Anatrack Ranges Support - User contributions [en]

Anatrack Ranges User Guide

2015-04-29T07:11:58Z

Admin: /* Offline Support */

Ranges is a comprehensive system for viewing, editing and analysing spatial location data. The current version is Ranges 9.

== Introduction ==

The Ranges suite of software has been evolving since the early 1980s, not merely as a convenient way to analyse the extensive data that can be gathered from radio-tagged, and increasingly gps-tagged, animals, but also to assist planning that makes the effort of data-gathering as efficient as possible. Early versions were written for the BBC micro but Ranges now has Windows and Apple Macintosh interfaces to help you to set up and run analyses.

Ranges includes comprehesive tools to allow you to input, view and export your animal location data. Not only does it have a long list of location analyses for estimating home range outlines but also supports analyses of how these outlines overlap and the dynamic interaction of location records with those of other animals or of sites that are important for feeding or sociality. It allows you to investigate availability and use of habitat in different ways and more recently adds modelling techniques to its tool box.

== New Features ==

Ranges 9 includes

* Resource Area Dependence analysis
* Kaplan-Meier Survival analysis
* An up-to-date look with a more user-friendly interface but without loosing the familiar Ranges feel
* Better data and map split positioning on screen with an adjustable divider to optimise space for each
* Map rendering improvements: both faster and with fewer artefacts
* Improved map furniture: coordinates, scale bar, zoom and pan controls, etc.
* Zoom to selection with right mouse button
* Zoom in and out to cursor with mouse scroll button
* Ability to create locations and vector points with CTRL + left mouse click, remove from the end with CTRL + right mouse click
* Improved data charts for utilization and incremental files, autocorrelation & interlocation analyses with axis-scaling, and better labels & headings
* Ability to make map backgrounds paler to improve visibility of foreground material
* Faster file loading
* Huge file handling including large location files from GPS devices and large raster maps
* Importing locations in latitidue-longitude format
* Exporting to KML using lat-lng
* Location file merging; edge file sampling and merging
* Display locations and analysis maps on Google Maps
* Save maps and plots to image file
* Range overlap analysis map output

For new features added to each version of Ranges see: [[New Features|New Features]]

== Installing Ranges ==

Ranges can be installed and run without purchasing a licence. Until it is licensed it will run in demo mode.

To install Ranges:

1. Install the latest version of the Java Runtime Environment (JRE). To do this, download the version suitable for your operating system here:

https://java.com/en/download/manual.jsp

<div style="color: red; font-weight:bold;border: solid 0px grey; padding-left:0px;">Note that if you are using a 64 bit version of Windows, you must install the 64 bit version of Java.</div>

2. Install Ranges by downloading and running the version suitable for your operating system from:

http://www.anatrack.com/download_ranges.php

Uninstall Windows Ranges through the '''Control Panel...Programs''' and Mac Ranges by deleting the folder in Programs.

== Licensing Ranges ==

To unlock and use the analyses in Ranges, you must purchase a licence depending on whether the software is to be used by only you (Single User licence) or by a number of people in the same organisation (Site licence).

Single User licences allows Ranges to be installed on two computers, e.g. for use on one in a lab and another in the field, provided both computers are not to be used at the same time.

A Site licence allows Ranges to be installed on up to ten computers. If you need to install Ranges on more than ten computers, please [http://www.anatrack.com/contact.php contact us].

Licences can be purchased here:

http://www.anatrack.com/buy_ranges.php

after which we will supply a licence key.

Once you have a licence key and have installed Ranges, navigate to the Ranges folder in Anatrack Ltd in your applications folder. Click on the License Ranges shortcut and follow the instructions on screen. When prompted enter the licence number.

== Using Ranges ==

An overview of Ranges functionality with links to more detailed descriptions of analyses and features can be found here: [[Ranges Overview|Ranges Overview]]

If you are new to Ranges, please work through [[Tutorial|the tutorial]].

== Citing Ranges ==

Please use the following citation in publications:

Kenward, R.E., Casey, N.M., Walls, S.S. & South A.B. (2014) Ranges9 : For the analysis of tracking and location data. Online manual. Anatrack Ltd. Wareham, UK.

== Offline Support ==

If you will be using Ranges where you do not have access to the Internet, this support wiki can be downloaded to your computer here:

http://www.anatrack.myzen.co.uk/Ranges9/Anatrack_Ranges9_Support.zip

To use it, unzip it to a suitable location, keeping the folder structure as it is. The wiki pages are accessed through

<InstallationFolder>\Anatrack Ranges 9 Support\ranges_support.html

Anatrack Ranges User Guide

2015-04-29T07:11:17Z

Admin: /* Offline Support */

Ranges is a comprehensive system for viewing, editing and analysing spatial location data. The current version is Ranges 9.

== Introduction ==

The Ranges suite of software has been evolving since the early 1980s, not merely as a convenient way to analyse the extensive data that can be gathered from radio-tagged, and increasingly gps-tagged, animals, but also to assist planning that makes the effort of data-gathering as efficient as possible. Early versions were written for the BBC micro but Ranges now has Windows and Apple Macintosh interfaces to help you to set up and run analyses.

Ranges includes comprehesive tools to allow you to input, view and export your animal location data. Not only does it have a long list of location analyses for estimating home range outlines but also supports analyses of how these outlines overlap and the dynamic interaction of location records with those of other animals or of sites that are important for feeding or sociality. It allows you to investigate availability and use of habitat in different ways and more recently adds modelling techniques to its tool box.

== New Features ==

Ranges 9 includes

* Resource Area Dependence analysis
* Kaplan-Meier Survival analysis
* An up-to-date look with a more user-friendly interface but without loosing the familiar Ranges feel
* Better data and map split positioning on screen with an adjustable divider to optimise space for each
* Map rendering improvements: both faster and with fewer artefacts
* Improved map furniture: coordinates, scale bar, zoom and pan controls, etc.
* Zoom to selection with right mouse button
* Zoom in and out to cursor with mouse scroll button
* Ability to create locations and vector points with CTRL + left mouse click, remove from the end with CTRL + right mouse click
* Improved data charts for utilization and incremental files, autocorrelation & interlocation analyses with axis-scaling, and better labels & headings
* Ability to make map backgrounds paler to improve visibility of foreground material
* Faster file loading
* Huge file handling including large location files from GPS devices and large raster maps
* Importing locations in latitidue-longitude format
* Exporting to KML using lat-lng
* Location file merging; edge file sampling and merging
* Display locations and analysis maps on Google Maps
* Save maps and plots to image file
* Range overlap analysis map output

For new features added to each version of Ranges see: [[New Features|New Features]]

== Installing Ranges ==

Ranges can be installed and run without purchasing a licence. Until it is licensed it will run in demo mode.

To install Ranges:

1. Install the latest version of the Java Runtime Environment (JRE). To do this, download the version suitable for your operating system here:

https://java.com/en/download/manual.jsp

<div style="color: red; font-weight:bold;border: solid 0px grey; padding-left:0px;">Note that if you are using a 64 bit version of Windows, you must install the 64 bit version of Java.</div>

2. Install Ranges by downloading and running the version suitable for your operating system from:

http://www.anatrack.com/download_ranges.php

Uninstall Windows Ranges through the '''Control Panel...Programs''' and Mac Ranges by deleting the folder in Programs.

== Licensing Ranges ==

To unlock and use the analyses in Ranges, you must purchase a licence depending on whether the software is to be used by only you (Single User licence) or by a number of people in the same organisation (Site licence).

Single User licences allows Ranges to be installed on two computers, e.g. for use on one in a lab and another in the field, provided both computers are not to be used at the same time.

A Site licence allows Ranges to be installed on up to ten computers. If you need to install Ranges on more than ten computers, please [http://www.anatrack.com/contact.php contact us].

Licences can be purchased here:

http://www.anatrack.com/buy_ranges.php

after which we will supply a licence key.

Once you have a licence key and have installed Ranges, navigate to the Ranges folder in Anatrack Ltd in your applications folder. Click on the License Ranges shortcut and follow the instructions on screen. When prompted enter the licence number.

== Using Ranges ==

An overview of Ranges functionality with links to more detailed descriptions of analyses and features can be found here: [[Ranges Overview|Ranges Overview]]

If you are new to Ranges, please work through [[Tutorial|the tutorial]].

== Citing Ranges ==

Please use the following citation in publications:

Kenward, R.E., Casey, N.M., Walls, S.S. & South A.B. (2014) Ranges9 : For the analysis of tracking and location data. Online manual. Anatrack Ltd. Wareham, UK.

== Offline Support ==

If you will be using Ranges where you do not have access to the Internet, this support wiki can be downloaded to your computer here:

http://www.anatrack.myzen.co.uk/Ranges9/Anatrack_Ranges9_Support.zip

To use it, unzip it to a suitable location keeping the folder structure in shape. The wiki pages are accessed through

<InstallationFolder>\Anatrack Ranges 9 Support\ranges_support.html

Anatrack Ranges User Guide

2015-04-29T07:10:40Z

Admin:

Ranges is a comprehensive system for viewing, editing and analysing spatial location data. The current version is Ranges 9.

== Introduction ==

The Ranges suite of software has been evolving since the early 1980s, not merely as a convenient way to analyse the extensive data that can be gathered from radio-tagged, and increasingly gps-tagged, animals, but also to assist planning that makes the effort of data-gathering as efficient as possible. Early versions were written for the BBC micro but Ranges now has Windows and Apple Macintosh interfaces to help you to set up and run analyses.

Ranges includes comprehesive tools to allow you to input, view and export your animal location data. Not only does it have a long list of location analyses for estimating home range outlines but also supports analyses of how these outlines overlap and the dynamic interaction of location records with those of other animals or of sites that are important for feeding or sociality. It allows you to investigate availability and use of habitat in different ways and more recently adds modelling techniques to its tool box.

== New Features ==

Ranges 9 includes

* Resource Area Dependence analysis
* Kaplan-Meier Survival analysis
* An up-to-date look with a more user-friendly interface but without loosing the familiar Ranges feel
* Better data and map split positioning on screen with an adjustable divider to optimise space for each
* Map rendering improvements: both faster and with fewer artefacts
* Improved map furniture: coordinates, scale bar, zoom and pan controls, etc.
* Zoom to selection with right mouse button
* Zoom in and out to cursor with mouse scroll button
* Ability to create locations and vector points with CTRL + left mouse click, remove from the end with CTRL + right mouse click
* Improved data charts for utilization and incremental files, autocorrelation & interlocation analyses with axis-scaling, and better labels & headings
* Ability to make map backgrounds paler to improve visibility of foreground material
* Faster file loading
* Huge file handling including large location files from GPS devices and large raster maps
* Importing locations in latitidue-longitude format
* Exporting to KML using lat-lng
* Location file merging; edge file sampling and merging
* Display locations and analysis maps on Google Maps
* Save maps and plots to image file
* Range overlap analysis map output

For new features added to each version of Ranges see: [[New Features|New Features]]

== Installing Ranges ==

Ranges can be installed and run without purchasing a licence. Until it is licensed it will run in demo mode.

To install Ranges:

1. Install the latest version of the Java Runtime Environment (JRE). To do this, download the version suitable for your operating system here:

https://java.com/en/download/manual.jsp

<div style="color: red; font-weight:bold;border: solid 0px grey; padding-left:0px;">Note that if you are using a 64 bit version of Windows, you must install the 64 bit version of Java.</div>

2. Install Ranges by downloading and running the version suitable for your operating system from:

http://www.anatrack.com/download_ranges.php

Uninstall Windows Ranges through the '''Control Panel...Programs''' and Mac Ranges by deleting the folder in Programs.

== Licensing Ranges ==

To unlock and use the analyses in Ranges, you must purchase a licence depending on whether the software is to be used by only you (Single User licence) or by a number of people in the same organisation (Site licence).

Single User licences allows Ranges to be installed on two computers, e.g. for use on one in a lab and another in the field, provided both computers are not to be used at the same time.

A Site licence allows Ranges to be installed on up to ten computers. If you need to install Ranges on more than ten computers, please [http://www.anatrack.com/contact.php contact us].

Licences can be purchased here:

http://www.anatrack.com/buy_ranges.php

after which we will supply a licence key.

Once you have a licence key and have installed Ranges, navigate to the Ranges folder in Anatrack Ltd in your applications folder. Click on the License Ranges shortcut and follow the instructions on screen. When prompted enter the licence number.

== Using Ranges ==

An overview of Ranges functionality with links to more detailed descriptions of analyses and features can be found here: [[Ranges Overview|Ranges Overview]]

If you are new to Ranges, please work through [[Tutorial|the tutorial]].

== Citing Ranges ==

Please use the following citation in publications:

Kenward, R.E., Casey, N.M., Walls, S.S. & South A.B. (2014) Ranges9 : For the analysis of tracking and location data. Online manual. Anatrack Ltd. Wareham, UK.

== Offline Support ==

If you will be using Ranges where you do not have access to the Internet, this support wiki can be downloaded to your computer:

http://www.anatrack.myzen.co.uk/Ranges9/Anatrack_Ranges9_Support.zip

To use it, unzip it to a suitable location keeping the folder structure in shape. The wiki pages are accessed through <InstallationFolder>\Anatrack Ranges 9 Support\ranges_support.html.

Anatrack Ranges User Guide

2015-04-29T07:09:19Z

Admin:

Ranges is a comprehensive system for viewing, editing and analysing spatial location data. The current version is Ranges 9.

== Introduction ==

The Ranges suite of software has been evolving since the early 1980s, not merely as a convenient way to analyse the extensive data that can be gathered from radio-tagged, and increasingly gps-tagged, animals, but also to assist planning that makes the effort of data-gathering as efficient as possible. Early versions were written for the BBC micro but Ranges now has Windows and Apple Macintosh interfaces to help you to set up and run analyses.

Ranges includes comprehesive tools to allow you to input, view and export your animal location data. Not only does it have a long list of location analyses for estimating home range outlines but also supports analyses of how these outlines overlap and the dynamic interaction of location records with those of other animals or of sites that are important for feeding or sociality. It allows you to investigate availability and use of habitat in different ways and more recently adds modelling techniques to its tool box.

== New Features ==

Ranges 9 includes

* Resource Area Dependence analysis
* Kaplan-Meier Survival analysis
* An up-to-date look with a more user-friendly interface but without loosing the familiar Ranges feel
* Better data and map split positioning on screen with an adjustable divider to optimise space for each
* Map rendering improvements: both faster and with fewer artefacts
* Improved map furniture: coordinates, scale bar, zoom and pan controls, etc.
* Zoom to selection with right mouse button
* Zoom in and out to cursor with mouse scroll button
* Ability to create locations and vector points with CTRL + left mouse click, remove from the end with CTRL + right mouse click
* Improved data charts for utilization and incremental files, autocorrelation & interlocation analyses with axis-scaling, and better labels & headings
* Ability to make map backgrounds paler to improve visibility of foreground material
* Faster file loading
* Huge file handling including large location files from GPS devices and large raster maps
* Importing locations in latitidue-longitude format
* Exporting to KML using lat-lng
* Location file merging; edge file sampling and merging
* Display locations and analysis maps on Google Maps
* Save maps and plots to image file
* Range overlap analysis map output

For new features added to each version of Ranges see: [[New Features|New Features]]

== Installing Ranges ==

Ranges can be installed and run without purchasing a licence. Until it is licensed it will run in demo mode.

To install Ranges:

1. Install the latest version of the Java Runtime Environment (JRE). To do this, download the version suitable for your operating system here:

https://java.com/en/download/manual.jsp

<div style="color: red; font-weight:bold;border: solid 0px grey; padding-left:0px;">Note that if you are using a 64 bit version of Windows, you must install the 64 bit version of Java.</div>

2. Install Ranges by downloading and running the version suitable for your operating system from:

http://www.anatrack.com/download_ranges.php

Uninstall Windows Ranges through the '''Control Panel...Programs''' and Mac Ranges by deleting the folder in Programs.

== Licensing Ranges ==

To unlock and use the analyses in Ranges, you must purchase a licence depending on whether the software is to be used by only you (Single User licence) or by a number of people in the same organisation (Site licence).

Single User licences allows Ranges to be installed on two computers, e.g. for use on one in a lab and another in the field, provided both computers are not to be used at the same time.

A Site licence allows Ranges to be installed on up to ten computers. If you need to install Ranges on more than ten computers, please [http://www.anatrack.com/contact.php contact us].

Licences can be purchased here:

http://www.anatrack.com/buy_ranges.php

after which we will supply a licence key.

Once you have a licence key and have installed Ranges, navigate to the Ranges folder in Anatrack Ltd in your applications folder. Click on the License Ranges shortcut and follow the instructions on screen. When prompted enter the licence number.

== Using Ranges ==

An overview of Ranges functionality with links to more detailed descriptions of analyses and features can be found here: [[Ranges Overview|Ranges Overview]]

If you are new to Ranges, please work through [[Tutorial|the tutorial]].

== Citing Ranges ==

Please use the following citation in publications:

Kenward, R.E., Casey, N.M., Walls, S.S. & South A.B. (2014) Ranges9 : For the analysis of tracking and location data. Online manual. Anatrack Ltd. Wareham, UK.

== Offline Support ==

If you will be using Ranges where you do not have access to the Internet, this support wiki can be downloaded to your computer:

http://www.anatrack.myzen.co.uk/Ranges9/Anatrack_Ranges9_Support.zip

To use it, unzip it to a suitable location keeping the folder structure in shape. The wiki pages are accessed through

<InstallationFolder>\Anatrack Ranges 9 Support\ranges_support.html

Anatrack Ranges User Guide

2015-04-29T07:08:07Z

Admin:

Ranges is a comprehensive system for viewing, editing and analysing spatial location data. The current version is Ranges 9.

== Introduction ==

The Ranges suite of software has been evolving since the early 1980s, not merely as a convenient way to analyse the extensive data that can be gathered from radio-tagged, and increasingly gps-tagged, animals, but also to assist planning that makes the effort of data-gathering as efficient as possible. Early versions were written for the BBC micro but Ranges now has Windows and Apple Macintosh interfaces to help you to set up and run analyses.

Ranges includes comprehesive tools to allow you to input, view and export your animal location data. Not only does it have a long list of location analyses for estimating home range outlines but also supports analyses of how these outlines overlap and the dynamic interaction of location records with those of other animals or of sites that are important for feeding or sociality. It allows you to investigate availability and use of habitat in different ways and more recently adds modelling techniques to its tool box.

== New Features ==

Ranges 9 includes

* Resource Area Dependence analysis
* Kaplan-Meier Survival analysis
* An up-to-date look with a more user-friendly interface but without loosing the familiar Ranges feel
* Better data and map split positioning on screen with an adjustable divider to optimise space for each
* Map rendering improvements: both faster and with fewer artefacts
* Improved map furniture: coordinates, scale bar, zoom and pan controls, etc.
* Zoom to selection with right mouse button
* Zoom in and out to cursor with mouse scroll button
* Ability to create locations and vector points with CTRL + left mouse click, remove from the end with CTRL + right mouse click
* Improved data charts for utilization and incremental files, autocorrelation & interlocation analyses with axis-scaling, and better labels & headings
* Ability to make map backgrounds paler to improve visibility of foreground material
* Faster file loading
* Huge file handling including large location files from GPS devices and large raster maps
* Importing locations in latitidue-longitude format
* Exporting to KML using lat-lng
* Location file merging; edge file sampling and merging
* Display locations and analysis maps on Google Maps
* Save maps and plots to image file
* Range overlap analysis map output

For new features added to each version of Ranges see: [[New Features|New Features]]

== Installing Ranges ==

Ranges can be installed and run without purchasing a licence. Until it is licensed it will run in demo mode.

To install Ranges:

1. Install the latest version of the Java Runtime Environment (JRE). To do this, download the version suitable for your operating system here:

: https://java.com/en/download/manual.jsp

<div style="color: red; font-weight:bold;border: solid 0px grey; padding-left:0px;">Note that if you are using a 64 bit version of Windows, you must install the 64 bit version of Java.</div>

2. Install Ranges by downloading and running the version suitable for your operating system from:

: http://www.anatrack.com/download_ranges.php

Uninstall Windows Ranges through the '''Control Panel...Programs''' and Mac Ranges by deleting the folder in Programs.

== Licensing Ranges ==

To unlock and use the analyses in Ranges, you must purchase a licence depending on whether the software is to be used by only you (Single User licence) or by a number of people in the same organisation (Site licence).

Single User licences allows Ranges to be installed on two computers, e.g. for use on one in a lab and another in the field, provided both computers are not to be used at the same time.

A Site licence allows Ranges to be installed on up to ten computers. If you need to install Ranges on more than ten computers, please [http://www.anatrack.com/contact.php contact us].

Licences can be purchased here:

: http://www.anatrack.com/buy_ranges.php

after which we will supply a licence key.

Once you have a licence key and have installed Ranges, navigate to the Ranges folder in Anatrack Ltd in your applications folder. Click on the License Ranges shortcut and follow the instructions on screen. When prompted enter the licence number.

== Using Ranges ==

An overview of Ranges functionality with links to more detailed descriptions of analyses and features can be found here: [[Ranges Overview|Ranges Overview]]

If you are new to Ranges, please work through [[Tutorial|the tutorial]].

== Citing Ranges ==

Please use the following citation in publications:

Kenward, R.E., Casey, N.M., Walls, S.S. & South A.B. (2014) Ranges9 : For the analysis of tracking and location data. Online manual. Anatrack Ltd. Wareham, UK.

== Offline Support ==

If you will be using Ranges where you do not have access to the Internet, this support wiki can be downloaded to your computer:

: http://www.anatrack.myzen.co.uk/Ranges9/Anatrack_Ranges9_Support.zip

To use it, unzip it to a suitable location keeping the folder structure in shape. The wiki pages are accessed through

: <InstallationFolder>\Anatrack Ranges 9 Support\ranges_support.html

Tutorial

2014-12-11T18:56:47Z

Admin: /* 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: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\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: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\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.

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Tutorial

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Admin: /* 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: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\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: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\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.

Tutorial

2014-12-11T18:53:32Z

Admin: /* 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: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: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.

Tutorial

2014-12-11T18:28:50Z

Admin: /* Clipping home ranges by a river outline */

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: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.

Tutorial

2014-12-11T18:28:27Z

Admin: /* Clipping home ranges by a river outline */

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: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.

Tutorial

2014-12-11T18:28:11Z

Admin: /* Fish analyses, midline and clipping */

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: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.

Tutorial

2014-12-11T18:27:37Z

Admin: /* Fish analyses, midline and clipping */

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: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.

Tutorial

2014-12-11T18:24:31Z

Admin: /* Fish analyses, midline and clipping */

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: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.

Tutorial

2014-12-11T18:23:47Z

Admin: /* Fish analyses, midline and clipping */

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: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.

Tutorial

2014-12-11T18:11:06Z

Admin: /* 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: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: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.

Tutorial

2014-12-11T18:10:07Z

Admin:

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|Press import and select ''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: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.

File:Location analysis7.png

2014-12-11T18:08:45Z

Admin:

2014-11-29T08:30:15Z

Admin:

# [[Main Page|Anatrack Ranges]]
## [[Main Page#Introduction|Introduction]]
## [[Main Page#New Features|New Features]]
## [[Main Page#Installing Ranges|Installing Ranges]]
## [[Main Page#Licensing Ranges|Licensing Ranges]]
## [[Main Page#Using Ranges|Using Ranges]]
## [[Main Page#Citing Ranges|Citing Ranges]]
# [[Ranges Overview|Ranges Overview]]
# [[Input & Graphics|Input & Graphics]]
## [[Input & Graphics#Introduction|Introduction]]
## [[Input & Graphics#Open|Open]]
## [[Input & Graphics#New|New]]
## [[Input & Graphics#Import|Import]]
## [[Input & Graphics#Modify|Modify]]
## [[Input & Graphics#Export|Export]]
## [[Input & Graphics#Save|Save]]
## [[Input & Graphics#Data Tables|Data Tables]]
## [[Input & Graphics#Map Display|Map Display]]
# [[Location Analysis|Location Analysis]]
## [[Location Analysis#Introduction|Introduction]]
## [[Location Analysis#Inter-location Measures|Inter-location Measures]]
## [[Location Analysis#Convex Polygons|Convex Polygons]]
## [[Location Analysis#Concave Polygons|Concave Polygons]]
## [[Location Analysis#Neighbour Linkage|Neighbour Linkage (OREP)]]
## [[Location Analysis#Ellipses|Ellipses]]
## [[Location Analysis#Harmonic Mean Contours|Harmonic Mean Contours]]
## [[Location Analysis#Kernel Contours|Kernel Contours]]
## [[Location Analysis#Midline Analyses (Interlocation, Linear Ranges and Clusters)|Midline Analyses]]
# [[Range Use Plots|Range Use Plots]]
## [[Range Use Plots#Introduction|Introduction]]
## [[Range Use Plots#Utilisation Plots|Utilisation Plots]]
## [[Range Use Plots#Incremental Area Analysis Plots|Incremental Area Analysis Plots]]
# [[Overlap Analysis|Overlap Analysis]]
## [[Overlap Analysis#Introduction|Introduction]]
## [[Overlap Analysis#Range Overlap|Range Overlap]]
## [[Overlap Analysis#Overlap Of Ranges On Locations|Overlap Of Ranges On Locations]]
# [[Interaction Analysis|Interaction Analysis]]
## [[Interaction Analysis#Introduction|Introduction]]
## [[Interaction Analysis#Autocorrelations|Autocorrelation Analysis]]
## [[Interaction Analysis#Dynamic interactions|Dynamic Interaction Analysis]]
## [[Interaction Analysis#Location-point distances|Location-point Distances]]
## [[Interaction Analysis#Range centre spacing|Range Centre Spacing]]
# [[Habitat Analysis|Habitat Analysis]]
## [[Habitat Analysis#Introduction|Introduction]]
## [[Habitat Analysis#Habitat content of a map|Habitat Content Of A Map]]
## [[Habitat Analysis#Habitat content of ranges |Habitat Content Of Ranges]]
## [[Habitat Analysis#Points within ranges|Points Within Ranges]]
## [[Habitat Analysis#Habitat at locations|Habitat At Locations]]
## [[Habitat Analysis#Habitat preference in ranges|Habitat Preference Within Ranges]]
## [[Habitat Analysis#Calculating areas|Calculating Areas]]
# [[Modelling Analysis|Modelling Analysis]]
## [[Modelling Analysis#Introduction|Introduction]]
## [[Modelling Analysis#Resource Area Dependence Analysis|Resource Area Dependence Analysis]]
## [[Modelling Analysis#Kaplan-Meier Survival|Kaplan-Meier Survival]]
# [[Selections|Selections]]
## [[Selections#Introduction|Introduction]]
## [[Selections#Selecting Ranges|Selecting Ranges]]
## [[Selections#Selecting Cores|Selecting Cores]]
## [[Selections#Selecting Locations|Selecting Locations]]
# [[Output Files|Output Files]]
## [[Output Files#Introduction|Introduction]]
## [[Output Files#Output filename codes for location analyses|Output Filename Codes]]
# [[Large Data And Java Memory|Large Data And Java Memory]]
# [[Tutorial|Tutorials]]
## [[Demo Tutorial|Demo Tutorial]]
## [[Tutorial|Full Tutorial]]
# [[Glossary|Glossary]]
# [[Bibliography|Bibliography]]

Modelling Analysis

2014-11-29T08:29:24Z

Admin:

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.

Large Data And Java Memory

2014-11-10T13:59:57Z

Admin:

Ranges can now handle huge files, the largest being raster files used to define habitats and to use as background maps.

64 bit operating systems can use essentially limitless amounts of computer memory (RAM). If you are running 64 bit Windows or Mac OS, you can run Ranges so that it also has access to the huge amounts of memory that your state-of-the-art computer has.

== The Ranges batch file ==

The Ranges large memory batch file (''ranges-largememory.bat'') in the Ranges installation folder can be tweaked to run Ranges with a large amount of memory depending the memory installed in your computer and your operating sysmte. Open this file in a plain text editor such as notepad to see the following:

<pre>
::ranges-largememory.bat : starts up java GUI with DOS command window
::adjust the -Xmx setting to run Ranges with more RAM if your computer has it
::
::e.g. to run Ranges with 4GB of memory use
::
::java -Xmx4096m -jar ranges.jar
::
::note that the maximum available to 32 bit Windows operating systems is about 1.4GB

java -Xmx1024m -jar ranges.jar

exit
</pre>

Following the instructions in the file, you can edit the java command line and increase the memory. Once you have edited and saved the file, run it to run Ranges with the increased memory.

Large Data And Java Memory

2014-11-10T13:59:15Z

Admin:

Ranges can now handle huge files, the largest being raster files used to define habitats and to use as background maps.

64 bit operating systems can use essentially limitless amounts of computer memory. If you are running 64 bit Windows or Mac OS, you can run Ranges so that it also has access to the huge amounts of memory (RAM) that your state-of-the-art computer has.

== The Ranges batch file ==

The Ranges large memory batch file (''ranges-largememory.bat'') in the Ranges installation folder can be tweaked to run Ranges with a large amount of memory depending the memory installed in your computer and your operating sysmte. Open this file in a plain text editor such as notepad to see the following:

<pre>
::ranges-largememory.bat : starts up java GUI with DOS command window
::adjust the -Xmx setting to run Ranges with more RAM if your computer has it
::
::e.g. to run Ranges with 4GB of memory use
::
::java -Xmx4096m -jar ranges.jar
::
::note that the maximum available to 32 bit Windows operating systems is about 1.4GB

java -Xmx1024m -jar ranges.jar

exit
</pre>

Following the instructions in the file, you can edit the java command line and increase the memory. Once you have edited and saved the file, run it to run Ranges with the increased memory.

Large Data And Java Memory

2014-11-10T13:55:03Z

Admin: Created page with "Ranges can now handle huge files, the largest being raster files used to define habitats and to use as background maps. 64 bit operating systems can use essentially limitless..."

Ranges can now handle huge files, the largest being raster files used to define habitats and to use as background maps.

64 bit operating systems can use essentially limitless amounts of computer memory. If you are running 64 bit Windows or Mac OS, you can run Ranges so that it also has access to the huge amounts of memory that your state-of-the-art computer has.

== The Ranges fatch file ==

The Ranges batch file (''<Ranges installation folder>\ranges.bat'') can be tweaked to run Ranges with any amount of memory less than that installed in you computer. Open this file in a plain text editor such as notepad to see the following:

<pre><code>

::ranges-largememory.bat : starts up java GUI with DOS command window
::adjust the -Xmx setting to run Ranges with more RAM if your computer has it
::
::e.g. to run Ranges with 4GB of memory use
::
::java -Xmx4096m -jar ranges.jar
::
::note that the maximum available to 32 bit Windows operating systems is about 1.4GB

java -Xmx1024m -jar ranges.jar

exit

</code></pre>

2014-11-10T13:27:39Z

Admin:

# [[Main Page|Anatrack Ranges]]
## [[Main Page#Introduction|Introduction]]
## [[Main Page#New Features|New Features]]
## [[Main Page#Installing Ranges|Installing Ranges]]
## [[Main Page#Licensing Ranges|Licensing Ranges]]
## [[Main Page#Using Ranges|Using Ranges]]
## [[Main Page#Citing Ranges|Citing Ranges]]
# [[Ranges Overview|Ranges Overview]]
# [[Input & Graphics|Input & Graphics]]
## [[Input & Graphics#Introduction|Introduction]]
## [[Input & Graphics#Open|Open]]
## [[Input & Graphics#New|New]]
## [[Input & Graphics#Import|Import]]
## [[Input & Graphics#Modify|Modify]]
## [[Input & Graphics#Export|Export]]
## [[Input & Graphics#Save|Save]]
## [[Input & Graphics#Data Tables|Data Tables]]
## [[Input & Graphics#Map Display|Map Display]]
# [[Location Analysis|Location Analysis]]
## [[Location Analysis#Introduction|Introduction]]
## [[Location Analysis#Inter-location Measures|Inter-location Measures]]
## [[Location Analysis#Convex Polygons|Convex Polygons]]
## [[Location Analysis#Concave Polygons|Concave Polygons]]
## [[Location Analysis#Neighbour Linkage|Neighbour Linkage (OREP)]]
## [[Location Analysis#Ellipses|Ellipses]]
## [[Location Analysis#Harmonic Mean Contours|Harmonic Mean Contours]]
## [[Location Analysis#Kernel Contours|Kernel Contours]]
## [[Location Analysis#Midline Analyses (Interlocation, Linear Ranges and Clusters)|Midline Analyses]]
# [[Range Use Plots|Range Use Plots]]
## [[Range Use Plots#Introduction|Introduction]]
## [[Range Use Plots#Utilisation Plots|Utilisation Plots]]
## [[Range Use Plots#Incremental Area Analysis Plots|Incremental Area Analysis Plots]]
# [[Overlap Analysis|Overlap Analysis]]
## [[Overlap Analysis#Introduction|Introduction]]
## [[Overlap Analysis#Range Overlap|Range Overlap]]
## [[Overlap Analysis#Overlap Of Ranges On Locations|Overlap Of Ranges On Locations]]
# [[Interaction Analysis|Interaction Analysis]]
## [[Interaction Analysis#Introduction|Introduction]]
## [[Interaction Analysis#Autocorrelations|Autocorrelation Analysis]]
## [[Interaction Analysis#Dynamic interactions|Dynamic Interaction Analysis]]
## [[Interaction Analysis#Location-point distances|Location-point Distances]]
## [[Interaction Analysis#Range centre spacing|Range Centre Spacing]]
# [[Habitat Analysis|Habitat Analysis]]
## [[Habitat Analysis#Introduction|Introduction]]
## [[Habitat Analysis#Habitat content of a map|Habitat Content Of A Map]]
## [[Habitat Analysis#Habitat content of ranges |Habitat Content Of Ranges]]
## [[Habitat Analysis#Points within ranges|Points Within Ranges]]
## [[Habitat Analysis#Habitat at locations|Habitat At Locations]]
## [[Habitat Analysis#Habitat preference in ranges|Habitat Preference Within Ranges]]
## [[Habitat Analysis#Calculating areas|Calculating Areas]]
# [[Modelling Analysis|Modelling Analysis]]
## [[Modelling Analysis#Introduction|Introduction]]
## [[Modelling Analysis#Resource Area Dependence|Resource Area Dependence]]
## [[Modelling Analysis#Kaplan Meier Survival|Kaplan Meier Survival]]
# [[Selections|Selections]]
## [[Selections#Introduction|Introduction]]
## [[Selections#Selecting Ranges|Selecting Ranges]]
## [[Selections#Selecting Cores|Selecting Cores]]
## [[Selections#Selecting Locations|Selecting Locations]]
# [[Output Files|Output Files]]
## [[Output Files#Introduction|Introduction]]
## [[Output Files#Output filename codes for location analyses|Output Filename Codes]]
# [[Large Data And Java Memory|Large Data And Java Memory]]
# [[Tutorial|Tutorials]]
## [[Demo Tutorial|Demo Tutorial]]
## [[Tutorial|Full Tutorial]]
# [[Glossary|Glossary]]
# [[Bibliography|Bibliography]]

Input & Graphics

2014-11-10T13:24:55Z

Admin: /* Location file from column text file */

== 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 [[Neighbour-linkage|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 Analaysis#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 (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 is editable. In the ranges table Age, Sex, the Month cells and Fate Codehave 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).

Anatrack Ranges User Guide

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Admin:

Ranges is a comprehensive system for viewing, editing and analysing spatial location data. The current version is Ranges 9.

== Introduction ==

The Ranges suite of software has been evolving since the early 1980s, not merely as a convenient way to analyse the extensive data that can be gathered from radio-tagged, and increasingly gps-tagged, animals, but also to assist planning that makes the effort of data-gathering as efficient as possible. Early versions were written for the BBC micro but Ranges now has Windows and Apple Macintosh interfaces to help you to set up and run analyses.

Ranges includes comprehesive tools to allow you to input, view and export your animal location data. Not only does it have a long list of location analyses for estimating home range outlines but also supports analyses of how these outlines overlap and the dynamic interaction of location records with those of other animals or of sites that are important for feeding or sociality. It allows you to investigate availability and use of habitat in different ways and more recently adds modelling techniques to its tool box.

== New Features ==

Ranges 9 includes

* Resource Area Dependence analysis
* Kaplan-Meier Survival analysis
* An up-to-date look with a more user-friendly interface but without loosing the familiar Ranges feel
* Better data and map split postioning on screen with an adjustable divider to optimise space for each
* Map rendering improvements: both faster and with less artifacts
* Improved map furniture: coordinates, scale bar, zoom and pan controls etc
* Zoom to selection with right mouse button
* Zoom in and out to cursor with mouse scroll button
* Ability to create locations and vector points with CTRL + left mouse click, remove from the end with CTRL + right mouse click
* Improved data charts for utilization and inc files, autocorrelation and interlocation analyses with scaling axes and better labels and headings
* Ability to make map backgrounds paler to make foreground show up better.
* Faster file loading
* Huge file handling including large location files from GPS devices and large raster maps
* Importing locations in latitidue-longitude format
* Exporting to KML using lat-lng
* Location file merging; edge file sampling and merging
* Display locations and analysis maps on Google Maps
* Save maps and plots to image file
* Range overlap analysis map output

For new features added to each version of Ranges see: [[New Features|New Features]]

== Installing Ranges ==

Ranges can be installed and run without purchasing a licence. Until it is licensed it will run in demo mode.

To install Ranges:

1. Install the latest version of the Java Runtime Environment (JRE). To do this, download the version suitable for your operating system here:

: https://java.com/en/download/manual.jsp

<div style="color: red; font-weight:bold;border: solid 0px grey; padding-left:0px;">Note that if you are using a 64 bit version of Windows, you must install the 64 bit version of Java.</div>

2. Install Ranges by downloading and running the version suitable for your operating system from:

: http://www.anatrack.com/download_ranges.php

Uninstall Windows Ranges through the '''Control Panel...Programs''' and Mac Ranges by deleting the folder in Programs.

== Licensing Ranges ==

To unlock and use the analyses in Ranges, you must purchase a licence depending on whether the software is to be used by only you (Single User licence) or by a team (Site licence).

Single User licences allows Ranges to be installed on two computers, e.g. for use in a lab and in the field, provided both computers are not to be used at the same time.

A Site licence allows Ranges to be installed on up to ten computers. If you need to install Ranges on more than ten computers, please [http://www.anatrack.com/contact.php contact us].

Licences can be purchased here:

http://www.anatrack.com/buy_ranges.php

where we will supply a licence key.

Once you have a licence key and have installed Ranges, navigate to the Ranges folder in Anatrack Ltd in your applications folder. Click on the License Ranges shortcut and follow the instructions on screen. When prompted enter the licence number.

== Using Ranges ==

An overview of Ranges functionality with links to more detailed descriptions of analyses and features can be found here: [[Ranges Overview|Ranges Overview]]

If you are new to Ranges, please work through [[Tutorial|the tutorial]].

== Citing Ranges ==

Please use the following citation in publications:

Kenward RE Walls SS South AB & Casey N, (2008) Ranges8 : For the analysis of tracking and location data. Online manual. Anatrack Ltd. Wareham, UK.

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Anatrack Ranges User Guide

Privacy Policy

2014-11-10T12:18:28Z

Admin: Created page with "This privacy policy sets out how Anatrack uses and protects any information that you give Anatrack when you use this website. Anatrack is committed to ensuring that your priv..."

This privacy policy sets out how Anatrack uses and protects any information that you give Anatrack when you use this website.

Anatrack is committed to ensuring that your privacy is protected. Should we ask you to provide certain information by which you can be identified when using this website, then you can be assured that it will only be used in accordance with this privacy statement.

Anatrack may change this policy from time to time by updating this page. You should check this page from time to time to ensure that you are happy with any changes. This policy is effective from 27 September 2010.

== What we collect ==

We may collect the following information:

* name and job title
* contact information including email address
* demographic information such as postcode, preferences and interests
*other information relevant to customer surveys and/or offers

== What we do with the information we gather ==

We require this information to understand your needs and provide you with a better service, and in particular for the following reasons:

* Internal record keeping.
* We may use the information to improve our products and services.
* We may periodically send promotional emails about new products, special offers or other information which we think you may find interesting using the email address which you have provided.
* From time to time, we may also use your information to contact you for market research purposes. We may contact you by email, phone, fax or mail. We may use the information to customise the website according to your interests.

== Security ==

We are committed to ensuring that your information is secure. In order to prevent unauthorised access or disclosure, we have put in place suitable physical, electronic and managerial procedures to safeguard and secure the information we collect online.

== How we use cookies ==

A cookie is a small file which asks permission to be placed on your computer's hard drive. Once you agree, the file is added and the cookie helps analyse web traffic or lets you know when you visit a particular site. Cookies allow web applications to respond to you as an individual. The web application can tailor its operations to your needs, likes and dislikes by gathering and remembering information about your preferences.

We use traffic log cookies to identify which pages are being used. This helps us analyse data about webpage traffic and improve our website in order to tailor it to customer needs. We only use this information for statistical analysis purposes and then the data is removed from the system.

Overall, cookies help us provide you with a better website by enabling us to monitor which pages you find useful and which you do not. A cookie in no way gives us access to your computer or any information about you, other than the data you choose to share with us.

You can choose to accept or decline cookies. Most web browsers automatically accept cookies, but you can usually modify your browser setting to decline cookies if you prefer. This may prevent you from taking full advantage of the website.

== Links to other websites ==

Our website may contain links to other websites of interest. However, once you have used these links to leave our site, you should note that we do not have any control over that other website. Therefore, we cannot be responsible for the protection and privacy of any information which you provide whilst visiting such sites and such sites are not governed by this privacy statement. You should exercise caution and look at the privacy statement applicable to the website in question.

== Controlling your personal information ==

You may choose to restrict the collection or use of your personal information in the following ways:

* whenever you are asked to fill in a form on the website, look for the box that you can click to indicate that you do not want the information to be used by anybody for direct marketing purposes
* if you have previously agreed to us using your personal information for direct marketing purposes, you may change your mind at any time by writing to or emailing us at info@anatrack.com or using our contact form

We will not sell, distribute or lease your personal information to third parties unless we have your permission or are required by law to do so. We may use your personal information to send you promotional information about third parties which we think you may find interesting if you tell us that you wish this to happen.

You may request details of personal information which we hold about you under the Data Protection Act 1998. A small fee will be payable. If you would like a copy of the information held on you please write to Anatrack Ltd, 52 Furzebrook Road, Wareham, BH20 5AX, Dorset,United Kingdom.

If you believe that any information we are holding on you is incorrect or incomplete, please write to or email us as soon as possible at the above address. We will promptly correct any information found to be incorrect.

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Modelling Analysis

2014-11-10T11:58:44Z

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== Introduction ==

== Resource area dependency analysis ==

== Kaplan Meier survival ==

Modelling Analysis

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Admin: /* Resource area dependency analyis */

== Introduction ==

== Resource area dependency analsyis ==

== Kaplan Meier Survival ==

Modelling Analysis

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Admin: Created page with "== Introduction == == Resource area dependency analyis == == Kaplan Meier Survival =="

== Introduction ==

== Resource area dependency analyis ==

== Kaplan Meier Survival ==

2014-11-10T11:56:15Z

Admin:

# [[Main Page|Anatrack Ranges]]
## [[Main Page#Introduction|Introduction]]
## [[Main Page#New Features|New Features]]
## [[Main Page#Installing Ranges|Installing Ranges]]
## [[Main Page#Licensing Ranges|Licensing Ranges]]
## [[Main Page#Using Ranges|Using Ranges]]
## [[Main Page#Citing Ranges|Citing Ranges]]
# [[Ranges Overview|Ranges Overview]]
# [[Input & Graphics|Input & Graphics]]
## [[Input & Graphics#Introduction|Introduction]]
## [[Input & Graphics#Open|Open]]
## [[Input & Graphics#New|New]]
## [[Input & Graphics#Import|Import]]
## [[Input & Graphics#Modify|Modify]]
## [[Input & Graphics#Export|Export]]
## [[Input & Graphics#Save|Save]]
## [[Input & Graphics#Data Tables|Data Tables]]
## [[Input & Graphics#Map Display|Map Display]]
# [[Location Analysis|Location Analysis]]
## [[Location Analysis#Introduction|Introduction]]
## [[Location Analysis#Inter-location Measures|Inter-location Measures]]
## [[Location Analysis#Convex Polygons|Convex Polygons]]
## [[Location Analysis#Concave Polygons|Concave Polygons]]
## [[Location Analysis#Neighbour Linkage|Neighbour Linkage (OREP)]]
## [[Location Analysis#Ellipses|Ellipses]]
## [[Location Analysis#Harmonic Mean Contours|Harmonic Mean Contours]]
## [[Location Analysis#Kernel Contours|Kernel Contours]]
## [[Location Analysis#Midline Analyses (Interlocation, Linear Ranges and Clusters)|Midline Analyses]]
# [[Range Use Plots|Range Use Plots]]
## [[Range Use Plots#Introduction|Introduction]]
## [[Range Use Plots#Utilisation Plots|Utilisation Plots]]
## [[Range Use Plots#Incremental Area Analysis Plots|Incremental Area Analysis Plots]]
# [[Overlap Analysis|Overlap Analysis]]
## [[Overlap Analysis#Introduction|Introduction]]
## [[Overlap Analysis#Range Overlap|Range Overlap]]
## [[Overlap Analysis#Overlap Of Ranges On Locations|Overlap Of Ranges On Locations]]
# [[Interaction Analysis|Interaction Analysis]]
## [[Interaction Analysis#Introduction|Introduction]]
## [[Interaction Analysis#Autocorrelations|Autocorrelation Analysis]]
## [[Interaction Analysis#Dynamic interactions|Dynamic Interaction Analysis]]
## [[Interaction Analysis#Location-point distances|Location-point Distances]]
## [[Interaction Analysis#Range centre spacing|Range Centre Spacing]]
# [[Habitat Analysis|Habitat Analysis]]
## [[Habitat Analysis#Introduction|Introduction]]
## [[Habitat Analysis#Habitat content of a map|Habitat Content Of A Map]]
## [[Habitat Analysis#Habitat content of ranges |Habitat Content Of Ranges]]
## [[Habitat Analysis#Points within ranges|Points Within Ranges]]
## [[Habitat Analysis#Habitat at locations|Habitat At Locations]]
## [[Habitat Analysis#Habitat preference in ranges|Habitat Preference Within Ranges]]
## [[Habitat Analysis#Calculating areas|Calculating Areas]]
# [[Modelling Analysis|Modelling Analysis]]
## [[Modelling Analysis#Introduction|Introduction]]
## [[Modelling Analysis#Resource Area Dependence|Resource Area Dependence]]
## [[Modelling Analysis#Kaplan Meier Survival|Kaplan Meier Survival]]
# [[Selections|Selections]]
## [[Selections#Introduction|Introduction]]
## [[Selections#Selecting Ranges|Selecting Ranges]]
## [[Selections#Selecting Cores|Selecting Cores]]
## [[Selections#Selecting Locations|Selecting Locations]]
# [[Output Files|Output Files]]
## [[Output Files#Introduction|Introduction]]
## [[Output Files#Output filename codes for location analyses|Output Filename Codes]]
# [[Tutorial|Tutorials]]
## [[Demo Tutorial|Demo Tutorial]]
## [[Tutorial|Full Tutorial]]
# [[Glossary|Glossary]]
# [[Bibliography|Bibliography]]

Kernel Contours

2014-11-10T11:53:51Z

Admin:

The pros & cons of different analysis techniques are discussed in detail in the [[Review Of Home Range Analyses|Review Of Home Range Analyses]] and for a more comprehensive recent review, see "A Manual for Wildlife Radio Tagging" (Kenward 2001) and Kenward et al. 2001.

== Introduction ==

Kernels and [[Harmonic Mean Contours|Harmonic means]] are both contour analyses which estimate density indices for locations at intersections of a matrix set across an animals range, and then interpolate contours between the values of that matrix.

([[Bibliography|Worton (1989)]] noted that the Harmonic Mean estimator was one of a family of Kernel estimators and that the bivariate normal estimator (among others) could handle d=0 without special treatment. The bivariate normal kernel used by ([[Bibliography|Worton (1989)]] uses a negative exponential function of location distance from estimation points for estimating location density indices. As exp(0)=1, this function has no problem handling locations that coincide with estimation points. However, the function is also inherently more smoothing than Harmonic Mean contours. This makes it more appropriate than Harmonic Mean approaches for obtaining stable estimates of range size with small samples of locations, but less precise for estimating cores to be used in analyses of habitat content and sociality, especially when there are distant outliers.

Smoothing of kernel analyses involves estimation of a smoothing parameter (h), sometimes called the reference bandwidth or window width (([[Bibliography|Seaman & Powell 1996]]). ([[Bibliography|Worton (1989)]] pointed out that his reference h might overestimate range areas by over-smoothing the distribution when ranges are strongly multimodal. He suggested the use of a fractional multiplier of h, and proposed estimating this smoothing factor by Least Squares Cross Validation (LSCV) of the mean integrated square error. See below for an explanation of how you can alter the [[#Smoothing|smoothing parameter]].

As for Harmonic Mean estimation, the contours can be based solely on the mean and variance of the density index distribution across locations, which is most appropriate for range size estimates, or fitted to selected proportions of the locations, which may better define cores for subsequent analyses of sociality and habitat. The matrix size can be varied from its default of 40x40, or frozen to prevent re-scaling. [[#Matrix size|Matrix size]] does not influence the kernel estimates greatly. However, the expansive nature of outermost kernel contours can result after re-scaling in ranges covering only 50% of the matrix, so selection of matrices larger than the default 40x40 may help to obtain smooth contours across multimodal distributions.

The majority of options for kernel contours are exactly the same as those for [[Harmonic Mean Contours|harmonic mean contours]] except [[#Kernel type|Kernel type]] and [[#Smoothing|Smoothing]] which replaces whether to centre locations between matrix intersections.

== Locations Kc and statistics ==

The density index can be estimated at each location. This enables estimation of statistics for the density distribution, and also provides values for interpolating contours either to the locations or based on location density alone. The Locations, Kc & statistics option runs more quickly than other options in contour analyses because the routine does not have to calculate a matrix of location density values.

The statistics produced can give a useful insight into the structure of the range based on the distribution of the locations. A range statistics output file can be specified in the [[Output Files|'''Output Files''']]. The statistics include range spread and the density score at the central fix, with the dispersion, skewness and kurtosis of the density distribution ([[Bibliography|Spencer & Barrett 1984]]).

== Selected cores ==

This option allows you to examine range structure and to define core areas. By excluding low density areas the edges enclose areas most used by the animal. See the introduction to [[Location Analysis|Location Analyses]] for more details.

You can choose one or more values for the percentage of locations or of location density to be included. Type them in ascending order, separated by either spaces or commas.

The display shows coordinates of the Kc (Kernel centre) and its distance from the focal site.

In the [[Output Files|'''Output Files''']] column you can specify a range areas and statistics output files. The estimates are in column format, suitable for spreadsheets. Each row has the 7 range variables, followed by X,Y coordinates for the range centre, followed by 5 range statistics followed by as many areas as there were core percentages. The statistics include the Kc coordinates, and the spread, dispersion, skew and kurtosis of the location distribution ([[Bibliography|Spencer & Barrett 1984]]).

== Cores at 5% intervals ==

This option provides plots which help to decide which locations are part of a core, and which are outliers.

You can choose to save both edge (polygon) and utilisation files the latter can be plotted in [[Input & Graphics|the main window]]. Density analyses such as this save edges from 20-99% (because 100% of the distribution cannot be estimated). The cores are saved at 5% intervals, a total of 17 sets.

The analysis produces a results screen which shows a map of the range edges, a table showing the area and % of total area of each % edge, and a graph of utilisation distribution.

Core ranges

Graphs of utilisation distribution can be used to assess (by eye) whether a sharp discontinuity in area, after the elimination of outlying locations, indicates a core range. Better estimation may be possible if the utilisation file is saved and plotted in [[Input & Graphics|the main window]].

== Incremental area analysis ==

Incremental area analysis is used to answer the question "how many locations do I need to estimate a home range?" Starting with the first three locations (the minimum needed to estimate a polygon area without a boundary strip), the new area is estimated as each location is added. This permits the consecutive areas, which tend to increase initially as the animal is observed using different parts of its range, to be plotted against number of locations until there is evidence of stability, which indicates that adding further locations will not improve the home range estimate. The default is to plot the edge round all the locations that have been added, but it is also possible to choose a single, smaller core. The results are saved to a ''.inc'' file which can be examined using opened in [[Input & Graphics|the main window]].

== Kernel Type ==

When [[Bibliography|Worton (1989)]] proposed the use of the bivariate normal kernel estimator, he noted that the smoothing parameter (h) can be adjusted in several ways. One approach is to vary h locally across the matrix, by weighting initial values to produce an "adaptive kernel".

==== Fixed kernels ====

These use the reference smoothing parameter (bandwidth), which is the standard deviation of x and y coordinates divided by the sixth root of the sample size.

==== Tail weighting, ‘adaptive’ ====

[[Bibliography|Worton (1989)]] suggested weighting by the inverse of the initial density index, to emphasise the tail of the distribution. Subsequent reviews show this to overestimate range sizes ([[Bibliography|Worton 1995]], [[Bibliography|Seaman & Powell 1996]]).

==== Core weighting ====

An alternative is to core-weight the estimates, which tends to de-emphasise the tail of the density distribution. However, it is probably best to base estimates on the default, fixed value.

== Contours ==

==== Contours based on location density alone (default) ====

In this option, contour plots are based solely on the mean and variance for the distribution of density indices across the locations. The contours estimate the probability of including a particular proportion of locations and may include more or less than the proportion of locations actually recorded. As in ellipse analyses, the outermost contour is estimated to include 99% of the location distribution, because the location density at 100% would be infinitely small. This classic approach is most appropriate for estimating stable range sizes, typically to include 95% of the density distribution, for which reason it is the default in Ranges 6.

==== Contours fitted to locations ====

When contours are fitted to locations, the density index values at locations are ranked. Contours are then plotted to just include a given percentage of the locations. This approach is most analogous to the polygon approach. For example, it puts the 100% contour through the outermost location. There tend also to be irregular gaps between contours fitted to locations, which simplify detection of a core by inspection of utilisation plots and may define cores best for analyses of sociality and habitat content.

== Smoothing multiplier, hRef and LSCV ==

==== hRef ====

The reference smoothing parameter (hRef) is the standard deviation of rescaled x and y coordinates divided by the sixth root of the number of locations.

==== Fixed multiplier ====

As the reference smoothing parameter tends to overestimate range areas, it can be multiplied by a fractional value ([[Bibliography|Worton 1989]]), in which case the contour areas from bivariate normal kernels tend to approach those of Harmonic Mean contours. Ranges allows multipliers between 0.1 (which often produces tight contours round locations) and 2.0 (which smooths contours highly).

==== LSCV (Least Squares Cross Validation) ====

LSCV provides an objective way to find a multiple of hRef. There are a number of potential ways of implementing LSCV. In Ranges, the routine starts with a multiplier of 1.51 and works downwards in steps of 0.02 to 0.09. The default implementation [LSCV Inflection] stops if it reaches an inflection, at which a decreasing downward slope either becomes an upward slope (indicating a local minimum) or increases again in a downward direction (indicating that a local minimum would have been likely with a much smaller step size than 0.02). [Ranges also supports LSCV Local minimum (in which case inflections other than true minima are ignored) and LSCV Global minimum (in which case the minimum that gives tightest smoothing is used). These options are denoted by LSCVI, LSCVL and LSCVG respectively.]

If no minimum or inflexion is found, the reference value (*1) is used. Thus, a multiplier of 1 is an indication that the routine has failed ( the start and interval value used for the local minimum search means that it can find an optimal multiplier of 0.99 or 1.01 but not 1 itself ).

If you have chosen to use least squares cross validation the message "OPTIMISING THE SMOOTHING CONSTANT" appears while the programme is running and the value of the multiplier is displayed.

LSCV can be applied on a range-by-range basis, but that makes the size of individual ranges dependent not only on the area covered by the locations but also on how they are distributed within that area ([[Bibliography|Kenward 2001]]). An alternative approach is to use all values that are not 1 (the reference value) to estimate a median fraction for the multiplier, and then apply that multiple of hRef to all the ranges. The value of this multiple should be stated when describing the analysis. To do this first run an LSCV analysis with a single selected core, and ‘Output stats and areas file’ selected, the multipliers will be in the ''xhRef'' column, then repeat the analysis selecting [[#Fixed multiplier|Fixed Multiplier] and entering the median value you have calculated.

LSCV tends not to work well with fewer than 30 locations or for data with large resolution relative to range size ([[Bibliography|Seaman et al. 1999]]). If a minimum is found only for very few ranges in a set, it may be better to use the reference value (hRef * 1), or to adopt a value that another study has found to be appropriate for the species.

== Matrix size ==

==== Matrix, set no. of cells ====

Contouring is most detailed when there are small distances between intersections of the estimation matrix. The default in Ranges is a 40x40 matrix, because this gives rapid runs, little change in definition for larger matrices and comparability with RangesV. However, Ranges lacks the memory constraints of previous versions and matrix size can be increased up to 200.

==== Matrix, set size of cells ====

This new option allows the size of matrix cells, rather than the number, to be set by the user. This allows you to retain the same plotting resolution for home ranges of very different size (perhaps predator and prey), but may result in somewhat coarse plots for the smaller home range. If you set the size of cells such that the resulting matrix would be greater than the maximum of 200 cells, cell size will be set to create a 200 cell matrix and the warning ‘Matrix interval enlarged’ will be displayed at the end of the run. The size of the matrix cells is displayed in the ‘interval’ column in the statistics output file.

== Matrix rescaling ==

Contours tend to extend beyond the outermost locations, especially when based on location density alone. To plot such contours, the matrix is set to extend beyond the locations. In Ranges, the default is to set the locations to span the central 70% of the matrix. If an initial estimation of density at grid edges indicates that the outermost contour will still extend beyond the matrix, the proportion of the matrix spanned is decreased automatically in steps of 5% until a fit is likely. Re-scaling of the matrix is prevented by selecting the Freeze matrix option. This option is not available if ‘Matrix, set size of cells’ is selected.

Differences that have been noted in contour estimates between different software packages ([[Bibliography|Larkin & Halkin 1994]]) are likely to depend partly on aspects of the matrix, such as whether the quoted size includes or excludes a "contour-completion" boundary. For comparability between packages, estimation conditions must be set carefully. For example, if you want a 25x25 grid across the locations in Ranges, where the proportion of matrix spanning the locations is by default 70%, you should select a 36x36 grid and freeze it.

Clusters

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The pros & cons of different analysis techniques are discussed in detail in the [[Review Of Home Range Analyses|Review Of Home Range Analyses]] and for a more comprehensive review, see "A Manual for Wildlife Radio Tagging" (Kenward 2001) and Kenward et al. 2001.

== Neighbour-linkage methods ==

Peripheral convex polygons were the earliest approach to range analysis. However, their size is strongly influenced by outlying locations and can include large areas not visited by animals. One way of addressing this was to use outlines based on density of locations, first as ellipses and then as contours. However, these too are outlier-sensitive and their parametric smoothing is prone to expand into unvisited areas. Another approach was to attribute a grid cell, with dimensions based on tracking accuracy, to locations at each point. However, this approach underestimated the areas visited unless either there were very large numbers of locations available, or "joining rules" were used to link grid cells. Joining rules that link neighbouring locations can estimate polygons that define visited areas with great accuracy, estimating range cores as polygons to which isolated grid cells at outlying locations contribute little area.

An early neighbour-linkage method involved restricting polygon edges plotted between locations to a fraction (initially half) of the span of maximum distance between any locations, which gave "concave" polygons. However, the span remains strongly influenced by outliers and the fraction was an aribitrary decision. A subsequent method defined clusters of locations, by minimising sums of nearest neighbour distances as locations with longer distances are added. The analysis starts the first cluster by identifying the two locations that are closest together and have the nearest 3rd location (i.e. the minimal sum of linkage distances). It then finds the location nearest to one in this initial cluster. If this is less than the distance to the 3rd location in any other potential cluster, the 4th location joins the original cluster. If not, a new cluster forms. If two clusters have nearest neighbours at equal distances, the location that joins is the one that minimises the distance to all locations in the cluster (i.e. a centroid rule resolves ties). If the nearest neighbour is already assigned to another cluster, the two clusters join. When the required percentage of locations has been assigned, a polygon (which was initially convex but can also be concave) is drawn around each cluster and their areas summed (Kenward 1987).

Four additions to the original Cluster Polygon implementation are available in Ranges: Objective cores, concave polygons, alternative joining rules and the ability to construct a single inclusive polygon.

On the results screens, statistics include the number of range nuclei for each % polygon. Outliers tend to have a stronger effect on areas than in other analyses, which makes utilisation plots very suitable for identifying range cores by inspection. Inspection and objective coring typically indicate that up to 15% of locations are used for excursive activity, so that 85% polygons often provide convenient cluster core boundaries. Core clusters often remain separate at this point, whereas separation distances that are less than outlier distances cause fusion when all the locations are included.

These are ''.csv'' files with column headers that can be double-clicked to open in Microsoft Excel or imported to an alternative spreadsheet.

== Selected cores ==

This option allows you to examine range structure and to define core areas. By excluding outlying locations the edges enclose areas most used by the animal. See the introduction to Location Analyses for more details.

You can choose one or more values for the percentage of locations or of location density to be included. Type them in ascending order, separated by either spaces or commas.

In the '''Output Files''' column you can specify a range areas and statistics output file. The estimates are in column format, suitable for spreadsheets. Each row has the 7 range variables, followed by X,Y coordinates for the range centre, followed by 5 range statistics followed by as many areas as there were core percentages. Structure statistics include, after the area estimate, the number of nuclei in a core, its partial area (the sum of areas of separate polygons / the area of a single polygon round all the clusters). Simpson’s Index for diversity of number of locations across clusters and Simpson’s Index for diversity of area across clusters. This is a .csv file with column headers that can be double-clicked to open in Microsoft Excel or imported to an alternative spreadsheet.

== Cores at 5% intervals ==

This option provides plots which help to decide which locations are part of a core, and which are outliers. You can choose to save both edge (polygon) and utilisation files. The cores are saved at 5% intervals, from 20-100, a total of 17 sets.

Utilisation files can be plotted in Input & Graphics.

== Objective cores ==

Rather than choosing a particular core size, it is more scientifically rigorous to have an objective core calculated from the distribution of the locations. The distribution of nearest-neighbour distances can be used to detect and exclusion of outlying locations (Kenward et al. 2001) resulting in an objective core. The ways in which outliers are excluded are discussed below. Objective coring sometimes estimates core areas larger than those from an equivalent number of locations in the standard analysis. This is because the standard approach estimates polygons as soon as a required percentage of polygons are included, whereas objective coring continues to merge clusters that are separated by less than the exclusion distance. In these cases, inclusive polygons give the same result for both methods.

== Incremental area analysis ==

Incremental area analysis is used to answer the question "how many locations do I need to estimate a home range?" Starting with the first three locations (the minimum needed to estimate a polygon area without a boundary strip), the new area is estimated as each location is added. This permits the consecutive areas, which tend to increase initially as the animal is observed using different parts of its range, to be plotted against number of locations until there is evidence of stability, which indicates that adding further locations will not improve the home range estimate. The default is to plot the edge round all the locations that have been added, but it is also possible to choose a single, smaller core. The consecutive area estimates have to be saved to an output file, so that the result can be examined using Input & Graphics.

== Convex or concave cluster polygons ==

Concave polygons are now offered as well as convex polygons. The edge restriction of concave polygons can be based on a fraction of the span of each cluster or have the edge-restriction fraction adapted to each individual cluster, ranging from 0.2 (i.e. strongly restricted) for a cluster of all the locations to 1 (i.e. convex) for small clusters. The concave polygon option can be set when animals use strips of non-linear habitat, and prevents the (very rare) overlap of a small cluster within the limits of a larger, curved cluster.

== Outlier exclusion ==

If objective cores are selected, exclusion can be of locations in the largest 5% of the nearest-neighbour distance distribution (by analogy with plotting contours or ellipses to 95% of the density distribution), which is the Ranges default. Alternatively, an iterative process excludes the location with the most extreme linkage distance if it is beyond 1%, 0.5% or 0.1% of the distribution estimated by the remainder, and repeats this process until all distances are within the chosen alpha-level on a normal distribution. The 0.1% alpha level excludes only the most extreme outliers. The display shows the Outlier Exclusion Distance (OED) beyond which locations are excluded. In cluster analyses, polygons then plot round clusters with no nearest-neighbour locations beyond this distance. For objective-restricted edges, the exclusion distance has a strip added equivalent to the resolution distances between locations.

== Objective-restricted-edge polygons ==

Although incremental cluster analysis conveniently defines groups of core locations separated from outliers, plotting outlines round clusters can be problematic. Convex polygons around separate clusters occasionally overlap (e.g. if a small cluster occurs within the horns of a crescent-shaped cluster) and simple concave solutions to that overlap problem use arbitrary or subjective edge distances. A better solution uses outlier exclusion distances to define Objective-Restricted-Edge Polygons.

OREPs are equivalent to polygons in cluster analysis when a core of locations is defined by an exclusion distance (OED) when outliers are excluded. However, instead of first identifying clusters of locations with the minimal sum of nearest-neighbour distances (which is slow to compute for many locations), OREPs are plotted immediately as concave polygons with an edge restriction based on the OED. OREPs have three advantages over clustering, namely (i) simplicity (hence speed), (ii) polygons cannot overlap and (iii) habitat at all locations is included (because a single grid cell is attributed to outliers beyond the OED).

Polygon edge distances can be based either on the distribution of Nearest-Neighbour Exclusion Distances (NNED), as used for objective coring in cluster analysis, or on the distribution of mean distances from each location to all others as estimated in kernel analyses. The Kernel Exclusion Distance (KED) is our default, because it (a) gives more normal distributions than nearest neighbour distances, (b) gives smoother outlines than NNED especially for small samples and (c) is analogous to exclusion of outlier locations to prevent their excessive influence on contours (reference).

Range cores defined by OREPs are equivalent both to cluster analysis with objective coring (Kenward et al. 2001), but without risk of polygon overlap, and also to the concave hulls derived from neighbour distances (Getz & Wilmers 2004), but with an objective choice of the edge-restriction distance. With kernel-based outlier exclusion distances, OREPs unify range analyses based on grid-cell, polygon and location density techniques.

== Joining priority ==

The third addition offers the centroid rule, of joining locations to clusters when all linkage distances are minimal, as a priority over the nearest-neighbour rule, which is then used only as a tie-breaker. Centroid priority suppresses chaining along linear habitats and is thus less appropriate than the nearest-neighbour priority for species (probably most species) that minimise their travel distances.

== Separate cluster polygons or Single inclusive polygon ==

The fourth addition is the option of plotting a single polygon round all the clusters. This excludes locations that are outliers to the main core but includes those between the clusters and which probably represent times when animals were detected on transition between clusters rather than making true excursions. This single polygon, called a "usual area" by Johnstone (1994), may provide a better estimate of a core territory.

Convex Polygons

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Convex Polygons

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Inter-location Measures

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This allows you to calculate simple measures between locations or groups of locations. You need to load a location file, choose a measure, select between which locations you want that to be calculated and then press the ‘Run location analysis’ button. The analysis will run – producing a summary of its progress and output the results to a file. What happens after the run is finished depends on the options you have selected.

If you select [[#FirstToLast|first to last]] or a [[#LocationInterval|location interval]] other than 1 then the output file will be displayed in the Statistics window.

For other options, after running the analysis a plot for the first range will appear in a separate window, and the user interface will switch to Input & Graphics and display the location file with an extra column added containing the newly calculated attribute. To show later ranges in the plot, select them in the Ranges table. The currently selected location in the Locations table is displayed in red in the plot. Running subsequent analyses on the same file will result in multiple plot windows which can be viewed at the same time. This helps to discover how and when a juvenile disperses or an animal migrates, whether the distance moved is constant all day etc.

==Headings==

Results are given as headings in 360 degrees, [[#Between Which Locations|between a user-defined number of locations]].

==Distances==

Results are given in metres either between locations, or from a focal site (e.g. a nest) to the location. When [[#FocalSiteToLocation|focal site to location]] is selected for distances the [[Dispersal Detection|dispersal detection]] option is enabled.

==Times==

Note that this option is only enabled if your input file has [[File Types#Location Qualifying Variables|location qualifying variables]] defining times for each location (these must have labels containing combinations of YY, MO, DD, HH, MI, SS). Results are given in minutes.

==Speeds==

Note that this option is only enabled if your input file has [[File Types#Location Qualifying Variables|location qualifying variables]] defining times for each location (these must have labels containing combinations of YY, MO, DD, HH, MI, SS). Results are given in metres per hour.

==Between Which Locations==

span first to last

Calculate the chosen metric between the first and last location of each range. The value calculated is the sum of the result between each consecutive location in the range (with the exception of headings, which just calculates the heading between the first and last locations).

location interval

Allows you to input the location interval between which the metric is calculated. Entering 1 will result in calculations being made between all locations. For values greater than 1 the result will be the sum of the calculation between each consecutive location, e.g. if locations were taken at hourly intervals, a location interval of 24 could be used to estimate the daily distance moved.

focal site to location

Calculate the chosen metric between the focal site and each location. This option is not offered for times and speeds because the focal site doesn’t have an associated time value.

When focal site to location is selected for distances the [[Dispersal Detection|Dispersal detection]] option is enabled.

==Dispersal Detection==

This option is only available when distances and focal site to location are selected, and when your input file has [[File Types#Location Qualifying Variables|location qualifying variables]] defining times for each location (these must have labels containing combinations of YY, MO, DD, HH, MI, SS). This latter requirement is because the question you are asking is "when did dispersal occur?".

In this options two attribute columns will be added to the loc file, the first contains the distance from the site to the location, and the second whether the individual is classed as having dispersed yet (0=no, 1=yes). This enables easy splitting of files into before and after dispersal using [[Input & Graphics#Modify|modify]], or estimation of home range areas before and after dispersal by using the [[Selections|Make Selections]] button in Location Analysis.

Minimum dispersal distance (m)

Set minimum distance to recognise dispersal. It is important to set a value such as 10 m for birds with initial locations in a nest, to prevent premature triggering when they leave the nest. Alternatively, if you would not classify a bird within 1000 m of the nest as a disperser, set this distance (see [[Bibliography|Walls & Kenward 1995, 1998]]).

Alpha for dispersal detection

none

Dispersal is classified as having occurred when the distance from the focal site is exceeded.

1%, 5% or 10%

The stochastic dispersal detection starts with the first 3 locations, and estimates their arithmetic mean centre (Ac), and their confidence limit for distance from the Ac, using the relevant probability level. It then estimates the arithmetic mean for the next n locations in the data set, where n is usually 3 (but see below), and defines the "dispersal" vector (i.e. average direction of dispersal) between these. Dispersal is recognised if the orthogonal distances of the n locations along this vector are all outside the confidence limit for the first N (i.e. 3). If not, N increments by 1, and the process repeats through the set of locations.

The use of a dispersal vector means that dispersal will not be recognised erroneously if an animal makes consecutive excursions in different directions. However, dispersal may be recognised late if the animal makes an initial movement in one direction, and then departs in another direction. The estimation is only rigorous with N+n locations where n > 3. Missing values in the dataset (recorded as -9, -9), are assumed to represent occasions when the animal was sought but not found, and was outside the confidence limit for the current N. Dispersal is, therefore, recognised with a minimum of 4 (3+1) locations if coordinates for the last location are -9, -9. It is advisable to set a minimum distance as well as a probability level. This will prevent premature detection of dispersal (e.g. when a bird leaves a nest after several records there, instead of leaving the natal area).

After running Dispersal detection, the screen will display a distance/time plot with a vertical red line just after the appropriate location.

==Add Stats To Loc File==

If you select the Add stats to loc file option in '''Output Files''' the new location file with the added attribute column will be saved with a new name. This enables the attribute to be used as a [[File Types#Location Qualifying Variables|location qualifying variables]] in subsequent analyses.

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# [[Main Page|Anatrack Ranges]]
## [[Main Page#Introduction|Introduction]]
## [[Main Page#New Features|New Features]]
## [[Main Page#Installing Ranges|Installing Ranges]]
## [[Main Page#Licensing Ranges|Licensing Ranges]]
## [[Main Page#Using Ranges|Using Ranges]]
## [[Main Page#Citing Ranges|Citing Ranges]]
# [[Ranges Overview|Ranges Overview]]
# [[Input & Graphics|Input & Graphics]]
## [[Input & Graphics#Introduction|Introduction]]
## [[Input & Graphics#Open|Open]]
## [[Input & Graphics#New|New]]
## [[Input & Graphics#Import|Import]]
## [[Input & Graphics#Modify|Modify]]
## [[Input & Graphics#Export|Export]]
## [[Input & Graphics#Save|Save]]
## [[Input & Graphics#Data Tables|Data Tables]]
## [[Input & Graphics#Map Display|Map Display]]
# [[Location Analysis|Location Analysis]]
## [[Location Analysis#Introduction|Introduction]]
## [[Location Analysis#Inter-location Measures|Inter-location Measures]]
## [[Location Analysis#Convex Polygons|Convex Polygons]]
## [[Location Analysis#Concave Polygons|Concave Polygons]]
## [[Location Analysis#Neighbour Linkage|Neighbour Linkage (OREP)]]
## [[Location Analysis#Ellipses|Ellipses]]
## [[Location Analysis#Harmonic Mean Contours|Harmonic Mean Contours]]
## [[Location Analysis#Kernel Contours|Kernel Contours]]
## [[Location Analysis#Midline Analyses (Interlocation, Linear Ranges and Clusters)|Midline Analyses]]
# [[Range Use Plots|Range Use Plots]]
## [[Range Use Plots#Introduction|Introduction]]
## [[Range Use Plots#Utilisation Plots|Utilisation Plots]]
## [[Range Use Plots#Incremental Area Analysis Plots|Incremental Area Analysis Plots]]
# [[Overlap Analysis|Overlap Analysis]]
## [[Overlap Analysis#Introduction|Introduction]]
## [[Overlap Analysis#Range Overlap|Range Overlap]]
## [[Overlap Analysis#Overlap Of Ranges On Locations|Overlap Of Ranges On Locations]]
# [[Interaction Analysis|Interaction Analysis]]
## [[Interaction Analysis#Introduction|Introduction]]
## [[Interaction Analysis#Autocorrelations|Autocorrelation Analysis]]
## [[Interaction Analysis#Dynamic interactions|Dynamic Interaction Analysis]]
## [[Interaction Analysis#Location-point distances|Location-point Distances]]
## [[Interaction Analysis#Range centre spacing|Range Centre Spacing]]
# [[Habitat Analysis|Habitat Analysis]]
## [[Habitat Analysis#Introduction|Introduction]]
## [[Habitat Analysis#Habitat content of a map|Habitat Content Of A Map]]
## [[Habitat Analysis#Habitat content of ranges |Habitat Content Of Ranges]]
## [[Habitat Analysis#Points within ranges|Points Within Ranges]]
## [[Habitat Analysis#Habitat at locations|Habitat At Locations]]
## [[Habitat Analysis#Habitat preference in ranges|Habitat Preference Within Ranges]]
## [[Habitat Analysis#Calculating areas|Calculating Areas]]
# [[Modelling Analysis|Modelling Analysis]]
## [[Modelling Analysis#Introduction|Introduction]]
## [[Modelling Analysis#Resource Area Dependence|Resource Area Dependence]]
## [[Modelling Analysis#Kaplan Meier Survival|Kaplan Meier Survival]]
# [[Selections|Selections]]
## [[Selections#Introduction|Introduction]]
## [[Selections#Selecting Ranges|Selecting Ranges]]
## [[Selections#Selecting Cores|Selecting Cores]]
## [[Selections#Selecting Locations|Selecting Locations]]
# [[Output Files|Output Files]]
## [[Output Files#Introduction|Introduction]]
## [[Output Files#Output filename codes for location analyses|Output Filename Codes]]
# [[Tutorial|Tutorials]]
## [[Demo Tutorial|Demo Tutorial]]
## [[Tutorial|Full Tutorial]]
# [[Glossary|Glossary]]
# [[Index|Index]]
# [[Bibliography|Bibliography]]

File Types

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== Introduction ==

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. Locations files (''.loc''), vector files (''.vep'', ''.vel'', & ''.ves'' , for point, line and shape maps), edge files (''.edg'', of range outlines), utilisation files (''.uti''), incremental files (''.inc'') and survival files (''.srv'') are mainly to be used as inputs for other Ranges analyses. They can also be viewed in a spreadsheet, but the data are arranged to save space rather than for ease of interpretation. Outputs from modelling analyses, RADA files (''.rda'') and Kaplan Meier Graph files (''.kms'') have no map data and are only useful for displaying output data and plots within Ranges. Ranges also outputs files for use in other software, e.g. ‘.csv’ files that can be used spreadsheets (simply double click on them to open in Excel), and ESRI shapefiles that can be opened in ArcView or ArcGIS.

== Location Files ==

Location files (''.loc'') are the main starting point for analyses. They contain the point location data and associated attribute information. Locations are stored in a series of ranges, which may represent an individual, a social group or a particular time period. Location files can be [[Input & Graphics#New|created]] from scratch, or [[Input & Graphics#Import|imported]]. To ensure that Ranges is suitable for tracking all animals (from ants to elephants), each file must include information about the [[#Tracking Resolution|tracking resolution]], [[#Scale|scale]] and whether a focal site (e.g. nest, den etc.) should be included in the range.

=== Location coordinates ===

The locations themselves must be recorded in a flat projection, such as UTM ( or for Britain the OS National Grid ). Ranges can convert to UTM from latitude-longitude during the [[Input & Graphics#Import|import procedure and an Excel spreadsheet for doing this is available cheaply from [[http://www.dmap.co.uk/ll2tm.htm|http://www.dmap.co.uk/ll2tm.htm]]. GPS receivers usually have the option to output coordinates in UTM rather than Lat/Long.

Location coordinates can be decimals, but they cannot be negative. If you have locations with negative coordinates you will need to first transform your data by adding a number to the Eastings and or Northings such that all of the coordinates become positive. (The added number will have to be greater than or equal to the magnitude of the most negative easting or northing). This can be accomplished in a spreadsheet such as Excel.

=== File attribute variables ===

==== Tracking Resolution ====

The resolution depends on the accuracy of your tracking. Accuracy is sometimes cited as the standard deviation of locations obtained in a trail. Greater comparability with other statistical selection criteria would be to use the 95% confidence distance. For tracking with a 2-3 element Yagi, a 1-in-10 rule is acceptable: if you make triangulations at up to 10m from a small animal, the tracking resolution is 1m, or 10m at 100m. For Yagi antennas with more elements, a 1-in-20 rule can apply, i.e. a resolution of 100m for triangulations at up to 2km from an animal. The resolution with GPS may vary from 10-50m depending on terrain and other conditions. For ARGOS satellite tracking it may be closer to 1 km and depend on location class. Tracking resolution is used to:

# Set the width of the boundary strip that is included in polygon edges and areas. The boundary strip is half the value of the resolution e.g. 0.5m if the resolution is 1m. This means that a coordinate with a real position between 10.5 and 11.5, can be entered as 11. If you wish to suppress the boundary strip you can set the tracking resolution to 0. This is useful if you need analysis results comparable with a system lacking boundary strip estimation.
# Estimate the size of a grid cell plotted around single outlying locations in concave polygon analyses, and multiple locations at one site in cluster analyses. The width of the grid cell is equal to the resolution.
# To define the truncation distance in one type of harmonic mean contouring. In this case, the allocation of an inappropriate resolution can substantially affect range areas and statistics.

==== Scale ====

Scale is the number of metres represented by each coordinate unit. A scale of 10m means that each coordinate unit (e.g. 8,8) is 10m from the next (e.g. 8,9). Scaling greater than 1 allows you to type in data with fewer digits. For example, you can use a scale of 100m and type 213 instead of 21300.

Warning! The scale parameter must match the scale parameter in any [[#Scale of coordinate units|vector]] or [[#Raster Files|raster]] maps with which you wish to compare your data.

The scale parameter does not influence the map display in Input & Graphics (which uses the untransformed coordinate values), so a location file may appear to overlay a vector map file, but if they have different scale parameters they may not overlay in, for example, habitat analysis.

If a file is [[Input & Graphics#Export|exported]] to an ArcView shapefile the coordinates are multiplied by scale to convert them to metres. If a file is exported to a text file the coordinates are not multiplied by the scale parameter and the scale parameter will have to be re-entered if the text file is re-imported into Ranges.

==== Include Nest/Focal Site In Locations ====

If you choose yes, the focal site for each range will be included as a location in later analyses.

==== Coordinate System Datum Ellipsoid ====

If your data is in UTM (Universal Transverse Mercator) coordinates, it can be converted to latitude-longitude coordinates for display on Google Maps or for export to KML. The '''Coordinate System Datum Ellipsoid''', the ellipsoid used to model the shape of the Earth, must be set to achieve this. Most UTM systems use WGS84.

==== UTM Latitude Zone and UTM Longitude Zone ====

These must be set to convert UTM coordinates to latitude-longitude.

==== Range attribute variables ====

A file may contain thousands of ranges from different individuals, or from the same individual during different tracking sessions, and these must be easily identified. Saving multiple ranges in the same file can make analyses much easier as you only need to run once per file. It is easy to [[Selections|select the ranges]] you wish to look at during the analysis (e.g. Only the males). You can define how you want to identify the ranges, but the defaults are ID number, Age, Sex, Month and Year. These are explained below:

All seven Range attribute variables are stored as numeric values (for sorting purposes). The first five variables (ID, Age, Sex, Month and Year) must be integers, whilst the focal site coordinates can be decimals. The Age and Sex variables can be given one letter labels to identify animals on the screen.

The default Range attribute variable labels are as follows:

{| class="wikitable"
| style="width: 200px;" |Age || 1=J, 2=Y, 3=A (for Juvenile, Yearling, Adult)
|-
| Sex || 1=M, 2=F (for Male, Female)
|}

There are default values for each range variable, newly created ranges will start with these values.

{| class="wikitable"
| style="width:200px;" | ID || sequence number, which increments by one for each consecutive range
|-
|AGE || ? (coded as 0)
|-
|SEX || ? (coded as 0)
|-
|MONTH || (missing, coded as -9)
|-
|YEAR || (missing, coded as -9)
|-
|FOCAL SITE COORD E || (missing, coded as -9)
|-
|FOCAL SITE COORD N || (missing, coded as -9)
|}

A typical label might be displayed as AF21 6/01 for Adult Female 21 tracked from (or during) June 2001. Missing variables appear on results screens as ''?''. If you only define IDs, the same label would be ??21 ?/?.

ID should be unique for each range ( e.g. you shouldn’t have a male and female both with ID 21). By using import and export and changing the ID you can [[Import Locations|subdivide your data]] in different ways, e.g. to look at range changes over time.

==== Location qualifying variables (LQVs) ====

It is often helpful to know what an animal is doing or what habitat an animal is in at each location, or when the location was recorded, or even a score of how accurate the location was. This is achieved by using Location Qualifying Variables, of which there can be up to 50. It is easy to [[Selections|select the locations]] you wish to look at during the analysis (e.g. excluding locations when the animal is sleeping).

==== Time LQVs ====

Labels for times must be capital letters, in combinations of 2, 4 or 6 letters of the following : YY, MO, DD, HH, MI, SS. e.g. YYDD, HHMI, YYMODD, DDMOYY. There is a limit of 6 characters in the time LQVs so that 010417 is OK for April 17 2001, but 20010417 is not. A useful tip. If time variables are entered as "combinations" in descending order, (eg. YYMODD or HHMI), you can use these in '''Make Selections''' to select runs of locations that cross period boundaries. Using single labels, it is difficult to select locations between 15 December 1994 and 1 February 1995 while excluding locations between 1-14 December 1994 and those in January 1994. However, combination labels make it easy to select locations between 941215 and 950201.

==== Accuracy ellipse LQVs ====

LQVs can also be used to represent accuracy ellipses in which case the labels must be defined by capitals as MARAD, MIRAD, THETA or X-VAR, Y-VAR, COVAR, which represent either the maximum radius, minimum radius and inclination of an ellipse or the variance and covariance of its distribution (see the output statistics from location analysis, ellipses for more details).

Labels for other LQVs can be upper or lower case and should ideally have 5 letters (e.g. ACTIV) for them to show best in displays. Please note that although LQV labels and their range of values are listed to help make selections during analyses, you still need to record (outside of Ranges) the numerical codes of these 5-letter labels (eg. ACTIV, 1=resting, 2=feeding, 3=preening).

== Vector Files ==

Vector files (''.vep'', ''.vel'', ''.ves'') can contain either point, line or shape information and are used for mapping habitats. Coordinates are stored in groups, each group representing a single shape, line or point group. Each group is assigned to a category which has an associated label and colour. Groups may have the same No. and ID, this is useful for the representation of holes and secondary polygons within shapes. A [[#Scale of coordinate units|scale]] parameter defines the m per coord unit.

Vector file attributes can be set in the vector properties window, which is displayed when '''new...vector''' or ‘modify’ is pressed from the [[Input & Graphics|main panel]]. Vector files can be [[Import Vectors|imported]] as text files with columns containing point coordinates or from ArcView shapefiles.

Vector files can be used in the following ways in Ranges:

# Background maps in location analyses: Point, line or shape files can be used as [[Input & Graphics#Background maps|backgrounds]] for location analyses in which case they are plotted in grey. Grey is used for maps in this option to avoid confusion with the several colouring options for range edges.
# In Habitat analyses: Vector shapes and points are also used in colour in habitat analyses.
# In Interaction analyses: Shapes can be used to define sampling areas in interaction analyses. Points can be used to see, for example, how close a bird goes to nest sites or feeding areas, allowing objective assessments of association or avoidance.
# In Location Analyses: Vector line files formatted as midline files can be used in [[Location Analysis#Midline Analyses (Interlocation, Linear Ranges and Clusters)|midline analyses]] to define potential routes between locations (e.g. for fish in rivers).

==== On-screen digitising to create Vector files ====

Use '''new''' to create an empty vector file.Points can be [[Input & Graphics#On-screen digitising|digitised]] by holding down the CTRL key and clicking the left mouse button, perhaps following an image background.

==== Vector file type - points, lines or shapes ====

Points files have no connections between coordinates. In lines files, lines are drawn between the coordinates within each line. In shapes files, coordinates in the same shape are connected by lines and the resultant shape is filled with colour.

Coordinates for shapes must be entered in a clockwise sequence, without lines that cross and must finish by repeating the first set of coordinates.

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.

Vector shapefiles including holes can be [[Input & Graphics#On-screen digitising|digitised]] and the coordinates copied to the following shape to fill in the hole.

==== Scale of coordinate units ====

The scale specifies the number of metres that each coordinate unit represents. For example if the scale is 1, a location at 1,1 will be 5m from a location at 1,5, with a scale of 10 this distance would be 50m.

==== Coordinate System Datum Ellipsoid ====

If your data is in UTM (Universal Transverse Mercator) coordinates, it can be converted to latitude-longitude coordinates for display on Google Maps or for export to KML. The '''Coordinate System Datum Ellipsoid''', the ellipsoid used to model the shape of the Earth, must be set to achieve this. Most UTM systems use WGS84.

==== UTM Latitude Zone and UTM Longitude Zone ====

These must be set to convert UTM coordinates to latitude-longitude.

==== Vector categories ====

The '''add category''' button can be used to add new categories. Within the table the category label can be edited by double clicking in its cell. Category labels can be words or numbers. If the labels are numbers (e.g. density values), they can be decimals of any length. If you use numbers, for example to denote density of food in particular areas, [[Habitat Analysis#Habitat content of ranges|Habitat content of ranges]] will produce an average value from the proportion of the different areas in each range.

Colour can be edited by a single click within the cell that will bring up a colour chooser. You will be forced to choose another colour if the colour chosen is too close to that of an existing category.

There is a limit of 50 vector categories within Ranges.

For ArcView shapefiles that have > 50 categories, in ArcView you can create two or more maps with a subset of the categories with the following procedure:

# Select the theme containing the whole map
# Theme, Query, category < 50th category
# Theme, Start editing
# Edit, Delete features
# Theme, Save edits as, new filename
# Repeat the above, changing the query in step 2) to >= 50th category

The maps can then be imported separately into Ranges.

== Raster Files ==

Raster files (''.rst'') are files that store information, usually habitat, as a grid of cells, each containing a single map value. They are generally used for land cover information, particularly when it is derived from remotely sensed data from satellites or aerial photography. The size of each raster cell is defined and cannot be altered, which means that cells are displayed and analysed as large squares relative to fine-scaled range polygons, whereas vector maps retain angular shapes at any scale. However, analyses that use raster maps are faster than shapes over large areas. Moreover, makers of mapping systems tend not to export vectors in a convenient format for other packages, but will export raster files. Be careful to choose a raster cell size that provides adequate detail for analysis but remember that large raster maps are memory-hungry.

Ranges stores raster data as a byte array with a text appendix (these files are not text files and so cannot be viewed using a text editor). Although Ranges currently only handles 15 raster categories during analysis, maps with many more categories can be used. Categories can be easily combined, e.g. Orchard could be combined with deciduous woodland, and most analyses end up being based on less than 10 combinations. It is also simple to set categories to be unclassified, so that one set of 15 types are used for a run, and another set for a repeat run.

Raster files can be created from scratch or imported from gridascii files. The byte format in Ranges is typically about a third the size of the equivalent gridascii file, and therefore requires less memory.

Older versions of Ranges used to limit the area of a raster file you could view at a time. With increased computer memory this is no longer necessary however if you open a raster file with more than 10 million cells, the cell values table will not be displayed.

If you have problems loading large rasters, it is likely that you are running Ranges in a Java Runtime Environment (JRE) with limited memory. It is straight forward to [[Large Memory Ranges|increase the memory reserved for Ranges]].

Further instructions on setting up raster files can be found here: [[Raster File Setup|Raster File Setup]].

== Edge Files ==

Edge files (''.edg'') store the coordinates of home-range shapes generated in [[Location Analysis|location analyses]].

They can store multiple ranges (which may represent different individuals or different tracking sessions), and for each range can store multiple [[Convex Polygons#Selected cores|cores]] representing different levels of use.

Edge files can be viewed and exported from the [[Input & Graphics|main window]], but edge shapes cannot be edited there. When opened in Input & Graphics (as either the primary file or a background map), if you hold the mouse pointer over the filename a description of the analysis used to create the analysis will be displayed.

Edge files are the principal input for [[Overlap Analysis|Overlap analyses]].

== Utilisation Files ==

Utilisation files (''.uti'') are created in location analysis and contain the areas of range cores at 5% intervals (e.g. for [[Convex Polygons#Cores at 5%|convex polygons]]). [[Input & Graphics#Utilisation plots|Utilisation plots]] can be viewed and printed from Input & Graphics, by selecting the '''open...Utilisation files''' option.

== Incremental Files ==

Incremental files (''.inc'') are created in location analysis 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#Incremental area|clusters]]). Incremental plots can be viewed and printed from Input & Graphics, by selecting the '''open...Incremental file''' option.

== Statistics Files ==

Many analyses have an option within [[Run Specifications|Run Specifications]] for outputting a statistics file. They are in CSV (comma-separated variable) format and are stored with the ''.csv'' extension. They have column headers and can be opened in the Ranges Statistics window, double-clicked to open in Microsoft Excel or imported to an alternative spreadsheet.

== Esri Shapefiles ==

Esri shapefiles can be [[Input & Graphics#Export|exported]] from Input & Graphics, and can be opened in ArcView, ArcGIS and other GIS packages. The ESRI shapefiles produced each consist of a minimum three files with the same root, ''.shp'', ''.shx'' and ''.dbf'', all three files are needed for it to be opened in another package. Shapefiles can also be imported into Ranges from Input & Graphics.

== Image Files ==

Image files (''.ima'') can be used as [[Input & Graphics#Background maps|backgrounds]]. They are created from standard image files, JPEG, PNG, GIF or bitmap, by importing into Ranges and aligning with a coordinate system.

== RADA Files ==

RADA files (''.rda'') are the output of RADA analyses and contain habitat core data for the RADA plots. They cannot be edited.

== Survival Files ==

Survival files (''.srv'') contain animal survival data and are used as the input to Kaplan Meier Survival analyses. Survival files have no location data, and therefore no map, but a number of extra range attribute variables in order to make survival analysis possible. These are Start Day, Start Month and Start Year, End Day, End Month and End Year, and Fate Code, the fate of the animal on the end date, which can be ? (Unknown), Lost, Lived or Died.

== Kaplan Meier Survival Graph Files ==

Kaplan Meier Survival Graph files (''.kms'') are the output of Kaplan Meier analyses and contain data for the Kaplan Meier plots. They cannot be edited.

File Types

2014-11-10T11:45:11Z

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