Tutorial

For a tutorial on the free demonstration version of Ranges, see the 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

Press import and select Location file from column text file.

Set Scale Of Coordinate Units and Tracking resolution to 10.

Open Ranges to the 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 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

Range and location data

Open Ranges to the 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

Display all ranges, selected range in blue, selected location in red.

Open Ranges to the 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

GPS-collected lion data animated by time

Open Ranges to the 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

Setting up the inter-location analysis.

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

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

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

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, 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.

Dispersal detection via inter-location distances

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

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 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

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

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

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).

Habitat in buffers around locations

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

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

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

Clipping home ranges: map output from 100% cores convex polygons analysis of the fish data.

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 (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 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 Hemson et al. 2004). 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.