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 I describe actions to perform.

Getting your data in and viewing

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

I Open Ranges to the main window
I Press import and select ‘Location column file’
I 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.

I 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.

I 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

I Open Ranges to the main window
I Press import and select Location file from column text file
I 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.

I 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.

I Press save to save this as a Ranges location file.

location data - coordinates, range attributes and location qualifying variables

I Open Ranges to the main window
I Press import and select Location file from column textfile.
I 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.

I 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.

I 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

I Open Ranges to the main window
I Press open and select <RangesFolder>\samples\buzzard\buzzards101.loc
I Above the map display, change from display selected range(s) to display all ranges
I Make sure the range colours next to the display option box is set to selection
I Click the left mouse button in the left column of the Ranges table.
I 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.
I Select the left column in the Locations table.
I Use the arrow keys to move between locations in the table (see how the selected location is circled in red).
I 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.
I 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.
I Change the range colour option box to ‘sex’. You will see males displayed in blue and females in red.

10.2.5 Viewing GPS collected movement paths with associated time information

• Select the ‘Input & Graphics’ tab

• Press ‘open’ and select ‘<RangesFolder>\samples\lion\lions.loc’

• above the map display change from ‘display selected range(s)’ to ‘display all ranges’

• change ‘Line colour and thickness’ to ‘sex’

You should see the male locations overlapping with those of the 2 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’

• under ‘Line colour and thickness’ change the lowest 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.

10.3 Location analyses

10.3.1 Inter-location distances

• Select the ‘Location analysis’ tab

• choose ‘inter-location measures’

• under ‘choose input file’ press ‘browse’ and find the file <RangesFolder>\samples\blackbird\blackbird.loc

• under analysis options, select ‘distances’, ‘location interval’ and leave the no. of locations set at 1

• press the red ‘Run location analysis’ button

The distances between each location in the first range will be displayed in a separate window.

• press ‘return to main screen’.

• select different ranges within the ranges table on the upper left and 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

10.3.2 100% Minimum convex polygons

• Select the ‘Location analysis’ tab

• choose ‘convex polygons’

• if a file isn’t loaded, under ‘choose input file’ press ‘browse’ and find the file <RangesFolder>\samples\blackbird\blackbird.loc

• under ‘analysis options’ select 100% cores

• in ‘run specifications’, select ‘Output edge file’ and accept the default filename (blackbird.edg).

• press the red ‘Run location analysis’ button

• when the analysis has finished press ‘return to main screen’

The edge file created will be displayed in ‘Input & Graphics’

• 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 only in background’ is ticked.

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

• from ‘Input & Graphics’ press ‘Export’, and select ‘ArcView shapefile’

10.3.3 Convex polygons at 5% intervals

• Select the ‘Location analysis’ tab

• choose ‘convex polygons’

• if a file isn’t loaded, under ‘choose input file’ press ‘browse’ and find the file <RangesFolder>\samples\blackbird\blackbird.loc

• under ‘analysis options’ select ‘cores at 5% intervals’

• under ‘Choose peel centre’ select ‘focal site’ (this means that locations will be excluded based upon their distance from the focal site)

• in ‘run specifications’, under ‘choose display option’ select ‘one range at a time’

• press the red ‘Run location analysis’ button, and ‘return to main screen’ when it appears

The cores, and a utilisation plot will be displayed in Input & Graphics 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.

10.3.4 Incremental area plots

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

• repeat the steps in 10.3.3, but before pressing ‘Run …’ change the following options :

• under ‘analysis options’ select ‘incremental area analysis’

• keep the core % at the default value of 100

• press ‘Run…’ followed by ‘return to main screen’

The incremental area plot will be displayed for each range in Input & Graphics

10.3.5 Dispersal detection via Inter-location distances

• Select the ‘Location analysis’ tab

• choose ‘inter-location measures’

• under ‘choose input file’ 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 ‘Min. dispersal distance’ to 1000m and ‘Alpha for dispersal detection’ to none.

• press the red ‘Run location analysis’ button, and ‘return to main screen’ when it appears

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.

10.4 Overlap analysis

10.4.1 Creating an overlap matrix

• if you haven’t already done so, run through 10.3.2 to create the file ‘blackbird.edg’

• select the ‘Overlap’ tab

• select ‘range overlap (2D)’

• press ‘browse’ and select the edge file ‘blackbird.edg’

• press the ‘Run overlap analysis’ button followed by ‘return to main screen’

The user interface will open the overlap matrix in Stats Viewer and you will be able to see the percentage overlap of the ranges in rows by the ranges in columns.

10.5 Interaction analysis

10.5.1 Autocorrelations

• select ‘Interaction’ tab

• select ‘autocorrelations’

• press ‘browse’ and select ‘<RangesFolder>\samples\buzzard\buzzards.loc’

• press ‘Run Interaction Analysis’

10.5.2 Dynamic interactions

• select ‘dynamic interactions’

• press ‘browse’ and select ‘<RangesFolder>\samples\lion\lions.loc’

• select ‘all’ for ‘use the following individuals’

• select ‘time attributes of locations’ for ‘same time obs. defined by’

• type 30 for ‘Input threshold between same-time observations (mins)’

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

• accept the default ‘max. randomisation sample of 5000’

• In ‘run specifications’ select ‘Means for each range’

• press ‘Run Interaction Analysis’ and ‘return to main screen’

The stats file will open in Stats Viewer. You should see that the Jacobs indices in the final 3 columns are less that 0.1 for all combinations except for the last one (which is for the 2nd female and the male). This generates Jacobs indices of >0.75 using the different means, indicating strong positive association between the movements.

10.6 Habitat analysis

10.6.1 Habitat content of ranges

• select ‘Habitat’ tab

• select ‘Habitat content of ranges’

• for the ‘map’ file, press browse & select : <RangesFolder>\samples\buzzard\buzzmap.rst

• for the ‘edge’ file, press browse & select : <RangesFolder>\samples\buzzard\buzzards.edg

• press ‘Run Habitat Analysis’ followed by ‘Return to main screen’

• look at the ranges in ‘Input & Graphics’, move to ‘Stats Viewer’ to see the stats results

• to use a vector habitat file rather than a raster file use the files : <RangesFolder>\samples\blackbird\blackbird_map.ves & <RangesFolder>\samples\blackbird\blackbird.edg (the latter created in 10.3.2).

10.6.2 Habitat in buffers around locations

• select ‘Habitat content of ranges’

• select ‘Habitat at locations’

• for the ‘location’ file, press browse & select : <RangesFolder>\samples\buzzard\buzzards.loc

• select ‘buffers around locations’

• change input circle radius to 100m

• press ‘Run Habitat Analysis’ followed by ‘Return to main screen’

• look at the circles in ‘Input & Graphics’, move to ‘Stats Viewer’ to see the stats results

10.7 Fish analyses, midline and clipping

10.7.1 Midline inter-location distances

• Select the ‘Location analysis’ tab

• choose ‘midline inter-location’

• under ‘choose input file’ for Locations, press ‘browse’ and find the file <RangesFolder>\samples\fish\fish.loc

• for Midline, press ‘browse’ and find the file <RangesFolder>\samples\fish\midline.vel

• under analysis options, select ‘distances’, ‘location interval’ and leave the no. of locations set at 1

• select ‘link midline to locations’

• press the red ‘Run location analysis’ button

• when the ‘return to main screen’ button becomes visible, press it.

The program will switch to Input & Graphics and display the paths between all locations.

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.

• switch to ‘stats viewer’ to see the distances file.

10.7.2 Midline linear ranges

Using the same input files as above

• select ‘midline linear ranges’

• press the red ‘Run location analysis’ button

• the length of each linear range will be displayed

• when the ‘return to main screen’ button becomes visible, press it.

The program will switch to Input & Graphics and display each linear range, with the locations in the background.

• switch to ‘stats viewer’ to see the distances file.

10.7.3 Clipping home ranges by a river outline

• Select the ‘Location analysis’ tab

• choose ‘convex polygons’, ‘100% cores’

• use the same location file as above (fish.loc)

• select ‘Output edge file’

• press the red ‘Run location analysis’ button & ‘return to main screen’ when it becomes visible

The program will switch to Input & Graphics and display each convex polygon, with the locations in the background.

• select ‘Habitat’ tab

• select ‘Habitat content of ranges’

• for the ‘map’ file, press browse & 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)

• select ‘Output clip file’

• press ‘Run Habitat Analysis’ followed by ‘Return to main screen’

The clip file created will be called fish_x_Hab_river_clip.edg. It will not be auto-loaded, but you can open it in ‘Input & Graphics’ and load the original file ‘fish_x.edg’ as a background to see the difference between them.

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, and 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 thicket some 200m away. 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 (Aebischer et al. 1993). The buzzard data were collected for a study of relationships between demography and habitat (Kenward et al. 2000, 2001, South & Kenward 2001, Walls et al. 1999). Note that some of the buzzard data has been altered slightly to avoid it being 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. 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.

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