''set 2 start date''' to the ''set 1 start date'' option.

* Set the '''set 2 end date''' to the ''set 2 end date'' option.

* Press the '''Run Analysis''' button.

The survival is poorer for juvenile males than for juvenile females due mainly to differences from October (month 4) onwards. The ''z'' values of 2.07 to 2.13 are higher than the value of 1.96 for alpha = 0.05, so ''P'' < 0.05.

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward (2001), Kenward et al. (2001)]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls & Kenward 1995, 1998, 2001]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission. Goshawk survival data were collected on the Swedish island of Gotland ([[Bibliography|Kenward et al. 1993, 1999]]); the natal year of all fledged cohorts has been set to 1980 in the example files.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel, buzzard and goshawk data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology), in the last case in cooperation with Uppsala University and the Swedish Hunters' Association. The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-12-11T10:51:17Z

RobertKenward: /* Kaplan Meier Survival Analysis */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

==== Plotting survival for a single data set ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''kaplan meier survival''.

* Under '''Analysis Options''' ensure ''one set'' is selected

* Under '''Input files''' press '''browse''' and find, for the ''set 1 survival file'' the file ''<RangesFolder>\samples\raptors\GoshawkJuvMale.srv''.

* Press the '''Run Analysis''' button.

Looking at the statistics window, the sample size was not adequate until the start of the second month, and became less than 30 animals due to moulting of tail-mounted radio tags after 30 April. Run the analysis again, selecting as '''set 1 start date''' the ''specified date'' and use the calendar to select 1 July 1980 (slightly after the fledging date), then in '''set 1 end date''' again select ''specified date'' and set 31 March 1981. This estimates juvenile male survival to the start of the next egg-laying period, as used in [[Bibliography|Kenward et al. (1999)]].

==== Comparing two sets of survival data ====

[[File:To be added]]

* Under '''Analysis Options''' select ''two sets for comparison''

* Under '''Input files''' check that the ''set 1 survival file'' is still ''<RangesFolder>\samples\raptors\GoshawkJuvMale.srv''.

* Check that '''set 1 start date''' has ''specified date'' selected, of 1 July 1980.

* Check that '''set 1 end date''' has ''specified date'' selected, of 31 March 1981.

* Press '''browse''' for the ''set 2 survival file'' and find ''<RangesFolder>\samples\raptors\GoshawkJuvFem.srv''.

* Set the '''set 2 start date'' to the ''set 1 start date'' option.

* Set the '''set 2 end date'' to the ''set 2 end date'' option.

* Press the '''Run Analysis''' button.

The survival is poorer for juvenile males than for juvenile females due mainly to differences from October (month 4) onwards. The ''z'' values of 2.07 to 2.13 are higher than the value of 1.96 for alpha = 0.05, so ''P'' < 0.05.

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward (2001), Kenward et al. (2001)]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls & Kenward 1995, 1998, 2001]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission. Goshawk survival data were collected on the Swedish island of Gotland ([[Bibliography|Kenward et al. 1993, 1999]]); the natal year of all fledged cohorts has been set to 1980 in the example files.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel, buzzard and goshawk data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology), in the last case in cooperation with Uppsala University and the Swedish Hunters' Association. The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Output File Headers

2014-12-09T20:25:02Z

RobertKenward: /* Kaplan Meier survival */

This page describes the column headers for statistics files. These are output from Ranges analyses and can be loaded in the Statistics window.

== Inter-location headings (all values) ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|LocE || Location easting
|-
|LocN || Location northing
|-
|Headings(degrees) || Heading angle from track to previous location
|}

== Inter-location headings (means for each range) ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|-
|N || Number of locations
|-
|Average || Average heading of locations in degrees
|-
|SE+- || Standard Error of heading
|-
|GeoMean || Geometric mean heading
|-
|SE*/ || Standard Error of geometric heading (when using logs you must multiply and divide rather than add and subtract the SE)
|}

== Inter-location distances (all values) ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|LocE || Location easting
|-
|LocN || Location northing
|-
|Distances(m) || Distance of location in metres
|-
|Dispersal(distx) || 1 if animal has dispersed by this location, 1 otherwise (only when dispersal detector selected).
|-
|LQV1 || as specified in the location file
|-
|... LQVn || as specified in the location file
|}

NB. It is possible to reimport this csv file and then use distances as an LQV. This means that they can be used for analyses of, say, "only locations at least 100m from den".

== Inter-location distances (means for each range) ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|N || Number of locations
|-
|Average || Average distance of locations (m)
|-
|SE+- || Standard Error of distance
|-
|GeoMean || Geometric mean distance
|-
|SE*/ || Standard Error of geometric distance (when using logs you must multiply and divide rather than add and subtract the SE)
|}

== Inter-location times (all values) ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|LocE || Location easting
|-
|LocN || Location northing
|-
|Times(minutes) || Time between locations
|}

== Inter-location times (means for each range) ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|N || Number of locations
|-
|Average || Average time between locations in minutes
|-
|SE+- || Standard Error of time between locations
|-
|GeoMean || Geometric mean time between locations
|-
|SE*/ || Standard Error of geometric time between locations (when using logs you must multiply and divide rather than add and subtract the SE)
|}

== Inter-location speeds (all values) ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|LocE || Location easting
|-
|LocN || Location northing
|-
|Speeds(km/h) || Speeds in kilometres per hour
|}

== Inter-location speeds (means for each range) ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|N || Number of locations
|-
|Average || Average speed
|-
|SE+- || Standard Error of speed
|-
|GeoMean || Geometric mean speed
|-
|SE*/ || Standard Error of geometric speed (when using logs you must multiply and divide rather than add and subtract the SE)
|}

== Convex polygons ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|CentE || Easting for the range centre
|-
|CentN || Northing for the range centre
|-
|Span || Maximum distance between locations
|-
|Mean || Mean distance of locations from range centre
|-
|Median || Median distance of locations from range centre
|-
|Max || Maximum distance of locations from range centre
|-
|dummy || Unused variable
|-
|Core1 || Core percentage
|-
|Area || Area of that core (ha)
|-
|Core2 || Core percentage
|-
|Area || Area of that core (ha)
|-
|Core3 || Core percentage
|-
|Area || Area of that core (ha)
|-
|etc ||
|}

== Concave polygons ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|Span || Maximum distance between locations
|-
|dummy || Unused variable
|-
|dummy || Unused variable
|-
|dummy || Unused variable
|-
|dummy || Unused variable
|-
|dummy || Unused variable
|-
|dummy || Unused variable
|-
|Core% || Core percentage, always 100 for concave polygons
|-
|Area || Area of that core (ha)
|}

== Neighbour-linkage ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|Core1 || Core percentage
|-
|Area || Area of that core (ha)
|-
|Nuclei || Number of nuclei
|-
|Partial || Partial area
|-
|DivLocs || Simpson's index for location diversity
|-
|DivArea || Simpson's index for area diversity
|-
|Core2 || Core percentage
|-
|Area || Area of that core (ha)
|-
|Nuclei || Number of nuclei
|-
|Partial || Partial area
|-
|DivLocs || Simpson's index for location diversity
|-
|DivArea || Simpson's index for area diversity
|-
|Core3 || Core percentage
|-
|Area || Area of that core (ha)
|-
|Nuclei || Number of nuclei
|-
|Partial || Partial area
|-
|DivLocs || Simpson's index for location diversity
|-
|DivArea || Simpson's index for area diversity
|-
|Core1 || Core percentage
|-
|Area || Area of that core (ha)
|-
|etc ||
|}

== Ellipses ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|CentE || Easting for the range centre
|-
|CentN || Northing for the range centre
|-
|MARAD || Radius of the major axis for the maximum core size selected
|-
|MIRAD || Radius of the minor axis for the maximum core size selected
|-
|THETA || Angle major axis is inclined from horizontal
|-
|X-VAR || Variance in eastings
|-
|Y-VAR || Variance in northings
|-
|COVAR || Covariance of eastings x northings
|-
|r-STAT || correlation coefficient
|-
|JTAsym || Standard deviation of the major axis divided by that of the minor axis.
|-
|Core1 || Core percentage
|-
|Area || Area of that core (ha)
|-
|Core2 || Core percentage
|-
|Area || Area of that core (ha)
|etc ||
|}

== Harmonic mean contours ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|CentE || Arithmetic mean of eastings (range centre if with CentN)
|-
|CentN || Arithmetic mean of northings (range centre if with CentE)
|-
|Value || Density score at the central location
|-
|Spread || Range spread at central location
|-
|Dispersion || An index of dispersion of the distribution is given by the peak density value (at the range centre
location) divided by the standard deviation of the density value across all the locations
|-
|Skew || An index of skew in the distribution is given by the Euclidean distance between the arithmetic mean centre and the location with the peak density value, divided by the standard deviation of the density value across all the locations
|-
|Kurtosis || Kurtosis of the location distribution
|-
|hRef || Not relevant to Harmonic means
|-
|hUsed || Not relevant to Harmonic means
|-
|Core1 || Core percentage
|-
|Area || Area of that core (ha)
|-
|Core2 || Core percentage
|-
|Area || Area of that core (ha)
|-
|Core3 || Core percentage
|-
|Area || Area of that core (ha)
|-
|etc ||
|}

== Kernel contours ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|CentE || Arithmetic mean of eastings (range centre if with CentN)
|-
|CentN || Arithmetic mean of northings (range centre if with CentE)
|-
|Value || Density score at the central location
|-
|Spread || Range spread at central location
|-
|Dispersion || An index of dispersion of the distribution is given by the peak density value (at the range centre
location) divided by the standard deviation of the density value across all the locations
|-
|Skew || An index of skew in the distribution is given by the Euclidean distance between the arithmetic mean centre and the location with the peak density value, divided by the standard deviation of the density value across all the locations
|-
|Kurtosis || Kurtosis of the location distribution
|-
|hRef || Not relevant to Harmonic means
|-
|hUsed || Not relevant to Harmonic means
|-
|xhRef ||Multiple of hRef used (user defined or calculated by LSCV)
|-
|interval || Size (m) of lattice cells used in kernel estimation
|-
|Core1 || Core percentage
|-
|Area || Area of that core (ha)
|-
|Core2 || Core percentage
|-
|Area || Area of that core (ha)
|-
|Core3 || Core percentage
|-
|Area || Area of that core (ha)
|-
|etc ||
|}

== Range overlap ==

{| class="wikitable"
| style="width: 200px;" | overlap_ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|CentE || Arithmetic mean of eastings (range centre if with CentN)
|-
|CORE(%) !! Core percentage
|-
|ID1(%) || Percentage of overlapID range overlaps with range ID1 for this core
|-
|ID2(%) || Percentage of overlapID range overlaps with range ID2 for this core
|-
|ID3(%) || Percentage of overlapID range overlaps with range ID3 for this core
|-
|ID4(%) || Percentage of overlapID range overlaps with range ID4 for this core
|-
|etc ||
|-
|ID1(m2) || Area of overlap for overlapID range and range ID1 for this core
|-
|ID2(m2) || Area of overlap for overlapID range and range ID2 for this core
|-
|ID3(m2) || Area of overlap for overlapID range and range ID3 for this core
|-
|ID4(m2) || Area of overlap for overlapID range and range ID4 for this core
|-
|etc ||
|}

== Overlap of range on locations ==

{| class="wikitable"
| style="width: 200px;" | overlap_ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|CentE || Arithmetic mean of eastings (range centre if with CentN)
|-
|CORE(%) !! Core percentage
|-
|ID1(%) || Percentage of overlapID range overlaps with locations in range ID1 for this core
|-
|ID2(%) || Percentage of overlapID range overlaps with locations in range ID2 for this core
|-
|ID3(%) || Percentage of overlapID range overlaps with locations in range ID3 for this core
|-
|ID4(%) || Percentage of overlapID range overlaps with locations in range ID4 for this core
|}

== Autocorrelations ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|SIpast1(h) || **TODO **
|-
|SIpast2(h) || **TODO **
|-
|Mins || **TODO **
|-
|1xMins || **TODO **
|-
|2xMins || **TODO **
|-
|3xMins || **TODO **
|-
|4xMins || **TODO **
|-
|5xMins || **TODO **
|-
|etc ||
|}

== Dynamic interactions ==

{| class="wikitable"
| style="width: 200px;" | range1ID || First individual's identification number
|-
|AGE || First individual's age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || First individual's sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || First individual's month tracking started
|-
|YEAR || First individual's year tracking started
|-
|FOC-E || First individual's focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || First individual's focal site Northing (e.g. nest, den, trap site etc)
|-
|range2ID || Second individual's identification number
|-
|AGE || Second individual's age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Second individual's sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Second individual's month tracking started
|-
|YEAR || Second individual's year tracking started
|-
|FOC-E || Second individual's focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Second individual's focal site Northing (e.g. nest, den, trap site etc)
|-
|Nobs || Number of observed distances
|-
|AMEANObs || Arithmetic mean of observed distances
|-
|SUMObs || Sum of observed distances
|-
|SoSobs || Sum of Squares of observed distances
|-
|GMEANobs || Geometric mean of the observed distances
|-
|LSUMobs || Sum of logged observed distances
|-
|LSoSobs || Sum of squares of logged observed distances
|-
|MEDobs || Median Observed distance
|-
|Nran || Number of random locations
|-
|AMEANran || Arithmetic mean of random distances
|-
|SUMran || Sum of random distances
|-
|SoSran || Sum of Squares of random distances
|-
|GMEANran || Geometric mean of the random distances
|-
|LSUMran || Sum of logged random distances
|-
|LSoSran || Sum of squares of logged random distances
|-
|MEDran || Median random distance
|-
|JacobsAMEAN || Jacob's index of arithmetic mean distances
|-
|JacobsGMEAN || Jacob's index of geometric mean distances
|-
|JacobsMED || Jacob's index of median distances
|}

== Location-point distances ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|Nobs || Number of observed distances
|-
|AMEANObs || Arithmetic mean of observed distances
|-
|SUMObs || Sum of observed distances
|-
|SoSobs || Sum of Squares of observed distances
|-
|GMEANobs || Geometric mean of the observed distances
|-
|LSUMobs || Sum of logged observed distances
|-
|LSoSobs || Sum of squares of logged observed distances
|-
|MEDobs || Median Observed distance
|-
|Nran || Number of random locations
|-
|AMEANran || Arithmetic mean of random distances
|-
|SUMran || Sum of random distances
|-
|SoSran || Sum of Squares of random distances
|-
|GMEANran || Geometric mean of the random distances
|-
|LSUMran || Sum of logged random distances
|-
|LSoSran || Sum of squares of logged random distances
|-
|MEDran || Median random distance
|-
|JacobsAMEAN || Jacob's index of arithmetic mean distances
|-
|JacobsGMEAN || Jacob's index of geometric mean distances
|-
|JacobsMED || Jacob's index of median distances
|}

== Range centre spacing ==

{| class="wikitable"
| style="width: 200px;" | Nobs || Number of observed distances
|-
|MEANobs || Arithmetic mean of observed distances
|-
|SUMobs || Sum of observed distances
|-
|SoSobs || Sum of Squares of observed distances
|-
|SEobs || Standard Error of observed distances
|-
|AREA || Area of range
|-
|MEANest || Estimated mean distance
|-
|SEest || Standard error of estimated distances
|-
|t-obs/est || Student's t-test for regular spacing of estimated observations
|-
|Nran || Number of random locations
|-
|MEANran || Arithmetic mean of random distances
|-
|SUMran || Sum of random distances
|-
|SoSran || Sum of Squares of random distances
|-
|SEran || Standard error of random distances
|-
|t-obs/ran || Student's t-test for regular spacing of random estimates
|}

== Habitat in a map rectangle ==

{| class="wikitable"
| style="width: 200px;" | W-edge || Western edge
|-
|E-edge || Eastern edge
|-
|S-edge || Southern Edge
|-
|N-edge || Northern edge
|-
|Area || Area of assessed rectangle
|-
|HabitatGroup1 || % of the area made up of this habitat
|-
|HabitatGroup2 || % of the area made up of this habitat
|-
|HabitatGroup3 || % of the area made up of this habitat
|-
|etc ||
|}

== Habitat in a map circle ==

{| class="wikitable"
| style="width: 200px;" | cent-E || Western edge
|-
|cent-N || Circle centre northing
|-
|radius || radius of circle in metres
|-
|Area || Area of circle
|-
|HabitatGroup1 || % of the area made up of this habitat
|-
|HabitatGroup2 || % of the area made up of this habitat
|-
|HabitatGroup3 || % of the area made up of this habitat
|-
|etc ||
|}

== Habitat content of ranges ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|Core1 || Core percent
|-
|Area || Area of core
|-
|HabitatGroup1 || % of the area made up of this habitat
|-
|HabitatGroup2 || % of the area made up of this habitat
|-
|HabitatGroup3 || % of the area made up of this habitat
|-
|etc ||
|-
|Core2 || Core size
|-
|Area || Area of core 2
|-
|HabitatGroup1 || % of the area made up of this habitat
|-
|HabitatGroup2 || % of the area made up of this habitat
|-
|HabitatGroup3 || % of the area made up of this habitat
|-
|etc ||
|}

== Habitat points within ranges ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|Core1 || Core percent
|-
|Area || Area of core 1
|-
|sites || Number of sites within core 1
|-
|Core2 || Core percent
|-
|Area || Area of core 2
|-
|sites || Number of sites within core 2
|-
|etc ||
|}

== Habitat at locations ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|N-locs || Number of locations
|-
|HabitatGroup1 || % of the locations (or ellipse area if error ellipses) of this habitat
|-
|HabitatGroup2 || % of the locations (or ellipse area if error ellipses) of this habitat
|-
|HabitatGroup3 || % of the locations (or ellipse area if error ellipses) of this habitat
|-
|etc ||
|}

== Habitat preference in ranges ==

{| class="wikitable"
| style="width: 200px;" | ID || Individual identification number
|-
|AGE || Age (e.g. 1 = Juvenile, 2 = Yearling, 3 = Adult)
|-
|SEX || Sex (e.g. 1 = Male, 2 = Female)
|-
|MONTH || Month tracking started
|-
|YEAR || Year tracking started
|-
|FOC-E || Focal site Easting (e.g. nest, den, trap site etc)
|-
|FOC-N || Focal site Northing (e.g. nest, den, trap site etc)
|-
|Core1 || Core percent
|-
|Area || Area of core
|-
|HabitatGroup1 || % of the area made up of this habitat
|-
|HabitatGroup2 || % of the area made up of this habitat
|-
|HabitatGroup3 || % of the area made up of this habitat
|-
|etc ||
|-
|Core2 || Core size
|-
|Area || Area of core 2
|-
|HabitatGroup1 || % of the area made up of this habitat
|-
|HabitatGroup2 || % of the area made up of this habitat
|-
|HabitatGroup3 || % of the area made up of this habitat
|-
|etc ||
|-
|N-locs || Number of locations
|-
|HabitatGroup1 || % of the locations (or ellipse area if error ellipses) of this habitat
|-
|HabitatGroup2 || % of the locations (or ellipse area if error ellipses) of this habitat
|-
|HabitatGroup3 || % of the locations (or ellipse area if error ellipses) of this habitat
|-
|etc ||
|}

== Resource area dependence ==

{| class="wikitable"
| style="width: 200px;" |Habitat || The habitat group name
|-
|Core || The core %
|-
|ExclusionStatus || Habitat Excluded or not
|-
|rObserved || Pearson's r for observations
|-
|bObserved || Slope of regression for observations
|-
|SEbObserved || Standard error of slope for observations
|-
|cObserved || Area at y-axis intercept for observations
|-
|0-Core%Observed || Number of observed habitat cores with zero core area
|-
|0-Habitat%Observed || Number of observed habitat cores without this habitat in the core
|-
|rMeanRandom || Mean Pearson's r for randomly placed range cores
|-
|rMedianRandom || Median Pearson's r for randomly placed range cores
|-
|z || z for for randomly placed range cores
|-
|+r95%CL || lower confidence limit for random r if normally distributed
|-
|r95%CL || upper confidence limit for random r if normally distributed
|-
|Beyondr || number of random r values more extreme than the observed r
|-
|bMeanRandom || Mean slope for randomly placed range cores
|-
|SEbMeanRandom || Mean standard error of slope for randomly placed range cores
|-
|cMeanRandom || Mean area at y-axis intercept for random rs
|-
|0-habitat%Random || number of random habitat cores without this habitat in the core
|}

== Kaplan Meier survival ==

{| class="wikitable"
| style="width: 200px;" | File || The name of the analysis survival file
|-
|Dates || The dates set for the analysis
|-
|Interval || the interval number
|-
|Ending || the end date of the interval
|-
|Present At Start || Individuals present at start of interval
|-
|Present At End || Individuals present at end of interval
|-
|Censor Dead || Individuals died during interval
|-
|Censor Lost || Individuals lost during interval
|-
|Alive at End || Individuals alive at end of interval
|-
|Added During || Individuals added during interval
|-
|Survival Total || Individuals survived for interval
|-
|Survival Decrease|| Decrease in individuals for interval
|-
|Variance Greenwood || Greenwood variance for interval
|-
|Variance Cox/Oakes || Cox/Oakes variance for interval
|-
|Tag days || Total number of days for all individuals
|}

Modelling Analysis

2014-12-09T20:19:59Z

RobertKenward: /* analysis options */

When Ranges 4 was launched in 1990, individual-based modelling of animal populations was in its infancy. However, it was becoming clear that not only was such modelling powerful for predicting population beyond the envelope of conditions in which individuals were measured, but also that radio-tracking could provide the linkages of habitats and sociality with persistence or dispersal, and survival and productivity, that would be needed for modelling. So the provision of a toolkit for modelling was a long-term aspiration for this type of software [[Bibliography|(Kenward 1992)]].

== Introduction ==

The initial contribution to modelling is a new approach to analysing resources, such as habitats, which can estimate minimal requirements of individual animals and hence enable individual-based modelling. There is also a method for estimating survival or dispersal rates that is convenient for data from radio-tagging. There are illustrated explanations of both methods in ([[Bibliography|Kenward 2001]]). Further components of a toolkit for modelling will be added to this tab in due course, with the ultimate aspiration of linking these in order to automate population modelling from location data and maps.

== Resource Area Dependence Analysis ==

The principle that underlies this analysis is that if an animal requires a particular amount of a resource, such as a particular tree or area of habitat, then it will extend its home-range to an extent necessary to contain than amount of resource. If the resource is rarer, range outlines will be larger. In this case, there will be a negative relationship between range area and resource content. For strong resource dependence, the relationship tends to become negative exponential ([[Bibliography|Kenward 1982]]), but is linear with negative correlation if the logarithm of resource content is plotted against the logarithm of range area. Moreover, the range area at a point where the resource proportion is 1 is an estimate of the minimum area of resource required.

Another important consideration is that a single patch of habitat enclosed within range outlines of varying size will show a negative relationship of proportion with area by chance. To avoid misinterpretation of random events, the significance of observed correlations should be compared with random range placement in the same areas. In the case of a single resource, its occurrence significantly more frequently in observed ranges than in random placements may be the best indication of its importance.

This analysis requires an edge file and a habitat file. Suitable example files are in the folder squirrel, as described for [[Habitat#sources|habitat analysis]].

=== analysis options ===

For a rapid examination of whether the prevalence of any of the habitats in a set correlate negatively with range size, analysis of observed values only is appropriate. The statistics available from such are run are the observed value of r, the slope b for the regression of (log) habitat prevalence on (log) range area, the standard error of b, the (log) area intercept c for 100% habitat, the percentage of ranges with no habitat at all in the core, and the percentage with none of the habitat in a particular row. On the graph, the green regression line is for the observed values.

To investigate significance, randomisations are available with 99, 199 and 999 iterations. During randomisation, outlines of all the observed ranges are randomly rotated and displaced within an envelope. By default, that envelope is the minimum convex polygon round all observed outlines for the largest core size among a set of core sizes. N outlines are chosen at random with replacement from the N observed outlines, and an r, b and c calculated in each case.

Statistics from randomisations include the mean and median values for r by randomisation, z for the difference of this r from the observedr, with associated 95% confidence limits, on the assumption that r is distributed normally. The next value is a more robust test statistic, which is the number of random r values more extremely negative than the observed value. In a two-tailed test, with 999 iterations, a value less than 25 indicates P<0.05, with 5 or less for P<=0.01 and 0 for P<=0.02. There are then mean values for b, its SE and c by randomisation, which are used to plot the yellow line on the graph, and finally the proportion of random placements of the range outlines that lack the relevant habitat. Percentages below the observed percentage of ranges without the habitat indicate non-random placement of observed range outlines with respect to that habitat.

=== zero handling ===

Animals may differ in their use of resources. Some may specialise in a quite different resource to the majority, either through choice or exclusion, so that it does not occur in their range. Excluded animals may have above average range size, in which case addition of a value below other values (which is done automatically for the replace zeros option), will tend to maintain negative correlations. However, if resource strategy is divergent, inclusion of missing (or very low) proportions of the resource may conceal a major effect. At present, a choice of excluding missing values is possible, with two options; resample zeros to obtain resource within all outlines is appropriate if it is suspected that large ranges are more likely to include habitat by chance; otherwise the ignore zeros option will give very similar results but will be faster and will estimate the proportion of randomly-placed outlines that lack the resource. When there are very low values of resource in some observed ranges, it may in future be possible to exclude these objectively as statistical outliers and then examine these ranges for different resource area dependence relationships.

=== exclude habitats ===

As in analyses of habitat preference, disproportionate use of one relatively abundant resource can conceal a dependence also on one or more uncommon resources. This effect can be avoided by removing the area of the first resource from the range and then re-analysing for the second, in a step-wise approach. Resource exclusion of this type is supported in Ranges 9. The Ctrl key can be held to select multiple habitats to exclude, and is also required to remove previous selections.

=== envelope ===

The default envelope, mcp around max edge file core may allow very little rotation and displacement of large ranges in a small area, which can greatly slow analyses. If resources have a wide distribution, a larger user defined envelope may be used to speed the randomisation, at least for a first quick test, by loading the envelope separately. This is also useful if analysis is focussed in small cores (say, 50% cluster cores), but a polygon around all the locations is being used to standardise the envelope.

== Kaplan-Meier Survival ==

The Kaplan-Meier approach ([[Bibliography|Kaplan & Meier 1958]]), as described for radio-tracking by [[Bibliography|Pollock et al. (1989)]], is provided as a first survival estimation technique. Its interval-based estimation procedure adapts well to the asynchronous (staggered) entries and departures for unknown reasons that are typical for groups of radio-tagged animals.

Example data are the trajectories in first 4 years of life for 152 buzzards that were tagged in or near their natal nests (***.srv in the folder buzzards). There are also files one.srv and two.srv in the folder squirrel, for two sets of squirrels subject to different short-term control measures as a damage-reduction strategy.

=== analysis options ===

Choice of one set will run an analysis on one survival file, with a plot that includes error bars for 95% confidence limits based on [[Bibliography|Cox-Oakes (1984)]] variance estimation. The statistics include, for each time interval in the analysis, the number of animals with active tags at the beginning and end of the interval, the number that died, had lost signals for unexplained reasons, were known to have lived through expiry of tag (e.g. due to battery exhaustion) or were added through tag attachment. There is then an estimate of the survival with two types of 95% confidence limits, and the survival decrease since the last period. The numbers in each category are summed at the bottom of the table, with a count of the total number of active tag-days. If the statistics file is saved, it can be opening in Excel or other spreadsheet for .csv files. The .kms graphics file can be opened at a later date in the graphics window.

Choice of two sets for comparison will run two plots as above, but also estimate statistics for the comparison between the survival rates. These are log-rank chi-square statistics with one degree of freedom, estimated in progressively more conservative ways, on the penultimate row of the table, and a comparison (see [[Bibliography|Pollock et al. (1989)]] and [[Bibliography|Kenward (2001)]] for further details. The two-sets option enables re-entry of the same file as for the first set, using a second '''[[Selections|Make Selections]]''' button and box to choose a different category of animal (e.g. adult rather than juvenile) within the file.

=== time interval ===

The length of time intervals for analysis should be great enough to provide opportunity for a number of deaths, but not too long to detect seasonal differences in timing of mortality. A choice of days rather than one month will bring up a box in which the number of days for each interval can be entered. Typically, monthly intervals are selected unless the period to be analysed is less than about 3 months (use e.g. 5-day intervals for the one.srv and two.srv squirrel example files).

=== set 1 start date ===

Although the default is the first animal start date, this often starts the analysis with too few animals in the first time interval; there should ideally be at least 20, because otherwise the confidence limits will be very large, with a tendency for differences between categories to lack significance. Even when many animals are marked within a short time, there may be a need to delay the start of analysis to exclude animals with possible adversely affects of capture or considered more vulnerable while adjusting to tags. Selecting specified date will bring up a calendar to assist the choice of date.

=== set 1 end date ===

The default of last animal end date will often result in very few individuals in the last sample interval, and hence undesirably large confidence limits. It is therefore possible either to set a specified date with a calendar, or to give a duration in days for the analysis.
=== set 2 start date and end date ===

For a comparison run, two further option boxes appear. For cases where the time period for comparison is the same in both files, or categories within the same file, it is convenient to be able to choose set 1 start date and set 1 end date, as well as having other options similar to those for the first set of data.

=== treat lost as dead ===

When carcases are found, the category of died is not hard to assign in survival files. Likewise, when tracking is stopped at a particular date, or tag cell is due to expire the fate category lived can be assigned. However, a problem arises when tracking animals for which deaths are frequently associated with destruction of the radio (e.g. through trauma) or severe loss of signal range or transport of the carcase away from a monitored area. In this case, survival is overestimated by the default of treating the lost signals as tag failure. For conservative estimates of survival during population modelling, it may be most appropriate to treat signals lost before the likely end of tag cell life as if they represent deaths, by ticking this box. The difference in survival estimated by merely censoring the radios will not be large if radios are highly reliable. Correction for“lost” animals that are subsequently retrapped or resighted after the study period can involve reclassifying their fate as lived; more sophisticated correction from such data ([[Bibliography|Kenward 2001]]) will be added in due course.

Modelling Analysis

2014-12-09T20:17:09Z

RobertKenward:

When Ranges 4 was launched in 1990, individual-based modelling of animal populations was in its infancy. However, it was becoming clear that not only was such modelling powerful for predicting population beyond the envelope of conditions in which individuals were measured, but also that radio-tracking could provide the linkages of habitats and sociality with persistence or dispersal, and survival and productivity, that would be needed for modelling. So the provision of a toolkit for modelling was a long-term aspiration for this type of software [[Bibliography|(Kenward 1992)]].

== Introduction ==

The initial contribution to modelling is a new approach to analysing resources, such as habitats, which can estimate minimal requirements of individual animals and hence enable individual-based modelling. There is also a method for estimating survival or dispersal rates that is convenient for data from radio-tagging. There are illustrated explanations of both methods in ([[Bibliography|Kenward 2001]]). Further components of a toolkit for modelling will be added to this tab in due course, with the ultimate aspiration of linking these in order to automate population modelling from location data and maps.

== Resource Area Dependence Analysis ==

The principle that underlies this analysis is that if an animal requires a particular amount of a resource, such as a particular tree or area of habitat, then it will extend its home-range to an extent necessary to contain than amount of resource. If the resource is rarer, range outlines will be larger. In this case, there will be a negative relationship between range area and resource content. For strong resource dependence, the relationship tends to become negative exponential ([[Bibliography|Kenward 1982]]), but is linear with negative correlation if the logarithm of resource content is plotted against the logarithm of range area. Moreover, the range area at a point where the resource proportion is 1 is an estimate of the minimum area of resource required.

Another important consideration is that a single patch of habitat enclosed within range outlines of varying size will show a negative relationship of proportion with area by chance. To avoid misinterpretation of random events, the significance of observed correlations should be compared with random range placement in the same areas. In the case of a single resource, its occurrence significantly more frequently in observed ranges than in random placements may be the best indication of its importance.

This analysis requires an edge file and a habitat file. Suitable example files are in the folder squirrel, as described for [[Habitat#sources|habitat analysis]].

=== analysis options ===

For a rapid examination of whether the prevalence of any of the habitats in a set correlate negatively with range size, analysis of observed values only is appropriate. The statistics available from such are run are the observed value of r, the slope b for the regression of (log) habitat prevalence on (log) range area, the standard error of b, the (log) area intercept c for 100% habitat, the percentage of ranges with no habitat at all in the core, and the percentage with none of the habitat in a particular row. On the graph, the green regression line is for the observed values.

To investigate significance, randomisations are available with 99, 199 and 999 iterations. During randomisation, outlines of all the observed ranges are randomly rotated and displaced within an envelope. By default, that envelope is the minimum convex polygon round all observed outlines for the largest core size among a set of core sizes. N outlines are chosen at random with replacement from the N observed outlines, and an r, b and c calculated in each case.

Statistics from randomisations include the mean and median values for r by randomisation, z for the difference of this r from the observedr, with associated 95% confidence limits, on the assumption that r is distributed normally. The next value is a more robust test statistic, which is the number of random r values more extremely negative than the observed value. In a two-tailed test, with 999 iterations, a value less than 25 indicates P<0.05, with 5 or less for P<=0.01 and 0 for P<=0.02. There are then mean values for b, its SE and c by randomisation, which are used to plot the yellow line on the graph, and finally the proportion of random placements of the range outlines that lack the relevant habitat. Percentages below the observed percentage of ranges without the habitat indicate non-random placement of observed range outlines with respect to that habitat.

=== zero handling ===

Animals may differ in their use of resources. Some may specialise in a quite different resource to the majority, either through choice or exclusion, so that it does not occur in their range. Excluded animals may have above average range size, in which case addition of a value below other values (which is done automatically for the replace zeros option), will tend to maintain negative correlations. However, if resource strategy is divergent, inclusion of missing (or very low) proportions of the resource may conceal a major effect. At present, a choice of excluding missing values is possible, with two options; resample zeros to obtain resource within all outlines is appropriate if it is suspected that large ranges are more likely to include habitat by chance; otherwise the ignore zeros option will give very similar results but will be faster and will estimate the proportion of randomly-placed outlines that lack the resource. When there are very low values of resource in some observed ranges, it may in future be possible to exclude these objectively as statistical outliers and then examine these ranges for different resource area dependence relationships.

=== exclude habitats ===

As in analyses of habitat preference, disproportionate use of one relatively abundant resource can conceal a dependence also on one or more uncommon resources. This effect can be avoided by removing the area of the first resource from the range and then re-analysing for the second, in a step-wise approach. Resource exclusion of this type is supported in Ranges 9. The Ctrl key can be held to select multiple habitats to exclude, and is also required to remove previous selections.

=== envelope ===

The default envelope, mcp around max edge file core may allow very little rotation and displacement of large ranges in a small area, which can greatly slow analyses. If resources have a wide distribution, a larger user defined envelope may be used to speed the randomisation, at least for a first quick test, by loading the envelope separately. This is also useful if analysis is focussed in small cores (say, 50% cluster cores), but a polygon around all the locations is being used to standardise the envelope.

== Kaplan-Meier Survival ==

The Kaplan-Meier approach ([[Bibliography|Kaplan & Meier 1958]]), as described for radio-tracking by [[Bibliography|Pollock et al. (1989)]], is provided as a first survival estimation technique. Its interval-based estimation procedure adapts well to the asynchronous (staggered) entries and departures for unknown reasons that are typical for groups of radio-tagged animals.

Example data are the trajectories in first 4 years of life for 152 buzzards that were tagged in or near their natal nests (***.srv in the folder buzzards). There are also files one.srv and two.srv in the folder squirrel, for two sets of squirrels subject to different short-term control measures as a damage-reduction strategy.

=== analysis options ===

Choice of one set will run an analysis on one survival file, with a plot that includes error bars for 95% confidence limits based on variance estimation. The statistics include, for each time interval in the analysis, the number of animals with active tags at the beginning and end of the interval, the number that died, had lost signals for unexplained reasons, were known to have lived through expiry of tag (e.g. due to battery exhaustion) or were added through tag attachment. There is then an estimate of the survival with two types of 95% confidence limits, and the survival decrease since the last period. The numbers in each category are summed at the bottom of the table, with a count of the total number of active tag-days. If the statistics file is saved, it can be opening in Excel or other spreadsheet for .csv files. The .kms graphics file can be opened at a later date in the graphics window.

Choice of two sets for comparison will run two plots as above, but also estimate statistics for the comparison between the survival rates. These are log-rank chi-square statistics with one degree of freedom, estimated in progressively more conservative ways, on the penultimate row of the table, and a comparison (see [[Bibliography|Pollock et al. (1989)]] and [[Bibliography|Kenward (2001)]] for further details. The two-sets option enables re-entry of the same file as for the first set, using a second '''[[Selections|Make Selections]]''' button and box to choose a different category of animal (e.g. adult rather than juvenile) within the file.

=== time interval ===

The length of time intervals for analysis should be great enough to provide opportunity for a number of deaths, but not too long to detect seasonal differences in timing of mortality. A choice of days rather than one month will bring up a box in which the number of days for each interval can be entered. Typically, monthly intervals are selected unless the period to be analysed is less than about 3 months (use e.g. 5-day intervals for the one.srv and two.srv squirrel example files).

=== set 1 start date ===

Although the default is the first animal start date, this often starts the analysis with too few animals in the first time interval; there should ideally be at least 20, because otherwise the confidence limits will be very large, with a tendency for differences between categories to lack significance. Even when many animals are marked within a short time, there may be a need to delay the start of analysis to exclude animals with possible adversely affects of capture or considered more vulnerable while adjusting to tags. Selecting specified date will bring up a calendar to assist the choice of date.

=== set 1 end date ===

The default of last animal end date will often result in very few individuals in the last sample interval, and hence undesirably large confidence limits. It is therefore possible either to set a specified date with a calendar, or to give a duration in days for the analysis.
=== set 2 start date and end date ===

For a comparison run, two further option boxes appear. For cases where the time period for comparison is the same in both files, or categories within the same file, it is convenient to be able to choose set 1 start date and set 1 end date, as well as having other options similar to those for the first set of data.

=== treat lost as dead ===

When carcases are found, the category of died is not hard to assign in survival files. Likewise, when tracking is stopped at a particular date, or tag cell is due to expire the fate category lived can be assigned. However, a problem arises when tracking animals for which deaths are frequently associated with destruction of the radio (e.g. through trauma) or severe loss of signal range or transport of the carcase away from a monitored area. In this case, survival is overestimated by the default of treating the lost signals as tag failure. For conservative estimates of survival during population modelling, it may be most appropriate to treat signals lost before the likely end of tag cell life as if they represent deaths, by ticking this box. The difference in survival estimated by merely censoring the radios will not be large if radios are highly reliable. Correction for“lost” animals that are subsequently retrapped or resighted after the study period can involve reclassifying their fate as lived; more sophisticated correction from such data ([[Bibliography|Kenward 2001]]) will be added in due course.

Modelling Analysis

2014-12-09T20:12:09Z

RobertKenward: /* analysis options */

When Ranges 4 was launched in 1990, individual-based modelling of animal populations was in its infancy. However, it was becoming clear that not only was such modelling powerful for predicting population beyond the envelope of conditions in which individuals were measured, but also that radio-tracking could provide the linkages of habitats and sociality with persistence or dispersal, and survival and productivity, that would be needed for modelling. So the provision of a toolkit for modelling was a long-term aspiration for this type of software [[Bibliography|(Kenward 1992)]].

== Introduction ==

The initial contribution to modelling is a new approach to analysing resources, such as habitats, which can estimate minimal requirements of individual animals and hence enable individual-based modelling. There is also a method for estimating survival or dispersal rates that is convenient for data from radio-tagging. There are illustrated explanations of both methods in ([[Bibliography|Kenward 2001]]). Further components of a toolkit for modelling will be added to this tab in due course, with the ultimate aspiration of linking these in order to automate population modelling from location data and maps.

== Resource Area Dependence Analysis ==

The principle that underlies this analysis is that if an animal requires a particular amount of a resource, such as a particular tree or area of habitat, then it will extend its home-range to an extent necessary to contain than amount of resource. If the resource is rarer, range outlines will be larger. In this case, there will be a negative relationship between range area and resource content. For strong resource dependence, the relationship tends to become negative exponential ([[Bibliography|Kenward 1982]]), but is linear with negative correlation if the logarithm of resource content is plotted against the logarithm of range area. Moreover, the range area at a point where the resource proportion is 1 is an estimate of the minimum area of resource required.

Another important consideration is that a single patch of habitat enclosed within range outlines of varying size will show a negative relationship of proportion with area by chance. To avoid misinterpretation of random events, the significance of observed correlations should be compared with random range placement in the same areas. In the case of a single resource, its occurrence significantly more frequently in observed ranges than in random placements may be the best indication of its importance.

This analysis requires an edge file and a habitat file. Suitable example files are in the folder squirrel, as described for [[Habitat#sources|habitat analysis]].

=== analysis options ===

For a rapid examination of whether the prevalence of any of the habitats in a set correlate negatively with range size, analysis of observed values only is appropriate. The statistics available from such are run are the observed value of r, the slope b for the regression of (log) habitat prevalence on (log) range area, the standard error of b, the (log) area intercept c for 100% habitat, the percentage of ranges with no habitat at all in the core, and the percentage with none of the habitat in a particular row. On the graph, the green regression line is for the observed values.

To investigate significance, randomisations are available with 99, 199 and 999 iterations. During randomisation, outlines of all the observed ranges are randomly rotated and displaced within an envelope. By default, that envelope is the minimum convex polygon round all observed outlines for the largest core size among a set of core sizes. N outlines are chosen at random with replacement from the N observed outlines, and an r, b and c calculated in each case.

Statistics from randomisations include the mean and median values for r by randomisation, z for the difference of this r from the observedr, with associated 95% confidence limits, on the assumption that r is distributed normally. The next value is a more robust test statistic, which is the number of random r values more extremely negative than the observed value. In a two-tailed test, with 999 iterations, a value less than 25 indicates P<0.05, with 5 or less for P<=0.01 and 0 for P<=0.02. There are then mean values for b, its SE and c by randomisation, which are used to plot the yellow line on the graph, and finally the proportion of random placements of the range outlines that lack the relevant habitat. Percentages below the observed percentage of ranges without the habitat indicate non-random placement of observed range outlines with respect to that habitat.

=== zero handling ===

Animals may differ in their use of resources. Some may specialise in a quite different resource to the majority, either through choice or exclusion, so that it does not occur in their range. Excluded animals may have above average range size, in which case addition of a value below other values (which is done automatically for the replace zeros option), will tend to maintain negative correlations. However, if resource strategy is divergent, inclusion of missing (or very low) proportions of the resource may conceal a major effect. At present, a choice of excluding missing values is possible, with two options; resample zeros to obtain resource within all outlines is appropriate if it is suspected that large ranges are more likely to include habitat by chance; otherwise the ignore zeros option will give very similar results but will be faster and will estimate the proportion of randomly-placed outlines that lack the resource. When there are very low values of resource in some observed ranges, it may in future be possible to exclude these objectively as statistical outliers and then examine these ranges for different resource area dependence relationships.

=== exclude habitats ===

As in analyses of habitat preference, disproportionate use of one relatively abundant resource can conceal a dependence also on one or more uncommon resources. This effect can be avoided by removing the area of the first resource from the range and then re-analysing for the second, in a step-wise approach. Resource exclusion of this type is supported in Ranges 9. The Ctrl key can be held to select multiple habitats to exclude, and is also required to remove previous selections.

=== envelope ===

The default envelope, mcp around max edge file core may allow very little rotation and displacement of large ranges in a small area, which can greatly slow analyses. If resources have a wide distribution, a larger user defined envelope may be used to speed the randomisation, at least for a first quick test, by loading the envelope separately. This is also useful if analysis is focussed in small cores (say, 50% cluster cores), but a polygon around all the locations is being used to standardise the envelope.

== Kaplan-Meier Survival ==

The Kaplan-Meier approach ([[Bibliography|Kaplan & Meier 1958]]), as described for radio-tracking by [[Bibliography|Pollock et al. (1989)]], is provided as a first survival estimation technique. Its interval-based estimation procedure adapts well to the asynchronous (staggered) entries and departures for unknown reasons that are typical for groups of radio-tagged animals.

Example data are the trajectories in first 4 years of life for 152 buzzards that were tagged in or near their natal nests (***.srv in the folder buzzards). There are also files one.srv and two.srv in the folder squirrel, for two sets of squirrels subject to different short-term control measures as a damage-reduction strategy.

=== analysis options ===

Choice of one set will run an analysis on one survival file, with a plot that includes error bars for 95% confidence limits based on [[Bibliography|Cox-Oates (1984)]] variance estimation. The statistics include, for each time interval in the analysis, the number of animals with active tags at the beginning and end of the interval, the number that died, had lost signals for unexplained reasons, were known to have lived through expiry of tag (e.g. due to battery exhaustion) or were added through tag attachment. There is then an estimate of the survival with two types of 95% confidence limits, and the survival decrease since the last period. The numbers in each category are summed at the bottom of the table, with a count of the total number of active tag-days. If the statistics file is saved, it can be opening in Excel or other spreadsheet for .csv files. The .kms graphics file can be opened at a later date in the graphics window.

Choice of two sets for comparison will run two plots as above, but also estimate statistics for the comparison between the survival rates. These are log-rank chi-square statistics with one degree of freedom, estimated in progressively more conservative ways, on the penultimate row of the table, and a comparison (see [[Bibliography|Pollock et al. (1989)]] and [[Bibliography|Kenward (2001)]] for further details. The two-sets option enables re-entry of the same file as for the first set, using a second '''[[Selections|Make Selections]]''' button and box to choose a different category of animal (e.g. adult rather than juvenile) within the file.

=== time interval ===

The length of time intervals for analysis should be great enough to provide opportunity for a number of deaths, but not too long to detect seasonal differences in timing of mortality. A choice of days rather than one month will bring up a box in which the number of days for each interval can be entered. Typically, monthly intervals are selected unless the period to be analysed is less than about 3 months (use e.g. 5-day intervals for the one.srv and two.srv squirrel example files).

=== set 1 start date ===

Although the default is the first animal start date, this often starts the analysis with too few animals in the first time interval; there should ideally be at least 20, because otherwise the confidence limits will be very large, with a tendency for differences between categories to lack significance. Even when many animals are marked within a short time, there may be a need to delay the start of analysis to exclude animals with possible adversely affects of capture or considered more vulnerable while adjusting to tags. Selecting specified date will bring up a calendar to assist the choice of date.

=== set 1 end date ===

The default of last animal end date will often result in very few individuals in the last sample interval, and hence undesirably large confidence limits. It is therefore possible either to set a specified date with a calendar, or to give a duration in days for the analysis.
=== set 2 start date and end date ===

For a comparison run, two further option boxes appear. For cases where the time period for comparison is the same in both files, or categories within the same file, it is convenient to be able to choose set 1 start date and set 1 end date, as well as having other options similar to those for the first set of data.

=== treat lost as dead ===

When carcases are found, the category of died is not hard to assign in survival files. Likewise, when tracking is stopped at a particular date, or tag cell is due to expire the fate category lived can be assigned. However, a problem arises when tracking animals for which deaths are frequently associated with destruction of the radio (e.g. through trauma) or severe loss of signal range or transport of the carcase away from a monitored area. In this case, survival is overestimated by the default of treating the lost signals as tag failure. For conservative estimates of survival during population modelling, it may be most appropriate to treat signals lost before the likely end of tag cell life as if they represent deaths, by ticking this box. The difference in survival estimated by merely censoring the radios will not be large if radios are highly reliable. Correction for“lost” animals that are subsequently retrapped or resighted after the study period can involve reclassifying their fate as lived; more sophisticated correction from such data ([[Bibliography|Kenward 2001]]) will be added in due course.

Modelling Analysis

2014-12-09T20:10:37Z

RobertKenward: /* analysis options */

When Ranges 4 was launched in 1990, individual-based modelling of animal populations was in its infancy. However, it was becoming clear that not only was such modelling powerful for predicting population beyond the envelope of conditions in which individuals were measured, but also that radio-tracking could provide the linkages of habitats and sociality with persistence or dispersal, and survival and productivity, that would be needed for modelling. So the provision of a toolkit for modelling was a long-term aspiration for this type of software [[Bibliography|(Kenward 1992)]].

== Introduction ==

The initial contribution to modelling is a new approach to analysing resources, such as habitats, which can estimate minimal requirements of individual animals and hence enable individual-based modelling. There is also a method for estimating survival or dispersal rates that is convenient for data from radio-tagging. There are illustrated explanations of both methods in ([[Bibliography|Kenward 2001]]). Further components of a toolkit for modelling will be added to this tab in due course, with the ultimate aspiration of linking these in order to automate population modelling from location data and maps.

== Resource Area Dependence Analysis ==

The principle that underlies this analysis is that if an animal requires a particular amount of a resource, such as a particular tree or area of habitat, then it will extend its home-range to an extent necessary to contain than amount of resource. If the resource is rarer, range outlines will be larger. In this case, there will be a negative relationship between range area and resource content. For strong resource dependence, the relationship tends to become negative exponential ([[Bibliography|Kenward 1982]]), but is linear with negative correlation if the logarithm of resource content is plotted against the logarithm of range area. Moreover, the range area at a point where the resource proportion is 1 is an estimate of the minimum area of resource required.

Another important consideration is that a single patch of habitat enclosed within range outlines of varying size will show a negative relationship of proportion with area by chance. To avoid misinterpretation of random events, the significance of observed correlations should be compared with random range placement in the same areas. In the case of a single resource, its occurrence significantly more frequently in observed ranges than in random placements may be the best indication of its importance.

This analysis requires an edge file and a habitat file. Suitable example files are in the folder squirrel, as described for [[Habitat#sources|habitat analysis]].

=== analysis options ===

For a rapid examination of whether the prevalence of any of the habitats in a set correlate negatively with range size, analysis of observed values only is appropriate. The statistics available from such are run are the observed value of r, the slope b for the regression of (log) habitat prevalence on (log) range area, the standard error of b, the (log) area intercept c for 100% habitat, the percentage of ranges with no habitat at all in the core, and the percentage with none of the habitat in a particular row. On the graph, the green regression line is for the observed values.

To investigate significance, randomisations are available with 99, 199 and 999 iterations. During randomisation, outlines of all the observed ranges are randomly rotated and displaced within an envelope. By default, that envelope is the minimum convex polygon round all observed outlines for the largest core size among a set of core sizes. N outlines are chosen at random with replacement from the N observed outlines, and an r, b and c calculated in each case.

Statistics from randomisations include the mean and median values for r by randomisation, z for the difference of this r from the observedr, with associated 95% confidence limits, on the assumption that r is distributed normally. The next value is a more robust test statistic, which is the number of random r values more extremely negative than the observed value. In a two-tailed test, with 999 iterations, a value less than 25 indicates P<0.05, with 5 or less for P<=0.01 and 0 for P<=0.02. There are then mean values for b, its SE and c by randomisation, which are used to plot the yellow line on the graph, and finally the proportion of random placements of the range outlines that lack the relevant habitat. Percentages below the observed percentage of ranges without the habitat indicate non-random placement of observed range outlines with respect to that habitat.

=== zero handling ===

Animals may differ in their use of resources. Some may specialise in a quite different resource to the majority, either through choice or exclusion, so that it does not occur in their range. Excluded animals may have above average range size, in which case addition of a value below other values (which is done automatically for the replace zeros option), will tend to maintain negative correlations. However, if resource strategy is divergent, inclusion of missing (or very low) proportions of the resource may conceal a major effect. At present, a choice of excluding missing values is possible, with two options; resample zeros to obtain resource within all outlines is appropriate if it is suspected that large ranges are more likely to include habitat by chance; otherwise the ignore zeros option will give very similar results but will be faster and will estimate the proportion of randomly-placed outlines that lack the resource. When there are very low values of resource in some observed ranges, it may in future be possible to exclude these objectively as statistical outliers and then examine these ranges for different resource area dependence relationships.

=== exclude habitats ===

As in analyses of habitat preference, disproportionate use of one relatively abundant resource can conceal a dependence also on one or more uncommon resources. This effect can be avoided by removing the area of the first resource from the range and then re-analysing for the second, in a step-wise approach. Resource exclusion of this type is supported in Ranges 9. The Ctrl key can be held to select multiple habitats to exclude, and is also required to remove previous selections.

=== envelope ===

The default envelope, mcp around max edge file core may allow very little rotation and displacement of large ranges in a small area, which can greatly slow analyses. If resources have a wide distribution, a larger user defined envelope may be used to speed the randomisation, at least for a first quick test, by loading the envelope separately. This is also useful if analysis is focussed in small cores (say, 50% cluster cores), but a polygon around all the locations is being used to standardise the envelope.

== Kaplan-Meier Survival ==

The Kaplan-Meier approach ([[Bibliography|Kaplan & Meier 1958]]), as described for radio-tracking by [[Bibliography|Pollock et al. (1989)]], is provided as a first survival estimation technique. Its interval-based estimation procedure adapts well to the asynchronous (staggered) entries and departures for unknown reasons that are typical for groups of radio-tagged animals.

Example data are the trajectories in first 4 years of life for 152 buzzards that were tagged in or near their natal nests (***.srv in the folder buzzards). There are also files one.srv and two.srv in the folder squirrel, for two sets of squirrels subject to different short-term control measures as a damage-reduction strategy.

=== analysis options ===

Choice of one set will run an analysis on one survival file, with a plot that includes error bars for 95% confidence limits based on [[Bibliography|Cox-Oakes (1984)]] variance estimation. The statistics include, for each time interval in the analysis, the number of animals with active tags at the beginning and end of the interval, the number that died, had lost signals for unexplained reasons, were known to have lived through expiry of tag (e.g. due to battery exhaustion) or were added through tag attachment. There is then an estimate of the survival with two types of 95% confidence limits, and the survival decrease since the last period. The numbers in each category are summed at the bottom of the table, with a count of the total number of active tag-days. If the statistics file is saved, it can be opening in Excel or other spreadsheet for .csv files. The .kms graphics file can be opened at a later date in the graphics window.

Choice of two sets for comparison will run two plots as above, but also estimate statistics for the comparison between the survival rates. These are log-rank chi-square statistics with one degree of freedom, estimated in progressively more conservative ways, on the penultimate row of the table, and a comparison (see [[Bibliography|Pollock et al. (1989)]] and [[Bibliography|Kenward (2001)]] for further details. The two-sets option enables re-entryof the same file as for the first set, using a second '''[[Selections|Make Selections]]''' button and box to choose a different category of animal (e.g. adult rather than juvenile) within the file.

=== time interval ===

The length of time intervals for analysis should be great enough to provide opportunity for a number of deaths, but not too long to detect seasonal differences in timing of mortality. A choice of days rather than one month will bring up a box in which the number of days for each interval can be entered. Typically, monthly intervals are selected unless the period to be analysed is less than about 3 months (use e.g. 5-day intervals for the one.srv and two.srv squirrel example files).

=== set 1 start date ===

Although the default is the first animal start date, this often starts the analysis with too few animals in the first time interval; there should ideally be at least 20, because otherwise the confidence limits will be very large, with a tendency for differences between categories to lack significance. Even when many animals are marked within a short time, there may be a need to delay the start of analysis to exclude animals with possible adversely affects of capture or considered more vulnerable while adjusting to tags. Selecting specified date will bring up a calendar to assist the choice of date.

=== set 1 end date ===

The default of last animal end date will often result in very few individuals in the last sample interval, and hence undesirably large confidence limits. It is therefore possible either to set a specified date with a calendar, or to give a duration in days for the analysis.
=== set 2 start date and end date ===

For a comparison run, two further option boxes appear. For cases where the time period for comparison is the same in both files, or categories within the same file, it is convenient to be able to choose set 1 start date and set 1 end date, as well as having other options similar to those for the first set of data.

=== treat lost as dead ===

When carcases are found, the category of died is not hard to assign in survival files. Likewise, when tracking is stopped at a particular date, or tag cell is due to expire the fate category lived can be assigned. However, a problem arises when tracking animals for which deaths are frequently associated with destruction of the radio (e.g. through trauma) or severe loss of signal range or transport of the carcase away from a monitored area. In this case, survival is overestimated by the default of treating the lost signals as tag failure. For conservative estimates of survival during population modelling, it may be most appropriate to treat signals lost before the likely end of tag cell life as if they represent deaths, by ticking this box. The difference in survival estimated by merely censoring the radios will not be large if radios are highly reliable. Correction for“lost” animals that are subsequently retrapped or resighted after the study period can involve reclassifying their fate as lived; more sophisticated correction from such data ([[Bibliography|Kenward 2001]]) will be added in due course.

Modelling Analysis

2014-12-09T20:09:20Z

RobertKenward: /* analysis options */

When Ranges 4 was launched in 1990, individual-based modelling of animal populations was in its infancy. However, it was becoming clear that not only was such modelling powerful for predicting population beyond the envelope of conditions in which individuals were measured, but also that radio-tracking could provide the linkages of habitats and sociality with persistence or dispersal, and survival and productivity, that would be needed for modelling. So the provision of a toolkit for modelling was a long-term aspiration for this type of software [[Bibliography|(Kenward 1992)]].

== Introduction ==

The initial contribution to modelling is a new approach to analysing resources, such as habitats, which can estimate minimal requirements of individual animals and hence enable individual-based modelling. There is also a method for estimating survival or dispersal rates that is convenient for data from radio-tagging. There are illustrated explanations of both methods in ([[Bibliography|Kenward 2001]]). Further components of a toolkit for modelling will be added to this tab in due course, with the ultimate aspiration of linking these in order to automate population modelling from location data and maps.

== Resource Area Dependence Analysis ==

The principle that underlies this analysis is that if an animal requires a particular amount of a resource, such as a particular tree or area of habitat, then it will extend its home-range to an extent necessary to contain than amount of resource. If the resource is rarer, range outlines will be larger. In this case, there will be a negative relationship between range area and resource content. For strong resource dependence, the relationship tends to become negative exponential ([[Bibliography|Kenward 1982]]), but is linear with negative correlation if the logarithm of resource content is plotted against the logarithm of range area. Moreover, the range area at a point where the resource proportion is 1 is an estimate of the minimum area of resource required.

Another important consideration is that a single patch of habitat enclosed within range outlines of varying size will show a negative relationship of proportion with area by chance. To avoid misinterpretation of random events, the significance of observed correlations should be compared with random range placement in the same areas. In the case of a single resource, its occurrence significantly more frequently in observed ranges than in random placements may be the best indication of its importance.

This analysis requires an edge file and a habitat file. Suitable example files are in the folder squirrel, as described for [[Habitat#sources|habitat analysis]].

=== analysis options ===

For a rapid examination of whether the prevalence of any of the habitats in a set correlate negatively with range size, analysis of observed values only is appropriate. The statistics available from such are run are the observed value of r, the slope b for the regression of (log) habitat prevalence on (log) range area, the standard error of b, the (log) area intercept c for 100% habitat, the percentage of ranges with no habitat at all in the core, and the percentage with none of the habitat in a particular row. On the graph, the green regression line is for the observed values.

To investigate significance, randomisations are available with 99, 199 and 999 iterations. During randomisation, outlines of all the observed ranges are randomly rotated and displaced within an envelope. By default, that envelope is the minimum convex polygon round all observed outlines for the largest core size among a set of core sizes. N outlines are chosen at random with replacement from the N observed outlines, and an r, b and c calculated in each case.

Statistics from randomisations include the mean and median values for r by randomisation, z for the difference of this r from the observedr, with associated 95% confidence limits, on the assumption that r is distributed normally. The next value is a more robust test statistic, which is the number of random r values more extremely negative than the observed value. In a two-tailed test, with 999 iterations, a value less than 25 indicates P<0.05, with 5 or less for P<=0.01 and 0 for P<=0.02. There are then mean values for b, its SE and c by randomisation, which are used to plot the yellow line on the graph, and finally the proportion of random placements of the range outlines that lack the relevant habitat. Percentages below the observed percentage of ranges without the habitat indicate non-random placement of observed range outlines with respect to that habitat.

=== zero handling ===

Animals may differ in their use of resources. Some may specialise in a quite different resource to the majority, either through choice or exclusion, so that it does not occur in their range. Excluded animals may have above average range size, in which case addition of a value below other values (which is done automatically for the replace zeros option), will tend to maintain negative correlations. However, if resource strategy is divergent, inclusion of missing (or very low) proportions of the resource may conceal a major effect. At present, a choice of excluding missing values is possible, with two options; resample zeros to obtain resource within all outlines is appropriate if it is suspected that large ranges are more likely to include habitat by chance; otherwise the ignore zeros option will give very similar results but will be faster and will estimate the proportion of randomly-placed outlines that lack the resource. When there are very low values of resource in some observed ranges, it may in future be possible to exclude these objectively as statistical outliers and then examine these ranges for different resource area dependence relationships.

=== exclude habitats ===

As in analyses of habitat preference, disproportionate use of one relatively abundant resource can conceal a dependence also on one or more uncommon resources. This effect can be avoided by removing the area of the first resource from the range and then re-analysing for the second, in a step-wise approach. Resource exclusion of this type is supported in Ranges 9. The Ctrl key can be held to select multiple habitats to exclude, and is also required to remove previous selections.

=== envelope ===

The default envelope, mcp around max edge file core may allow very little rotation and displacement of large ranges in a small area, which can greatly slow analyses. If resources have a wide distribution, a larger user defined envelope may be used to speed the randomisation, at least for a first quick test, by loading the envelope separately. This is also useful if analysis is focussed in small cores (say, 50% cluster cores), but a polygon around all the locations is being used to standardise the envelope.

== Kaplan-Meier Survival ==

The Kaplan-Meier approach ([[Bibliography|Kaplan & Meier 1958]]), as described for radio-tracking by [[Bibliography|Pollock et al. (1989)]], is provided as a first survival estimation technique. Its interval-based estimation procedure adapts well to the asynchronous (staggered) entries and departures for unknown reasons that are typical for groups of radio-tagged animals.

Example data are the trajectories in first 4 years of life for 152 buzzards that were tagged in or near their natal nests (***.srv in the folder buzzards). There are also files one.srv and two.srv in the folder squirrel, for two sets of squirrels subject to different short-term control measures as a damage-reduction strategy.

=== analysis options ===

Choice of one set will run an analysis on one survival file, with a plot that includes error bars for 95% confidence limits based on [[Bibliography|Cox-Oates (1984)]] variance estimation. The statistics include, for each time interval in the analysis, the number of animals with active tags at the beginning and end of the interval, the number that died, had lost signals for unexplained reasons, were known to have lived through expiry of tag (e.g. due to battery exhaustion) or were added through tag attachment. There is then an estimate of the survival with two types of 95% confidence limits, and the survival decrease since the last period. The numbers in each category are summed at the bottom of the table, with a count of the total number of active tag-days. If the statistics file is saved, it can be opening in Excel or other spreadsheet for .csv files. The .kms graphics file can be opened at a later date in the graphics window.

Choice of two sets for comparison will run two plots as above, but also estimate statistics for the comparison between the survival rates. These are log-rank chi-square statistics with one degree of freedom, estimated in progressively more conservative ways, on the penultimate row of the table, and a comparison (see [[Bibliography|Pollock et al. (1989)]] and [[Bibliography|Kenward (2001)]] for further details. The two-sets option enables re-entryof the same file as for the first set, using a second '''[[Selections|Make Selections]]''' button and box to choose a different category of animal (e.g. adult rather than juvenile) within the file.

=== time interval ===

The length of time intervals for analysis should be great enough to provide opportunity for a number of deaths, but not too long to detect seasonal differences in timing of mortality. A choice of days rather than one month will bring up a box in which the number of days for each interval can be entered. Typically, monthly intervals are selected unless the period to be analysed is less than about 3 months (use e.g. 5-day intervals for the one.srv and two.srv squirrel example files).

=== set 1 start date ===

Although the default is the first animal start date, this often starts the analysis with too few animals in the first time interval; there should ideally be at least 20, because otherwise the confidence limits will be very large, with a tendency for differences between categories to lack significance. Even when many animals are marked within a short time, there may be a need to delay the start of analysis to exclude animals with possible adversely affects of capture or considered more vulnerable while adjusting to tags. Selecting specified date will bring up a calendar to assist the choice of date.

=== set 1 end date ===

The default of last animal end date will often result in very few individuals in the last sample interval, and hence undesirably large confidence limits. It is therefore possible either to set a specified date with a calendar, or to give a duration in days for the analysis.
=== set 2 start date and end date ===

For a comparison run, two further option boxes appear. For cases where the time period for comparison is the same in both files, or categories within the same file, it is convenient to be able to choose set 1 start date and set 1 end date, as well as having other options similar to those for the first set of data.

=== treat lost as dead ===

When carcases are found, the category of died is not hard to assign in survival files. Likewise, when tracking is stopped at a particular date, or tag cell is due to expire the fate category lived can be assigned. However, a problem arises when tracking animals for which deaths are frequently associated with destruction of the radio (e.g. through trauma) or severe loss of signal range or transport of the carcase away from a monitored area. In this case, survival is overestimated by the default of treating the lost signals as tag failure. For conservative estimates of survival during population modelling, it may be most appropriate to treat signals lost before the likely end of tag cell life as if they represent deaths, by ticking this box. The difference in survival estimated by merely censoring the radios will not be large if radios are highly reliable. Correction for“lost” animals that are subsequently retrapped or resighted after the study period can involve reclassifying their fate as lived; more sophisticated correction from such data ([[Bibliography|Kenward 2001]]) will be added in due course.

Tutorial

2014-11-30T08:52:55Z

RobertKenward: /* Data Sources */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

==== Plotting survival for a single data set ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''kaplan meier survival''.

* Under '''Analysis Options''' ensure ''one set'' is selected

* Under '''Input files''' press '''browse''' and find, for the ''set 1 survival file'' the file ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Press the '''Run Analysis''' button.

Looking at the statistics window, the sample size was not adequate until the start of the second month, and became less than 30 animals due to moulting of tail-mounted radio tags after 30 April. Run the analysis again, selecting as '''set 1 start date''' the ''specified date'' and use the calendar to select 1 July 1980, then in '''set 1 end date''' again select ''specified date'' and set 31 March 1981. This estimates juvenile female survival to the start of the next egg-laying period, as used in [[Bibliography|Kenward et al. (1999)]].

==== Comparing two sets of survival data ====

[[File:To be added]]

* Under '''Analysis Options''' select ''two sets for comparison''

* Under '''Input files''' check that the ''set 1 survival file'' is still ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Check that '''set 1 start date''' has ''specified date'' selected, of 1 July 1980.

* Check that '''set 1 end date''' has ''specified date'' selected, of 31 March 1981.

* Press '''browse''' for the ''set 2 survival file'' and find ''<RangesFolder>\samples\raptors\goshawkjuvmal.srv''.

* Set the '''set 2 start date'' to the ''set 1 start date'' option.

* Set the '''set 2 end date'' to the ''set 2 end date'' option.

* Press the '''Run Analysis''' button.

The survival is poorer for juvenile males than for juvenile females due mainly to differences from October (month 4) onwards. The ''z'' values of 2.07 to 2.13 are higher than the value of 1.96 for alpha = 0.05, so ''P'' < 0.05.

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward (2001), Kenward et al. (2001)]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls & Kenward 1995, 1998, 2001]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission. Goshawk survival data were collected on the Swedish island of Gotland ([[Bibliography|Kenward et al. 1993, 1999]]); the natal year of all fledged cohorts has been set to 1980 in the example files.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel, buzzard and goshawk data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology), in the last case in cooperation with Uppsala University and the Swedish Hunters' Association. The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-30T08:52:06Z

RobertKenward: /* Data Sources */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

==== Plotting survival for a single data set ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''kaplan meier survival''.

* Under '''Analysis Options''' ensure ''one set'' is selected

* Under '''Input files''' press '''browse''' and find, for the ''set 1 survival file'' the file ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Press the '''Run Analysis''' button.

Looking at the statistics window, the sample size was not adequate until the start of the second month, and became less than 30 animals due to moulting of tail-mounted radio tags after 30 April. Run the analysis again, selecting as '''set 1 start date''' the ''specified date'' and use the calendar to select 1 July 1980, then in '''set 1 end date''' again select ''specified date'' and set 31 March 1981. This estimates juvenile female survival to the start of the next egg-laying period, as used in [[Bibliography|Kenward et al. (1999)]].

==== Comparing two sets of survival data ====

[[File:To be added]]

* Under '''Analysis Options''' select ''two sets for comparison''

* Under '''Input files''' check that the ''set 1 survival file'' is still ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Check that '''set 1 start date''' has ''specified date'' selected, of 1 July 1980.

* Check that '''set 1 end date''' has ''specified date'' selected, of 31 March 1981.

* Press '''browse''' for the ''set 2 survival file'' and find ''<RangesFolder>\samples\raptors\goshawkjuvmal.srv''.

* Set the '''set 2 start date'' to the ''set 1 start date'' option.

* Set the '''set 2 end date'' to the ''set 2 end date'' option.

* Press the '''Run Analysis''' button.

The survival is poorer for juvenile males than for juvenile females due mainly to differences from October (month 4) onwards. The ''z'' values of 2.07 to 2.13 are higher than the value of 1.96 for alpha = 0.05, so ''P'' < 0.05.

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward (2001), Kenward et al. (2001)]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls & Kenward 1995, 1998, 2001]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission. Goshawk survival data were collected on the Swedish island of Gotland ([[Bibliography|Kenward et al. 1993, 1999]]); the natal year of all fledged cohorts has been set to 1980 for use in this example.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel, buzzard and goshawk data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology), in the last case in cooperation with Uppsala University and the Swedish Hunters' Association. The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Bibliography

2014-11-30T07:58:27Z

RobertKenward:

Aebischer, N.J., Robertson, P.A. and Kenward, R.E. 1993. Compositional analysis of habitat use from animal radio-tracking data. Ecology 74 (5): 1313-1325.

Anderson, D.J. 1982. The home range: a new non-parametric estimation technique. Ecology 63:103-112.

Burt, W.H. 1943. Territoriality and home range concepts as applied to mammals. Journal of Mammalogy 24, 346-352.

Calhoun, J.B. and Casby, J.U. 1958. Calculation of Home Range and Density of Small Mammals. United States Public Health Service, Public Health Monograph 55.

Clarke, P.J. and Evans, F.C.1954. Distance to nearest neighbour as a measure of spatial relationships in populations. Ecology 35:445-453.

Cox, D.R. and Oakes, D. 1984. Analysis of survival data. Chapman and Hall, New York.

Dalke, P.D. and Sime, P.R. 1938. Home and seasonal ranges of the eastern cottontail in Connecticut. Transcripts of the North American Wildlife Conference 3: 659-669.

Dixon, K.R. and Chapman, J.A. 1980. Harmonic mean measure of animal activity areas. Ecology 61:1040-1047.

Don, B.A.C. and Rennolls, K. 1983. A home range model incorporating biological attraction points. Journal of Animal Ecology 52:69-81.

Ford, G. and Krumme, D.W. 1979. The analysis of space use patterns. Journal of Theoretical Biology 76:125-155.

Getz, W.M. and Wilmers, C.C. 2004. A local nearest-neighbor convex-hull construction of home ranges and utilization distributions. Ecography 27: 489-505.

Getz, W.M., Fortmann-Roe, S., Scott, P.C., Lyons, A.J., Ryan, S.J. and Wilmers, C.C. 2007. LoCoH: nonparameteric kernel methods for constructing home ranges and utilization distributions. PLoS ONE 2(2): e207. doi:10.1371/journal.pone.0000207.

Glendinning, R.H. 1991. The convex hull of a dependent vector-valued process. Journal of Statistical Computation and Simulation 38: 219-237.

Hartigan, J.A. 1987. Estimation of a convex density contour in two dimensions. Journal of the American Statistical Association 82:267-270.

Harvey, M.J. and Barbour, R.W. 1965. Home range of Microtus ochrogaster as determined by a modified minimum area method. Journal of Mammalogy 46:398-402.

Harris, S., Cresswell, W.J., Forde, P.G., Trewella, W.J., Woollard, T. and Wray, S. 1990. Home-range analysis using radio-tracking data - a review of problems and techniques particularly as applied to the study of mammals. Mammal Review 20:97-123.

Harrison, J.L. 1958. Range and movements of some Malayan rats. Journal of Mammalogy 39: 190-206.

Hayne, D.W. 1949. Calculation of size of home range. Journal of Mammalogy 30:1-18.

Hemson, G., Macdonald, D.W., Ginsberg, J., Kenward, R.E., Ripley, R. and South, A.B. 2005. Are Kernels the mustard, an assessment of kernel home range estimators using GPS data from lions. Journal of Animal Ecology. 74 (3), 455-463.

Hodder, K. H., Kenward, R. E., Walls, S. S. and Clarke, R. T. 1998. Estimating core ranges: a comparison of techniques using the common buzzard (Buteo buteo). Journal of Raptor Research 32(2): 82-89.

Hodder, K. H., Masters J.E.G., Beaumont W.R.C., Welton, J.S., Kenward, R.E., Pinder A C. and Gozlan R.E. 2007. Techniques for evaluating the spatial behaviour of river fish. Hydrobiologia 582:257-269.

Jacobs, J. 1974. Quantitative measurements of food selection. Oecologia 14:413-417.

Jamsa, K. 1991 DOS: the complete reference. 3rd Ed. Osbourne McGraw-Hill, London.

Jennrich, R.J. and Turner, F.B. 1969. Measurement of non-circular home range. Journal of Theoretical Biology 22:227-237.

Johnstone, I.G. 1992. Home range utilization and roost selection by non-breeding territorial European robins (Erithacus rubecula). In "Wildlife Telemetry - Remote Monitoring and Tracking of Animals" (I.G. Priede, and S.M. Swift, eds), 495-509. Ellis Horwood, Chichester, UK.

Kaplan, E.L. and Meier, P. 1958. Nonparametric estimation from incomplete observations. Journal of the American Statistical Association 53, 457-481.

Kenward, R.E. 1982. Goshawk hunting behaviour, and range size as a function of habitat availability. Journal of Animal Ecology 51:69-80.

Kenward, R.E. 1987. Wildlife radio tagging: equipment, field techniques and data analysis. Academic Press, London, UK.

Kenward, R.E. 1992. Quantity versus quality: programmed collection and analysis of radio-tracking data. pp. 231-246 in I.G. Priede and S.M.Swift (Eds). Wildlife telemetry: remote monitoring and tracking of animals. Ellis Horwood, Chichester, UK.

Kenward, R.E. 2001. A Manual for Wildlife Radio Tagging. Academic Press, London, UK.

Kenward, R. E., Clarke, R. T., Hodder, K. H. and Walls, S. S. 2001. Distance and density estimators of home range: Defining multi-nuclear cores by nearest neighbor clustering. Ecology 82(7): 1905-1920.

Kenward, R.E., Marcström, V. and Karlbom, M. 1993. Post-nestling behaviour in goshawks, Accipiter gentilis. II. Sex differences in sociality and nest switching. Animal Behaviour 46:371-378.

Kenward, R.E., Marcström, V. & Karlbom, M. 1999. Demographic estimates from radio-tagging: models of age-specific survival and breeding in the goshawk. Journal of Animal Ecology 68:1020-1033.

Knight, C.M., Kenward, R.E., Gozlan, R.E., Hodder, K.H., Walls, S.S. & Lucas, M.C. 2009. Home range estimation within a restricted linear environment: importance of method selection in detecting seasonal change. Wildlife Research 36: 213–224.

Larkin, R.P. and Halkin, D. 1994. A review of software packages for estimating animla home ranges. Wildlife Society Bulletin 22:274-287.

Macdonald, D.W., Ball, F.G. and Hough, N.G. 1980. The evaluation of home range size and configuration using radio tracking data. A Handbook on Biotelemetry and Radio Tracking (C.J. Amlaner and D.W. Macdonald, eds), 405-424. Pergamon Press, Oxford, UK.

Michener, G.R. 1979. Spatial relationships of adult Richardson’s ground squirrels. Canadian Zoology 57, 125-139.

Otis, D.L. and White, G.C. 1999. Autocorrelation of location estimates and the analysis of radiotracking data. Journal of Wildlife Management 63, 1039-1044.

Pollock, K.H., Winterstein, S.R., Bunck, C.M. and Curtiss, P.D. 1989. Survival analysis in telemetry studies: the staggered entry design. Journal of Wildlife Management 53, 7-14.

Robertson, P.A., N.J. Aebischer, R.E. Kenward, I.K. Hanski and N.P. Williams. (1998). Simulation and jack-knifing assessment of home-range indices based on underlying trajectories. Journal of Applied Ecology 35, 928-940.

Spencer, W.D. and Barrett, R.H. 1984. An evaluation of the harmonic mean method for evaluating carnivore activity areas. Acta Zoologica Fennica 171:255-259.

Swihart, R.K. and Slade, N.A. 1985. Testing for independence of observations in animal movements. Ecology 66:1176-1184.

Voight, D.R. & Tinline, R.R. 1980. Strategies for analysing radio-tracking data. pp.387-404 in Amlaner, C.J. & Macdonald, D.W. (eds) A Handbook on Biotelemetry and Radio Tracking, Pergamon Press, Oxford, UK.

Walls S.S. and Kenward R.E., 1995. Movements of radio-tagged Common Buzzards Buteo buteo in their first year. Ibis 137: 177-182.

Walls S.S. and Kenward R.E., 1998. Movements of radio-tagged common buzzards in early life. Ibis 140: 561-568.

Walls S.S. and Kenward R.E. 2001. Spatial consequences of relatedness and age in buzzards. Animal Behaviour 61: 1069-1078.

White, G.C. and Garrott, R.A. 1990. Analysis of wildlife tracking data. Academic Press, New York, USA.

Worton, B.J. 1989. Kernel methods for estimating the utilisation distribution in home range studies. Ecology 70:164-168.

Worton, B.J. 1995a. A convex hull-based estimator of home-range size. Biometrics 51, 1206-1215.

Worton, B.J. 1995b. Using MonteCarlo simulation to evaluate kernel-based home-range estimators. Journal of Wildlife Management 59, 794-800.

Wray, S., Cresswell, W.J. and Rogers, D. 1992. Dirichlet tessellations: a new, non-parametric approach to home range analysis. pp 247-255 in Priede & Swift.

Bibliography

2014-11-30T07:57:10Z

RobertKenward:

Aebischer, N.J., Robertson, P.A. and Kenward, R.E. 1993. Compositional analysis of habitat use from animal radio-tracking data. Ecology 74 (5): 1313-1325.

Anderson, D.J. 1982. The home range: a new non-parametric estimation technique. Ecology 63:103-112.

Burt, W.H. 1943. Territoriality and home range concepts as applied to mammals. Journal of Mammalogy 24, 346-352.

Calhoun, J.B. and Casby, J.U. 1958. Calculation of Home Range and Density of Small Mammals. United States Public Health Service, Public Health Monograph 55.

Clarke, P.J. and Evans, F.C.1954. Distance to nearest neighbour as a measure of spatial relationships in populations. Ecology 35:445-453.

Cox, D.R. and Oakes, D. 1984. Analysis of survival data. Chapman and Hall, New York.

Dalke, P.D. and Sime, P.R. 1938. Home and seasonal ranges of the eastern cottontail in Connecticut. Transcripts of the North American Wildlife Conference 3: 659-669.

Dixon, K.R. and Chapman, J.A. 1980. Harmonic mean measure of animal activity areas. Ecology 61:1040-1047.

Don, B.A.C. and Rennolls, K. 1983. A home range model incorporating biological attraction points. Journal of Animal Ecology 52:69-81.

Ford, G. and Krumme, D.W. 1979. The analysis of space use patterns. Journal of Theoretical Biology 76:125-155.

Getz, W.M. and Wilmers, C.C. 2004. A local nearest-neighbor convex-hull construction of home ranges and utilization distributions. Ecography 27: 489-505.

Getz, W.M., Fortmann-Roe, S., Scott, P.C., Lyons, A.J., Ryan, S.J. and Wilmers, C.C. 2007. LoCoH: nonparameteric kernel methods for constructing home ranges and utilization distributions. PLoS ONE 2(2): e207. doi:10.1371/journal.pone.0000207.

Glendinning, R.H. 1991. The convex hull of a dependent vector-valued process. Journal of Statistical Computation and Simulation 38: 219-237.

Hartigan, J.A. 1987. Estimation of a convex density contour in two dimensions. Journal of the American Statistical Association 82:267-270.

Harvey, M.J. and Barbour, R.W. 1965. Home range of Microtus ochrogaster as determined by a modified minimum area method. Journal of Mammalogy 46:398-402.

Harris, S., Cresswell, W.J., Forde, P.G., Trewella, W.J., Woollard, T. and Wray, S. 1990. Home-range analysis using radio-tracking data - a review of problems and techniques particularly as applied to the study of mammals. Mammal Review 20:97-123.

Harrison, J.L. 1958. Range and movements of some Malayan rats. Journal of Mammalogy 39: 190-206.

Hayne, D.W. 1949. Calculation of size of home range. Journal of Mammalogy 30:1-18.

Hemson, G., Macdonald, D.W., Ginsberg, J., Kenward, R.E., Ripley, R. and South, A.B. 2005. Are Kernels the mustard, an assessment of kernel home range estimators using GPS data from lions. Journal of Animal Ecology. 74 (3), 455-463.

Hodder, K. H., Kenward, R. E., Walls, S. S. and Clarke, R. T. 1998. Estimating core ranges: a comparison of techniques using the common buzzard (Buteo buteo). Journal of Raptor Research 32(2): 82-89.

Hodder, K. H., Masters J.E.G., Beaumont W.R.C., Welton, J.S., Kenward, R.E., Pinder A C. and Gozlan R.E. 2007. Techniques for evaluating the spatial behaviour of river fish. Hydrobiologia 582:257-269.

Jacobs, J. 1974. Quantitative measurements of food selection. Oecologia 14:413-417.

Jamsa, K. 1991 DOS: the complete reference. 3rd Ed. Osbourne McGraw-Hill, London.

Jennrich, R.J. and Turner, F.B. 1969. Measurement of non-circular home range. Journal of Theoretical Biology 22:227-237.

Johnstone, I.G. 1992. Home range utilization and roost selection by non-breeding territorial European robins (Erithacus rubecula). In "Wildlife Telemetry - Remote Monitoring and Tracking of Animals" (I.G. Priede, and S.M. Swift, eds), 495-509. Ellis Horwood, Chichester, UK.

Kaplan, E.L. and Meier, P. 1958. Nonparametric estimation from incomplete observations. Journal of the American Statistical Association 53, 457-481.

Kenward, R.E. 1982. Goshawk hunting behaviour, and range size as a function of habitat availability. Journal of Animal Ecology 51:69-80.

Kenward, R.E. 1987. Wildlife radio tagging: equipment, field techniques and data analysis. Academic Press, London, UK.

Kenward, R.E. 1992. Quantity versus quality: programmed collection and analysis of radio-tracking data. pp. 231-246 in I.G. Priede and S.M.Swift (Eds). Wildlife telemetry: remote monitoring and tracking of animals. Ellis Horwood, Chichester, UK.

Kenward, R.E., Marcström, V. & Karlbom, M. 1999. Demographic estimates from radio-tagging: models of age-specific survival and breeding in the goshawk. Journal of Animal Ecology 68:1020-1033.

Kenward, R.E. 2001. A Manual for Wildlife Radio Tagging. Academic Press, London, UK.

Kenward, R. E., Clarke, R. T., Hodder, K. H. and Walls, S. S. 2001. Distance and density estimators of home range: Defining multi-nuclear cores by nearest neighbor clustering. Ecology 82(7): 1905-1920.

Kenward, R.E., Marcström, V. and Karlbom, M. 1993. Post-nestling behaviour in goshawks, Accipiter gentilis. II. Sex differences in sociality and nest switching. Animal Behaviour 46:371-378.

Knight, C.M., Kenward, R.E., Gozlan, R.E., Hodder, K.H., Walls, S.S. & Lucas, M.C. 2009. Home range estimation within a restricted linear environment: importance of method selection in detecting seasonal change. Wildlife Research 36: 213–224.

Larkin, R.P. and Halkin, D. 1994. A review of software packages for estimating animla home ranges. Wildlife Society Bulletin 22:274-287.

Macdonald, D.W., Ball, F.G. and Hough, N.G. 1980. The evaluation of home range size and configuration using radio tracking data. A Handbook on Biotelemetry and Radio Tracking (C.J. Amlaner and D.W. Macdonald, eds), 405-424. Pergamon Press, Oxford, UK.

Michener, G.R. 1979. Spatial relationships of adult Richardson’s ground squirrels. Canadian Zoology 57, 125-139.

Otis, D.L. and White, G.C. 1999. Autocorrelation of location estimates and the analysis of radiotracking data. Journal of Wildlife Management 63, 1039-1044.

Pollock, K.H., Winterstein, S.R., Bunck, C.M. and Curtiss, P.D. 1989. Survival analysis in telemetry studies: the staggered entry design. Journal of Wildlife Management 53, 7-14.

Robertson, P.A., N.J. Aebischer, R.E. Kenward, I.K. Hanski and N.P. Williams. (1998). Simulation and jack-knifing assessment of home-range indices based on underlying trajectories. Journal of Applied Ecology 35, 928-940.

Spencer, W.D. and Barrett, R.H. 1984. An evaluation of the harmonic mean method for evaluating carnivore activity areas. Acta Zoologica Fennica 171:255-259.

Swihart, R.K. and Slade, N.A. 1985. Testing for independence of observations in animal movements. Ecology 66:1176-1184.

Voight, D.R. & Tinline, R.R. 1980. Strategies for analysing radio-tracking data. pp.387-404 in Amlaner, C.J. & Macdonald, D.W. (eds) A Handbook on Biotelemetry and Radio Tracking, Pergamon Press, Oxford, UK.

Walls S.S. and Kenward R.E., 1995. Movements of radio-tagged Common Buzzards Buteo buteo in their first year. Ibis 137: 177-182.

Walls S.S. and Kenward R.E., 1998. Movements of radio-tagged common buzzards in early life. Ibis 140: 561-568.

Walls S.S. and Kenward R.E. 2001. Spatial consequences of relatedness and age in buzzards. Animal Behaviour 61: 1069-1078.

White, G.C. and Garrott, R.A. 1990. Analysis of wildlife tracking data. Academic Press, New York, USA.

Worton, B.J. 1989. Kernel methods for estimating the utilisation distribution in home range studies. Ecology 70:164-168.

Worton, B.J. 1995a. A convex hull-based estimator of home-range size. Biometrics 51, 1206-1215.

Worton, B.J. 1995b. Using MonteCarlo simulation to evaluate kernel-based home-range estimators. Journal of Wildlife Management 59, 794-800.

Wray, S., Cresswell, W.J. and Rogers, D. 1992. Dirichlet tessellations: a new, non-parametric approach to home range analysis. pp 247-255 in Priede & Swift.

Bibliography

2014-11-30T07:56:06Z

RobertKenward:

Aebischer, N.J., Robertson, P.A. and Kenward, R.E. 1993. Compositional analysis of habitat use from animal radio-tracking data. Ecology 74 (5): 1313-1325.

Anderson, D.J. 1982. The home range: a new non-parametric estimation technique. Ecology 63:103-112.

Burt, W.H. 1943. Territoriality and home range concepts as applied to mammals. Journal of Mammalogy 24, 346-352.

Calhoun, J.B. and Casby, J.U. 1958. Calculation of Home Range and Density of Small Mammals. United States Public Health Service, Public Health Monograph 55.

Clarke, P.J. and Evans, F.C.1954. Distance to nearest neighbour as a measure of spatial relationships in populations. Ecology 35:445-453.

Cox, D.R. and Oakes, D. 1984. Analysis of survival data. Chapman and Hall, New York.

Dalke, P.D. and Sime, P.R. 1938. Home and seasonal ranges of the eastern cottontail in Connecticut. Transcripts of the North American Wildlife Conference 3: 659-669.

Dixon, K.R. and Chapman, J.A. 1980. Harmonic mean measure of animal activity areas. Ecology 61:1040-1047.

Don, B.A.C. and Rennolls, K. 1983. A home range model incorporating biological attraction points. Journal of Animal Ecology 52:69-81.

Ford, G. and Krumme, D.W. 1979. The analysis of space use patterns. Journal of Theoretical Biology 76:125-155.

Getz, W.M. and Wilmers, C.C. 2004. A local nearest-neighbor convex-hull construction of home ranges and utilization distributions. Ecography 27: 489-505.

Getz, W.M., Fortmann-Roe, S., Scott, P.C., Lyons, A.J., Ryan, S.J. and Wilmers, C.C. 2007. LoCoH: nonparameteric kernel methods for constructing home ranges and utilization distributions. PLoS ONE 2(2): e207. doi:10.1371/journal.pone.0000207.

Glendinning, R.H. 1991. The convex hull of a dependent vector-valued process. Journal of Statistical Computation and Simulation 38: 219-237.

Hartigan, J.A. 1987. Estimation of a convex density contour in two dimensions. Journal of the American Statistical Association 82:267-270.

Harvey, M.J. and Barbour, R.W. 1965. Home range of Microtus ochrogaster as determined by a modified minimum area method. Journal of Mammalogy 46:398-402.

Harris, S., Cresswell, W.J., Forde, P.G., Trewella, W.J., Woollard, T. and Wray, S. 1990. Home-range analysis using radio-tracking data - a review of problems and techniques particularly as applied to the study of mammals. Mammal Review 20:97-123.

Harrison, J.L. 1958. Range and movements of some Malayan rats. Journal of Mammalogy 39: 190-206.

Hayne, D.W. 1949. Calculation of size of home range. Journal of Mammalogy 30:1-18.

Hemson, G., Macdonald, D.W., Ginsberg, J., Kenward, R.E., Ripley, R. and South, A.B. 2005. Are Kernels the mustard, an assessment of kernel home range estimators using GPS data from lions. Journal of Animal Ecology. 74 (3), 455-463.

Hodder, K. H., Kenward, R. E., Walls, S. S. and Clarke, R. T. 1998. Estimating core ranges: a comparison of techniques using the common buzzard (Buteo buteo). Journal of Raptor Research 32(2): 82-89.

Hodder, K. H., Masters J.E.G., Beaumont W.R.C., Welton, J.S., Kenward, R.E., Pinder A C. and Gozlan R.E. 2007. Techniques for evaluating the spatial behaviour of river fish. Hydrobiologia 582:257-269.

Jacobs, J. 1974. Quantitative measurements of food selection. Oecologia 14:413-417.

Jamsa, K. 1991 DOS: the complete reference. 3rd Ed. Osbourne McGraw-Hill, London.

Jennrich, R.J. and Turner, F.B. 1969. Measurement of non-circular home range. Journal of Theoretical Biology 22:227-237.

Johnstone, I.G. 1992. Home range utilization and roost selection by non-breeding territorial European robins (Erithacus rubecula). In "Wildlife Telemetry - Remote Monitoring and Tracking of Animals" (I.G. Priede, and S.M. Swift, eds), 495-509. Ellis Horwood, Chichester, UK.

Kaplan, E.L. and Meier, P. 1958. Nonparametric estimation from incomplete observations. Journal of the American Statistical Association 53, 457-481.

Kenward, R.E. 1982. Goshawk hunting behaviour, and range size as a function of habitat availability. Journal of Animal Ecology 51:69-80.

Kenward, R.E. 1987. Wildlife radio tagging: equipment, field techniques and data analysis. Academic Press, London, UK.

Kenward, R.E. 1992. Quantity versus quality: programmed collection and analysis of radio-tracking data. pp. 231-246 in I.G. Priede and S.M.Swift (Eds). Wildlife telemetry: remote monitoring and tracking of animals. Ellis Horwood, Chichester, UK.

Kenward, R.E., Marcström, V. & Karlbom, M. 1999. Demographic estimates from radio-tagging: models of age-specific survival and breeding in the goshawk. Journal of Animal Ecology 68:1020-1033.

Kenward, R.E. 2001. A Manual for Wildlife Radio Tagging. Academic Press, London, UK.

Kenward, R. E., Clarke, R. T., Hodder, K. H. and Walls, S. S. 2001. Distance and density estimators of home range: Defining multi-nuclear cores by nearest neighbor clustering. Ecology 82(7): 1905-1920.

Kenward, R.E., Marcstrom, V. and Karlbom, M. 1993. Post-nestling behaviour in goshawks, Accipiter gentilis. II. Sex differences in sociality and nest switching. Animal Behaviour 46:371-378.

Knight, C.M., Kenward, R.E., Gozlan, R.E., Hodder, K.H., Walls, S.S. & Lucas, M.C. 2009. Home range estimation within a restricted linear environment: importance of method selection in detecting seasonal change. Wildlife Research 36: 213–224.

Larkin, R.P. and Halkin, D. 1994. A review of software packages for estimating animla home ranges. Wildlife Society Bulletin 22:274-287.

Macdonald, D.W., Ball, F.G. and Hough, N.G. 1980. The evaluation of home range size and configuration using radio tracking data. A Handbook on Biotelemetry and Radio Tracking (C.J. Amlaner and D.W. Macdonald, eds), 405-424. Pergamon Press, Oxford, UK.

Michener, G.R. 1979. Spatial relationships of adult Richardson’s ground squirrels. Canadian Zoology 57, 125-139.

Otis, D.L. and White, G.C. 1999. Autocorrelation of location estimates and the analysis of radiotracking data. Journal of Wildlife Management 63, 1039-1044.

Pollock, K.H., Winterstein, S.R., Bunck, C.M. and Curtiss, P.D. 1989. Survival analysis in telemetry studies: the staggered entry design. Journal of Wildlife Management 53, 7-14.

Robertson, P.A., N.J. Aebischer, R.E. Kenward, I.K. Hanski and N.P. Williams. (1998). Simulation and jack-knifing assessment of home-range indices based on underlying trajectories. Journal of Applied Ecology 35, 928-940.

Spencer, W.D. and Barrett, R.H. 1984. An evaluation of the harmonic mean method for evaluating carnivore activity areas. Acta Zoologica Fennica 171:255-259.

Swihart, R.K. and Slade, N.A. 1985. Testing for independence of observations in animal movements. Ecology 66:1176-1184.

Voight, D.R. & Tinline, R.R. 1980. Strategies for analysing radio-tracking data. pp.387-404 in Amlaner, C.J. & Macdonald, D.W. (eds) A Handbook on Biotelemetry and Radio Tracking, Pergamon Press, Oxford, UK.

Walls S.S. and Kenward R.E., 1995. Movements of radio-tagged Common Buzzards Buteo buteo in their first year. Ibis 137: 177-182.

Walls S.S. and Kenward R.E., 1998. Movements of radio-tagged common buzzards in early life. Ibis 140: 561-568.

Walls S.S. and Kenward R.E. 2001. Spatial consequences of relatedness and age in buzzards. Animal Behaviour 61: 1069-1078.

White, G.C. and Garrott, R.A. 1990. Analysis of wildlife tracking data. Academic Press, New York, USA.

Worton, B.J. 1989. Kernel methods for estimating the utilisation distribution in home range studies. Ecology 70:164-168.

Worton, B.J. 1995a. A convex hull-based estimator of home-range size. Biometrics 51, 1206-1215.

Worton, B.J. 1995b. Using MonteCarlo simulation to evaluate kernel-based home-range estimators. Journal of Wildlife Management 59, 794-800.

Wray, S., Cresswell, W.J. and Rogers, D. 1992. Dirichlet tessellations: a new, non-parametric approach to home range analysis. pp 247-255 in Priede & Swift.

Tutorial

2014-11-30T07:52:18Z

RobertKenward: /* Data Sources */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

==== Plotting survival for a single data set ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''kaplan meier survival''.

* Under '''Analysis Options''' ensure ''one set'' is selected

* Under '''Input files''' press '''browse''' and find, for the ''set 1 survival file'' the file ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Press the '''Run Analysis''' button.

Looking at the statistics window, the sample size was not adequate until the start of the second month, and became less than 30 animals due to moulting of tail-mounted radio tags after 30 April. Run the analysis again, selecting as '''set 1 start date''' the ''specified date'' and use the calendar to select 1 July 1980, then in '''set 1 end date''' again select ''specified date'' and set 31 March 1981. This estimates juvenile female survival to the start of the next egg-laying period, as used in [[Bibliography|Kenward et al. (1999)]].

==== Comparing two sets of survival data ====

[[File:To be added]]

* Under '''Analysis Options''' select ''two sets for comparison''

* Under '''Input files''' check that the ''set 1 survival file'' is still ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Check that '''set 1 start date''' has ''specified date'' selected, of 1 July 1980.

* Check that '''set 1 end date''' has ''specified date'' selected, of 31 March 1981.

* Press '''browse''' for the ''set 2 survival file'' and find ''<RangesFolder>\samples\raptors\goshawkjuvmal.srv''.

* Set the '''set 2 start date'' to the ''set 1 start date'' option.

* Set the '''set 2 end date'' to the ''set 2 end date'' option.

* Press the '''Run Analysis''' button.

The survival is poorer for juvenile males than for juvenile females due mainly to differences from October (month 4) onwards. The ''z'' values of 2.07 to 2.13 are higher than the value of 1.96 for alpha = 0.05, so ''P'' < 0.05.

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward (2001), Kenward et al. (2001)]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission. Goshawk survival data were collected on the Swedish island of Gotland ([[Bibliography|Kenward et al. 1993, 1999]]); although there are 5 year-cohorts, the natal year for all birds has been set to 1980 for use in this example.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel, buzzard and goshawk data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology), in the last case in cooperation with Uppsala University and the Swedish Hunters' Association. The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-30T07:48:56Z

RobertKenward: /* Kaplan Meier Survival Analysis */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

==== Plotting survival for a single data set ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''kaplan meier survival''.

* Under '''Analysis Options''' ensure ''one set'' is selected

* Under '''Input files''' press '''browse''' and find, for the ''set 1 survival file'' the file ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Press the '''Run Analysis''' button.

Looking at the statistics window, the sample size was not adequate until the start of the second month, and became less than 30 animals due to moulting of tail-mounted radio tags after 30 April. Run the analysis again, selecting as '''set 1 start date''' the ''specified date'' and use the calendar to select 1 July 1980, then in '''set 1 end date''' again select ''specified date'' and set 31 March 1981. This estimates juvenile female survival to the start of the next egg-laying period, as used in [[Bibliography|Kenward et al. (1999)]].

==== Comparing two sets of survival data ====

[[File:To be added]]

* Under '''Analysis Options''' select ''two sets for comparison''

* Under '''Input files''' check that the ''set 1 survival file'' is still ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Check that '''set 1 start date''' has ''specified date'' selected, of 1 July 1980.

* Check that '''set 1 end date''' has ''specified date'' selected, of 31 March 1981.

* Press '''browse''' for the ''set 2 survival file'' and find ''<RangesFolder>\samples\raptors\goshawkjuvmal.srv''.

* Set the '''set 2 start date'' to the ''set 1 start date'' option.

* Set the '''set 2 end date'' to the ''set 2 end date'' option.

* Press the '''Run Analysis''' button.

The survival is poorer for juvenile males than for juvenile females due mainly to differences from October (month 4) onwards. The ''z'' values of 2.07 to 2.13 are higher than the value of 1.96 for alpha = 0.05, so ''P'' < 0.05.

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward (2001), Kenward et al. (2001)]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission. Goshawk survival data were collected on the Swedish island of Gotland ([[Bibliography|Kenward et al. 1993, 1999]]).

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel, buzzard and goshawk data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology), in the last case in cooperation with Uppsala University and the Swedish Hunters' Association. The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-30T07:42:46Z

RobertKenward: /* Data Sources */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

==== Plotting survival for a single data set ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''kaplan meier survival''.

* Under '''Analysis Options''' ensure ''one set'' is selected

* Under '''Input files''' press '''browse''' and find, for the ''set 1 survival file'' the file ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Press the '''Run Analysis''' button.

Looking at the statistics window, the sample size was not adequate until the start of the second month, and became less than 30 animals due to moulting of tail-mounted radio tags after 30 April. Run the analysis again, selecting as '''set 1 start date''' the ''specified date'' and use the calendar to select 1 July 1980, then in '''set 1 end date''' again select ''specified date'' and set 31 March 1981. This estimates juvenile female survival of 71% to the start of the next egg-laying period, as used in [[Bibliography|Kenward et al. 1999]].

==== Comparing two sets of survival data ====

[[File:To be added]]

* Under '''Analysis Options''' select ''two sets for comparison''

* Under '''Input files''' check that the ''set 1 survival file'' is still ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Press '''browse''' for the ''set 2 survival file'' and find ''<RangesFolder>\samples\raptors\goshawkjuvmal.srv''.

* Set the '''set 2 start date'' to the ''set 1 start date'' option.

* Set the '''set 2 end date'' to the ''set 2 end date'' option.

* Press the '''Run Analysis''' button.

The survival is poorer for juvenile males than for juvenile females due mainly to differences from October (month 4) onwards. The ''z'' values of 2.07 to 2.13 are higher than the value of 1.96 for alpha = 0.05, so ''P'' < 0.05.

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward (2001), Kenward et al. (2001)]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission. Goshawk survival data were collected on the Swedish island of Gotland ([[Bibliography|Kenward et al. 1993, 1999]]).

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel, buzzard and goshawk data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology), in the last case in cooperation with Uppsala University and the Swedish Hunters' Association. The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-30T07:40:51Z

RobertKenward: /* Data Sources */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

==== Plotting survival for a single data set ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''kaplan meier survival''.

* Under '''Analysis Options''' ensure ''one set'' is selected

* Under '''Input files''' press '''browse''' and find, for the ''set 1 survival file'' the file ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Press the '''Run Analysis''' button.

Looking at the statistics window, the sample size was not adequate until the start of the second month, and became less than 30 animals due to moulting of tail-mounted radio tags after 30 April. Run the analysis again, selecting as '''set 1 start date''' the ''specified date'' and use the calendar to select 1 July 1980, then in '''set 1 end date''' again select ''specified date'' and set 31 March 1981. This estimates juvenile female survival of 71% to the start of the next egg-laying period, as used in [[Bibliography|Kenward et al. 1999]].

==== Comparing two sets of survival data ====

[[File:To be added]]

* Under '''Analysis Options''' select ''two sets for comparison''

* Under '''Input files''' check that the ''set 1 survival file'' is still ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Press '''browse''' for the ''set 2 survival file'' and find ''<RangesFolder>\samples\raptors\goshawkjuvmal.srv''.

* Set the '''set 2 start date'' to the ''set 1 start date'' option.

* Set the '''set 2 end date'' to the ''set 2 end date'' option.

* Press the '''Run Analysis''' button.

The survival is poorer for juvenile males than for juvenile females due mainly to differences from October (month 4) onwards. The ''z'' values of 2.07 to 2.13 are higher than the value of 1.96 for alpha = 0.05, so ''P'' < 0.05.

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission. Goshawk survival data were collected on the Swedish island of Gotland ([[Bibliography|Kenward et al. 1993, 1999]]).

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel, buzzard and goshawk data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology), in the last case in cooperation with Uppsala University and the Swedish Hunters' Association. The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T18:57:02Z

RobertKenward: /* Kaplan Meier Survival Analysis */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

==== Plotting survival for a single data set ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''kaplan meier survival''.

* Under '''Analysis Options''' ensure ''one set'' is selected

* Under '''Input files''' press '''browse''' and find, for the ''set 1 survival file'' the file ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Press the '''Run Analysis''' button.

Looking at the statistics window, the sample size was not adequate until the start of the second month, and became less than 30 animals due to moulting of tail-mounted radio tags after 30 April. Run the analysis again, selecting as '''set 1 start date''' the ''specified date'' and use the calendar to select 1 July 1980, then in '''set 1 end date''' again select ''specified date'' and set 31 March 1981. This estimates juvenile female survival of 71% to the start of the next egg-laying period, as used in [[Bibliography|Kenward et al. 1999]].

==== Comparing two sets of survival data ====

[[File:To be added]]

* Under '''Analysis Options''' select ''two sets for comparison''

* Under '''Input files''' check that the ''set 1 survival file'' is still ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Press '''browse''' for the ''set 2 survival file'' and find ''<RangesFolder>\samples\raptors\goshawkjuvmal.srv''.

* Set the '''set 2 start date'' to the ''set 1 start date'' option.

* Set the '''set 2 end date'' to the ''set 2 end date'' option.

* Press the '''Run Analysis''' button.

The survival is poorer for juvenile males than for juvenile females due mainly to differences from October (month 4) onwards. The ''z'' values of 2.07 to 2.13 are higher than the value of 1.96 for alpha = 0.05, so ''P'' < 0.05.

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T18:42:22Z

RobertKenward: /* Kaplan Meier Survival Analysis */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

==== Plotting survival for a single data set ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''kaplan meier survival''.

* Under '''Analysis Options''' ensure ''one set'' is selected

* Under '''Input files''' press '''browse''' and find, for the ''set 1 survival file'' the file ''<RangesFolder>\samples\raptors\goshawkjuvfem.srv''.

* Press the '''Run Analysis''' button.

Looking at the statistics window, the sample size was not adequate until the start of the second month, and became less than 30 animals due to moulting of tail-mounted radio tags after 30 April. Run the analysis again, selecting as '''set 1 start date''' the ''specified date'' and use the calendar to select 1 July 1980, then in '''set 1 end date''' again select ''specified date'' and set 31 March 1981. This estimates juvenile survival to the start of the next egg-laying period, as used in [[Bibliography|Kenward et al. 1999]].

==== Comparing two sets of survival data ====

[[File:To be added]]

* Under '''Analysis Options''' select ''two sets for comparison''

* Under '''Input files''' check that the ''set 1 survival file'' is still ''<RangesFolder>\samples\squirrel\Warfarin.srv''.

* Press '''browse''' for the ''set 2 survival file'' and find ''<RangesFolder>\samples\squirrel\LeggMulti.srv''.

* Check that the '''time interval''' remains set to ''days '' and accept the default of ''1'' day with all other defaults.

* Press the '''Run Analysis''' button.

The survival is initially poorer for animals caught with with Legg Multiple Capture traps but then

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T14:39:53Z

RobertKenward: /* Comparing observed and random data */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope''' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T14:38:33Z

RobertKenward: /* Comparing observed and random data */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options''' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope'' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T14:37:22Z

RobertKenward: /* Comparing observed and random data */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options'' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope'' select ''user defined'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T14:34:47Z

RobertKenward: /* Modelling */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options'' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope'' select ''user define'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and in tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T14:32:09Z

RobertKenward: /* Plotting observed data only */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line. The prediction of minimum woodland area required, from the intercept ''c'', is 10^-1 and therefore about 0.1 ha.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options'' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope'' select ''user define'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and in tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T14:24:22Z

RobertKenward: /* Comparing observed and random data */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options'' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5. For ''WOODL''and, there are no random values beyond the observed (i.e. ''P'' < 0.01), nor in repeated runs with 999 iterations (i.e. ''P'' < 0.002).

* Now under '''envelope'' select ''user define'', after making a file with an expansive outline (e.g. 99% ellipses)

You will find with this particular file that, due to the greater availability of sea round the island for random outlines, nearly 10% of the random outlines are in the sea if using either the default ''replace zeros'' or the option ''ignore zeros''. In these circumstances the random regressions have a tendency to be positive, because small range outlines have a greater chance of including no island or woodland. The option ''resample zeros'' is then most conservative, because it forces random samples to contain habitat and in tends to produce regression with ''b''=0.

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T13:59:23Z

RobertKenward: /* Comparing observed and random data */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line.

==== Comparing observed and random data ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options'' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the graph includes a yellow line based on the mean slope ''b'' and intercept ''c'' for the regressions from 199 random samplings with replacement among the 15 observed range outlines, each of which was randomly rotated and displaced within the envelope round all the observed outlines [[Glossary|see Glossary]] in a separate window; these mean values are given in the statistics window, also with 95% confidence limits for ''r'' assuming a normal distribution, and a z value for the difference between the observed ''r'' and that mean value. However, the most robust statistic for tests is in the next column: the number of negative random values beyond the observed ''r''. The value will vary with each run, but will average about 3. In a two-tailed test with 200 samples (including the observed), ''P'' < 0.05 for a value less than 5.

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T13:45:19Z

RobertKenward: /* Plotting observed data only */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which repeats in the statistics window. If you click ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line.

==== Comparing observed and random data ====

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options'' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the g [[Glossary|see Glossary]] in a separate window.

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T13:43:33Z

RobertKenward: /* Plotting observed data only */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island ''inclusive of woodland'' (and thus unlike the exclusive habitat areas in most habitat analysis), it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which also shows in the statistics window. If you click on ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line.

==== Comparing observed and random data ====

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options'' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the g [[Glossary|see Glossary]] in a separate window.

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T13:13:57Z

RobertKenward: /* Plotting observed data only */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''.
If that file is not in the folder, you need to create it in the Tutorial sequence [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island, it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which also shows in the statistics window. If you click on ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line.

==== Comparing observed and random data ====

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options'' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the g [[Glossary|see Glossary]] in a separate window.

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T13:12:51Z

RobertKenward: /* Modelling */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Select ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''. If that file is not in the folder, you need to create it in the Tutorial sequence above [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the log proportion of resource on the log area of the range. As the first resource is the area of island, it fills the range of most of the 15 squirrels, but six of them also included appreciable proportions of oil-extraction area which is not included as usable island; as these squirrels also had the larger range outlines there is a negative correlation (''r'' = -0.579), which also shows in the statistics window. If you click on ''WOODL'' at the top left of the main window, the graph shows a stronger relationship (''r'' = -0.863) with steeper green regression line.

==== Comparing observed and random data ====

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options'' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the g [[Glossary|see Glossary]] in a separate window.

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T12:52:40Z

RobertKenward: /* Plotting observed data only */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Choose ''resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''. If that file is not in the folder, you need to create it in the Tutorial sequence above [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the . [[Glossary|see Glossary]] in a separate window.

==== Comparing observed and random data ====

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options'' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the g

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T12:50:50Z

RobertKenward: /* Resource Area Dependence Analysis */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

==== Plotting observed data only ====

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Choose "resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''. If that file is not in the folder, you need to create it in the Tutorial sequence above [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options''' select ''observed only''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the . [[Glossary|see Glossary]] in a separate window.

==== Comparing observed and random data ====

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options'' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the g

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T12:45:40Z

RobertKenward: /* Resource Area Dependence Analysis */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Choose "resource area dependence''.

* Under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''. If that file is not in the folder, you need to create it in the Tutorial sequence above [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options'' select ''observed only and 199 random iterations''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the . [[Glossary|see Glossary]] in a separate window.

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options'' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the g

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T12:44:01Z

RobertKenward: /* Resource Area Dependence Analysis */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

[[File:To be added]]

* Click on the '''Modelling''' button to open the setup window. 

* Choose "resource area dependence''.

* If a file is not loaded, under '''Map file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furhab.ves''.

* Similarly, under '''Edge file''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey_cxoi01s.edg''. If that file is not in the folder, you need to create it in the Tutorial sequence above [[Tutorial#Cluster analysis with objective cores| Cluster analysis with objective cores]].

* Under '''Analysis Options'' select ''observed only and 199 random iterations''

* Press the '''Run Analysis''' button.

The computer does 15 habitat analyses and displays the results in a graph of the

[[Glossary|see Glossary]] in a separate window.

* Click on the '''Modelling''' button to open the setup window. 

All the previous options and files should still be selected, but make them again if not

* Under '''Analysis Options'' select ''observed and 199 random iterations''

* Press the '''Run Analysis''' button.

* Have a cup of tea or coffee while your computer does more than 3,000 habitat analyses.

This time the g

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T12:24:36Z

RobertKenward: /* Modelling */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate resource-requirement and survival parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

=== Kaplan Meier Survival Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T11:58:00Z

RobertKenward:

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate survival and resource-requirement parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Kaplan Meier Survival Analysis ===

=== Resource Area Dependence Analysis ===

== Data Sources ==

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was used to illustrate the effectiveness of [[Glossary|Cluster analysis]] in [[Bibliography|Kenward 2001, Kenward et al. 2001]].

The buzzard data were collected for a study of relationships between demography and habitat conducted from Furzebrook Research Station ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The squirrel and buzzard data came from work funded by the UK Natural Environment Research Council in its Centre for Ecology and Hydrology (formerly Institute of Terrestrial Ecology). The blackbird and lion data were collected during student and post-graduate projects from the University of Oxford, the first supervised externally within NERC-CEH. The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T11:47:24Z

RobertKenward:

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate survival and resource-requirement parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Kaplan Meier Survival Analysis ===

=== Resource Area Dependence Analysis ===

== Data Sources ==

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The squirrel data were collected in the 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. One set, which was collected at Elton Estate in work conducted from Monks Wood Experimental Station, was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]). A second set, collected on Furzey Island in Poole Harbour in work conducted from Furzebrook Research Station, was

The buzzard data were collected for a study of relationships between demography and habitat ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T11:41:47Z

RobertKenward:

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Modelling ==

These routines estimate survival and resource-requirement parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

=== Resource Area Dependence Analysis ===

== Data Sources ==

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The squirrel data were collected in the early 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. They were collected in a study of habitat use that was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]).

The buzzard data were collected for a study of relationships between demography and habitat ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T11:40:38Z

RobertKenward:

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

=== Modelling ===

These routines estimate survival and resource-requirement parameters which can be used in modelling. Future work will focus on refining these parameters and providing new ones with further automated analyses of the type being conducted in Resource Area Dependence Analysis.

==== Resource Area Dependence Analysis ====

== Data Sources ==

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The squirrel data were collected in the early 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. They were collected in a study of habitat use that was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]).

The buzzard data were collected for a study of relationships between demography and habitat ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The files within the folder fish are a simulated dataset created by Sean Walls.

Tutorial

2014-11-29T10:53:12Z

RobertKenward: /* Cluster analysis with objective cores */

For a tutorial on the free demonstration version of Ranges, see the [[Demo Tutorial|Demo Tutorial]].

== Introduction ==

This is a brief tutorial to work you through the basics of using Ranges. It concentrates on the practical steps you need to take to perform different analyses. It contains little explanation of what the routines do (see overview and links from there for that).

Lines starting with a bullet point (•) describe actions to perform. Click on the images to the right to enlarge them.

== Getting your data in and viewing ==

==== Location data, the simplest option - just coordinates for a single range ====

[[File:Import locations1.png|thumb|right|upright=1.6|Press import and select ''Location file from column text file''.]]
[[File:Import locations2.png|thumb|right|upright=1.6|Set Scale Of Coordinate Units and Tracking resolution to 10.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location column file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_indiv1_coords_only.txt

If you look at this file in a spreadsheet you’ll see it contains 2 columns of data with the headers E & N.

The import routine detects the file contents, and sets up the defaults accordingly.

* Set '''Scale Of Coordinate Units''' and '''Tracking resolution''' to 10. Press '''OK''' to accept other defaults

This will have read the two columns in as a single range, the points will be displayed in the map display and you can alter range attributes in the ''Ranges'' table, or the coordinates themselves in the ''Location'' table.

* Press '''save''' to save this as a Ranges location file that can be used as an input in other Ranges routines.

(Note that an alternative way of doing this is to press '''new''', then open the text file in Excel, copy the coordinates and paste them into the empty '''locations''' table).

==== Location data - coordinates for multiple ranges ====

* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column text file'' 
* Select the file <RangesFolder>\samples\blackbird\blackbird_ids_and_coords.txt

If you look at this file in a spreadsheet you’ll see it contains 3 columns of data with the headers ID, E & N.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges according to the ID specified in the first column.

* Press '''save''' to save this as a Ranges location file.

==== Location data - coordinates, range attributes and location qualifying variables ====

[[File:Import locations3.png|thumb|right|upright=1.6|Range and location data]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''import''' and select ''Location file from column textfile''. 
* Select the file <RangesFolder>\samples\blackbird\blackbird.txt

If you look at this file in a spreadsheet you’ll see it contains 17 columns of data.

* Set '''Scale Of Coordinate Units''' and '''Tracking Resolution''' to 10. Press '''OK''' to accept the defaults.

This will have read the coordinates into four ranges as above, but it will also have read in range attribute data that will be displayed in the ''Ranges'' table and location qualifying variables that will be displayed in the ''Locations'' table.

* Press '''save''' to save this as a Ranges location file, but note that an identical file named blackbird.loc is already provided in the blackbird directory.

==== Viewing a large multi-range file ====

[[File:Import locations4.png|thumb|right|upright=1.6|Display all ranges, selected range in blue, selected location in red.]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select <RangesFolder>\samples\buzzard\buzzards101.loc 
* Above the map display, change from ''display selected range(s)'' to ''display all ranges'' 
* Make sure the '''range colours''' next to the display option box is set to ''selection'' 
* Click the left mouse button in the left column of the ''Ranges'' table. 
* Use the arrow keys to move down the table (see how the selected range is displayed in blue, and the data for the selected range is displayed in the ''Locations'' table. 
* Select the left column in the ''Locations'' table. 
* Use the arrow keys to move between locations in the table.

See how the selected location is circled in red.

* Left click on a blue location in the map display while holding down the SHIFT key.

See how the corresponding row in the ''Locations'' table becomes selected, and the location is coloured red to show that it is selected.

* Try editing the E or N values for a location in the ''Locations'' table and see how its position in the map display is changed. 
* Change the '''range colour''' option box to ‘sex’.

You will see males displayed in blue and females in red.

==== Viewing GPS collected movement paths with associated time information ====

[[File:Import locations5.png|thumb|right|upright=1.6|GPS-collected lion data animated by time]]
* Open Ranges to the [[Input & Graphics| main window]] 
* Press '''open''' and select ''<RangesFolder>\samples\lion\lions.loc'' 
* Above the map display change from ''display selected range(s)'' to ''display all ranges'' 
* Change the range colour to ''sex''.

You should see the male locations overlapping with those of the two females.

* Tick '''Background map''' and browse to select ''lions.loc'' as the background file too. 
* Above the map display, change from ''display all ranges'' to ''animate locations by time''. 
* Change the option from ''Play fast'' to ''Play med'' or slower

You should be able to follow the movements of the 3 individuals over time, the first female enters the area covered by the male on the 20th of October and leaves on the 21st, the male doesn’t enter the area covered by the first female until the 27th.

== Location analyses ==

==== Inter-location distances ====

[[File:Location analysis1.png|thumb|right|upright=1.6|Setting up the inter-location analysis.]]
[[File:Location analysis2.png|thumb|right|upright=1.6|Inter-location analysis data, map and plot.]]
* Click on the '''Location''' button to open the Location Analysis setup window. 
* Choose ''inter-location measures''. 
* Under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''. 
* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at 1. 
* Press the ''Run Analysis'' button.

The progress window will flash up (this is a fast-running analysis. Then the Statistics window and a Plot window will be displayed over the main window.

* Select different ranges within the ranges table on the upper left.

The results for them will be displayed in the Plot window.

* Select different locations in the locations table on the lower left and the corresponding location will be displayed in red in the plot. 

Note that a new column ''Distances(m)'' has been added to the file in the Locations table.

==== 100% Minimum convex polygons ====

[[File:Location analysis3.png|thumb|right|upright=1.6|100% convex polygon results with selected in background option.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options''' select ''100% cores''.

* In '''Output Files''', select ''Output edge file'' and accept the default filename (''blackbird_x.edg'').

* Press the '''Run Analysis''' button.

The edge file created will be displayed in main window.

* Select different ranges in the Edge shapes table at the upper left.

The range edge and the locations used to create it will be displayed ( the latter occurs because the tickbox for ''selected'' is the current option for the '''Background'''.

If you wish to export the polygon edge file to ArcView or another GIS package do the following :

* From the main window press '''export''', and select ''ArcView Shapefile Polyline''.

==== Convex polygons at 5% intervals ====

[[File:Location analysis4-1.png|thumb|right|upright=1.6|5% intervals convex polygon results with plot, map and statistics. See the core size and area columns in the statistics window.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\blackbird\blackbird.loc''.

* Under '''Analysis Options'' select ''cores at 5% intervals''

* Under '''Peel centre''' select ''focal site'' (this means that locations will be excluded based upon their distance from the focal site).

* Press the '''Run Analysis''' button.

The cores, and a utilisation plot will be displayed in the main window for the first range.

* Select the first row in the upper left table and use the arrow key to move down through the range cores and on to the next ranges.

==== Incremental area plots ====

[[File:Location analysis5.png|thumb|right|upright=1.6|Incremental area analysis plot.]]

Incremental area plots display how the area of an estimated home range core changes as successive locations are added.

* repeat the steps in [[#Convex polygons at 5% intervals|Convex polygons at 5% intervals]], but before pressing '''Run Analysis''' change the following options :

* Under '''Analysis Options''' select ''incremental area analysis''

* Keep the core % at the default value of ''100''.

* Press the '''Run Analysis''' button.

The incremental area plot will be displayed for each range in the main window.

==== Cluster analysis with objective cores ====

[[File:To be added]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose "neighbour-linkage''.

* If a file is not loaded, under '''Input Files''' press '''browse''' and find the file ''<RangesFolder>\samples\squirrel\furzey.loc''.

* Under '''Analysis Options'' select ''objective cores''

* Under '''Linkage method''' select ''cluster convex polygons''

* Leave '''Inclusive or cluster''' at the default of ''separate cluster polygons''

* Leave '''Polygon display method''' at the default of ''corner & cell polygons''; these options give the classic cluster analysis from [[Bibliography|Kenward (1987), Kenward et al. (2001)]]).

* Under '''Outlier exclusion''' select ''iterative alpha 0.1%'' (this choice gives the most conservative exclusive of outlying locations – i.e. the [[Glossary|outlier exclusion distances]] are large) and hence only the most extremely excursive locations are excluded.

* Under '''Output files''' click the box to select ''output edge''; this should create a file ''furzey_cxoi01s.edg''

* Press the '''Run Analysis''' button.

The edges will be displayed in the main window for the first range, with cluster analysis statistics [[Glossary|see nuclei, partial area, diversity of areas and diversity of locations in the Glossary]] in a separate window.

* In the '''Outlier exclusion''' box at the top of the graphics screen, select ''display all''.

* In the '''Background''' box above the graphics screen, press the (third) ''open'' button and select the file ''furhab.ves''; in the same box select ''all'' instead of ''clipped'' in the second box.

The map of Furzey Island will plot in brown under the range outlines, with the (Scots pine) woodland used by the red squirrels shown in black. The island is surrounded by sea, and has two areas large of concrete used for oil-drilling within the woodland. Note that one squirrel location was on the beach to the north of the island, and (if you open the file ''furzey.loc'' instead of the edges in the '''Data''' box and select the (first) button to display the map ''faint'' in the '''Background''' box) that squirrels rarely used the oil-extraction sites.

==== Dispersal detection via inter-location distances ====

[[File:Location analysis6.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''inter-location measures''

* Under '''Input files''' press ''browse'' and find the file ''<RangesFolder>\samples\buzzard\buzzard_dispersal.loc''.

* Under '''Analysis Options''', select ''distances'', ''site to location''

* Tick the '''dispersal detection''' box

* Set '''Minimum dispersal distance’ to '''1000''' and '''Alpha for dispersal detection''' to ''none''.

* Press the '''Run Analysis''' button.

The distances from the focal site to each location over time for the first range will be displayed in a separate window, with a red vertical line marking where dispersal was classed to occur by the entered criteria.

* Select different ranges within the ranges table on the upper left and the results for them will be displayed in the plot window.

Note that new columns ''Distances*'' and ''Dispersal*'' have been added to the file in the Locations table. The latter contains 0 prior to dispersal and 1 after it.

== Overlap analysis ==

==== Creating an overlap matrix ====

[[File:Overlap analysis 1.png|thumb|right|upright=1.6|Dispersal detection map and plot. Note the new columns in the Locations table.]]

* If you have not already done so, run through [[#100% Minimum convex polygons|100% Minimum convex polygons]] to create the file ''blackbird_x.edg]].

* Click on the '''Overlap''' button.

* Select ''range overlap''.

* Press '''browse''' and select the edge file ''<RangesFolder>\samples\blackbird\blackbird_x.edg''

* Press the '''Run Analysis''' button.

In the statistics window and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns followed by the area itself. A new map has been built of the union of each range's overlap with all the others.

== Interaction analysis ==

==== Autocorrelations ====

[[File:Interaction analysis1.png|thumb|right|upright=1.6|Autocorrelation analysis results.]]

* Click on the '''Interaction''' button.

* Select ''autocorrelations''.

* Press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, click the Log button to see the ''time to independence (Schoeners 1) '' for each range. These are displayed in the plot.

==== Dynamic interactions ====

[[File:Interaction analysis2.png|thumb|right|upright=1.6|Dynamic interation statistics showing strong positive association between the movements of the second female and the male lions.]]

* Click on the '''Interaction''' button.

* Select '''dynamic interactions'''.

* Press '''browse''' and select ''<RangesFolder>\samples\lion\lions.loc''.

* Select ''all'’ for ''Individual selection''

* Select ''time attributes of locations'' for '''Same time observations defined by'''.

* Enter ''30'' for '''Input threshold between same-time observations (minutes)'''.

Locations were collected approximately hourly; this will allow for the slight variation while not considering consecutive locations as being taken at the same time.

* Leave the default '''Maximum randomisation sample''' (5000).

* In '''Output files''' select 'means for each range''.

* Press the '''Run Analysis''' button.

On completion, you should see in the statistics file that the Jacobs indices in the final three columns are less than 0.1 for all combinations except for the last one (which is for the second female and the male). This generates Jacobs indices of > 0.75 using the different means, indicating strong positive association between the movements.

== Habitat analysis ==
[[File:Habitat analysis1-1.png|thumb|right|upright=1.6|Habitat content of ranges analysis results map and statistics.]]

==== Habitat content of ranges ====

* Click on the '''Habitat''' button.

* Select ''habitat content of ranges''.

* For the '''map''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* for the '''edge''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.edg''.

* Press the '''Run Analysis''' button.

When the analysis completes, the statistics window will contain the area calculations for each habitat in each range.

The map in the main window contains the edge file in the foreground with the habitat raster in the background ''clipped'' to the edges and ''faint'' to make the edge lines clearer.

* To use a vector habitat file rather than a raster file use the files ''<RangesFolder>\samples\blackbird\blackbird_map.ves'' and ''<RangesFolder>\samples\blackbird\blackbird_x.edg'' (the latter created in [[#100% Minimum convex polygons|100% Minimum convex polygons]]).

==== Habitat in buffers around locations ====

[[File:Habitat analysis2.png|thumb|right|upright=1.6|Habitat at locations analysis map results.]]

* Click on the '''Habitat''' button.

* Select ''habitat at locations''.

* The map file should be already set but if not, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzmap.rst''.

* For the '''location''' file, press '''browse''' and select ''<RangesFolder>\samples\buzzard\buzzards.loc''.

* In '''Analysis Options''', select '''buffers around locations'''

* Change '''Input circle radius''' to ''100''.

* Press the '''Run Analysis''' button.

* When the analysis has finished, circles around each habitat will be displayed on the map.

== Fish analyses, midline and clipping ==

==== Midline inter-location distances ====

[[File:Midline analysis1.png|thumb|right|upright=1.6|Results of midline inter=location distances showing a section between two locations. The blue line first goes from the location to the midline at right angles, then along the midline until it is parallel with the next location.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''midline inter-location''.

* Under '''Input Files''' for location file, press '''browse''' and find the file ''<RangesFolder>\samples\fish\fish.loc''.

* For the midline file, press ''browse'' and find the file ''<RangesFolder>\samples\fish\midline.vel''.

* Under '''Analysis Options''', select ''distances'', ''location interval'' and leave the '''Per number of locations''' set at ''1''.

* Click the '''link midline to locations''' checkbox.

* Press the '''Run Analysis''' button.

The statistics file will contain the distances file. The main window map will display the paths between all locations on the map. To view each path individually:

* change from ‘display all’ to ‘display selected edge(s)’, and use the mouse or cursor keys to select different paths within the upper left table.

==== Midline linear ranges ====

[[File:Midline analysis2.png|thumb|right|upright=1.6|Midline linear ranges results map showing the linear range in blue with the locations as a background map. Only the area covered by the fish is shown.]]

Using the same input files as above

* Select ''midline linear ranges''

* Press the '''Run Analysis''' button.

The length of each linear range will be displayed in the statistics file. The main window map will display each linear range, with the locations in the background.

* Try changing the background map to ''<RangesFolder>\samples\fish\midline.vel'' to see how far the river extends beyond the fishes' range.

==== Clipping home ranges by a river outline ====

[[File:Midline analysis3.png|thumb|right|upright=1.6|Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.]]
[[File:Midline analysis4.png|thumb|right|upright=1.6|Clipping home ranges: edge file overlayed on the map of the river.]]

* Click on the '''Location''' button to open the Location Analysis setup window. 

* Choose ''convex polygons'', ''100% cores''

* Use the same location file as above (''<RangesFolder>\samples\fish\fish.loc''.)

* Check '''Output edge file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x.edg''.

* Press the '''Run Analysis''' button.

When the analysis is complete the map will show the convex polygon, with the locations in the background.

* Click on the '''Habitat''' button to open the Habitat Analysis setup window. 

* Select ‘habitat content of ranges’

* For the '''map file''', press '''browse''' and select ''<RangesFolder>\samples\fish\river.ves''.

* For the '''edge file''', press '''browse''' & select ''<RangesFolder>\samples\fish\fish_x.edg (created at the start of this exercise)

* Check '''Output clip file''' in '''Output Files''' to create file ''<RangesFolder>\samples\fish\fish_x_Hab_river_clip.edg''.

* Press the '''Run Analysis''' button.

The clip file be loaded in the main window. You can load the original file ''fish_x.edg'' as a background to see the difference between them. The statistics will show the total area of the MCP, then the percentage of that area that is in the main river (dark blue) and tributary (light blue).

== Data Sources ==

The blackbird data represent material on an abundant European passerine species collected by Ben Kenward during a pilot study for work on garden birds. There are two adult males, an adult female that was incubating eggs and one that was not breeding at the time. All but the breeding female foraged in a garden during the day and roosted at night in a Rhododendron thicket some 200m away across an open field. The birds were tracked on foot, and locations for triangulation taken from less than 100m away, giving a tracking resolution of about 10m. For this reason, coordinates were entered in 10m units.

The squirrel data were collected in the early 1980s, before the introduction of location qualifying variables: the data therefore consist of simple x,y coordinates. They were collected in a study of habitat use that was used to illustrate the introduction of compositional analysis ([[Bibliography|Aebischer et al. 1993]]).

The buzzard data were collected for a study of relationships between demography and habitat ([[Bibliography|Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999]]). Note that some of the buzzard data have been altered slightly to avoid use used without the authors' permission.

The lion data come from 3 lions (2 females and 1 male), GPS collared in Botswana by Graham Hemson of the Wildlife Conservation Research Unit, Oxford (see [[Bibliography|Hemson et al. 2005]]). The collars were scheduled to take 15 locations in every 24 hour period and the sample given here is for October 2001. The data coordinates are expressed in the UTM projection. In the first half of the month the movements of the first female are restricted to an area approximately 10 x 10 km in the west. Then over the following 10 days she makes a return trip of over 70 km coinciding with the start of the zebra and wildebeest migrations. The movements of the 2nd female and the male are very similar at the start of the month. Later in the month the male makes an excursion into an area crossed by the first female about a week beforehand.

The files within the folder fish are a simulated dataset created by Sean Walls.