Introduction

On this page we pull together links and advice for obtaining and installing the software used in other parts of the site and in our various courses and workshops.

The versions here are for MS Windows® or MS Vista®. See the sites for information on versions for other platforms.

All the software on this page is available without payment. In some cases, users are asked to give brief details of themselves or their intended uses for the software; this information helps the developers to justify their funding and ensure further improvements.

Original downloads from these sites should be free of viruses, but it is always good to scan them yourself with an up-to-date virus-checker before running them. It is also advisable to set a Windows restore point (go to Start > Programs > Accessories > System Tools > System Restore) before installation.

If you don't have the necessary permissions to install software on your computer and need help from your system administrator, check the notes next to the padlock icons below.

It is good practice to cite the software you use in any paper or report, and recommended citations are given.

DISTANCE

Performs analysis of distance sampling data: line transects, point transects and trapping webs. Also has facilities for the design of surveys.

Download: Go to the DISTANCE website at the University of St. Andrews (UK):

http://www.ruwpa.st-and.ac.uk/distance/distance60download.html

Fill in the registration form and download the installer for the latest version of the software.

Current version: DISTANCE 6.0 release 2 in ‘d60setup.exe’ (as at 20 March 2010).

Installation note: DISTANCE requires MS Windows Script 5.6 or later and you have the option to install the English language version of this as part of the program setup. If Windows Script is already installed on your computer, or you wish to install a non-English version, then you should click "No" when the Distance setup program asks if you want to install its version.

Documentation:

• DISTANCE has a good help facility which includes a 'User's Manual' in PDF format. Example files are included with the distribution.
• The Help menu also includes links to the DISTANCE home page and a DISTANCE-SAMPLING forum.
• For detailed information, refer to "Introduction to Distance Sampling" (Buckland et al, 2001) and "Advanced Distance Sampling" (Buckland et al, 2004).

Citation: Thomas, L., Laake, J.L., Strindberg, S., Marques, F.F.C., Buckland, S.T., Borchers, D.L., Anderson, D.R., Burnham, K.P., Hedley, S.L., Pollard, J.H., Bishop, J.R.B. and Marques, T.A. 2006. Distance 6.0. Release 2. Research Unit for Wildlife Population Assessment, University of St. Andrews, UK. http://www.ruwpa.st-and.ac.uk/distance/ (Check the release number in Help > About Distance... and use the one for your installation: results may differ slightly between releases.)

Examples on this site: Analysis of line transect observations of orangutan nests.

EstimateS

Analysis of data on species assemblages, producing (a) estimates of species richness, accumulation curves, and rarefaction information, and (b) indices of similarity between species assemblages.

Download: Go to the EstimateS web site:

http://purl.oclc.org/EstimateS

and fill in the registration form. Then download the installer for the latest version of the software.

When you first open EstimateS, a file navigation window may pop up asking you to select a "Data File": choose the file called Statistics.4DD, or click on New then Save to create a new file.

Current version: EstimateS 8.2.0 in ‘SetupEstimateS820Win.exe’ (as at 20 March 2010).

Documentation: The Users' Guide is available online here (there is also a link from a button on the Help > About... screen in EstimateS).

Citation: Colwell, R. K. 2006. EstimateS: Statistical estimation of species richness and shared species from samples. Version 8. Persistent URL <purl.oclc.org/estimates>

Examples on this site: (Awaiting revision!)

MARK

Carries out a wide range of different kinds of analyses related to capture-recapture designs.

Download: The best place to download the latest version of MARK is:

www.phidot.org/software/mark/download/

This page also has a facility to allow you to check the date of the current version of the installer, which is generally a few days after the dates of the main files as shown in Help > About... in MARK. As at 14 August 2010 the current version was MARK 6.0, with the 'mark.exe' file dated 24 July 2010 and 'mark_int.exe' dated 13 July 2010.

During installation you may get an error message saying "Unable to register component C:\WINDOWS\system32\Graphdtc.ocx". Just click OK, as MARK seems to work fine without this.

MARK's input files are text files (which can be created and edited in Notepad) but must have the ".inp" extension - and ".inp.txt" won't work either! The user therefore needs to be able to change the file extension.

Documentation:

• MARK has a very thorough Help facility, but it is rather technical.
• An excellent tutorial on MARK and the statistical concepts underlying the analysis is Cooch & White (2008), freely available online here.
• There is a forum devoted to MARK and related packages here.
• More information is available in the book edited by Amstrup et al (2005)

Citation: White, G.C. and K. P. Burnham. 1999. Program MARK: Survival estimation from populations of marked animals. Bird Study 46 Supplement, 120-138.

Examples on this site: simulation using cards; analysis of tiger data from Kanha.

OpenBUGS and WinBUGS

Performs Bayesian analysis of complex models using Markov chain Monte Carlo (MCMC) methods. BUGS stands for "Bayesian analysis Using Gibbs Sampler", the Gibbs Sampler algorithm being a component of the MCMC method.

Two versions of BUGS are available, WinBUGS from the Medical Research Council in the UK and OpenBUGS from the University of Helsinki in Finland.

The currently maintained version is OpenBUGS. Recent releases come as a Windows installer, and you do not need additional patches or keys. Several changes have been made in OpenBUGS - in particular, selection of updaters - and I have come across models which failed to converge in WinBUGS but worked fine in OpenBUGS; these included models in Link & Barker (2010). So I recommend switching to OpenBUGS. On the other hand, there are models which work in WinBUGS but not in OpenBUGS, so don't bin WinBUGS yet!

WinBUGS is the older and better-known program, but it will no longer be updated. Books such as Gelman & Hill (2007), Bolker (2008) and Royle & Dorazio (2008) all provide code designed for WinBUGS, which will work in OpenBUGS with minor modifications. Details of the differences are here.

OpenBUGS

Download : Go to the OpenBUGS site:

http://www.openbugs.info/w/

In the navigation bar on the left of the home page, go to Downloads. Download and run the setup file for Windows.

The native format for OpenBUGS documents is .ODC. In Windows this is used for "Office Data Connection" files, so you'll probably want to change this: right-click on an OpenBUGS .odc file (eg. Abbey.odc, an example file in Program Files\OpenBUGS\Examples) and select Open With. If "OpenBUGS" appears in the next window, select that, otherwise click on Choose Program... You may have to use the Browse... button to navigate to OpenBUGS.exe on your hard disk. Make sure you check the box labelled "Always use the selected program to open this kind of file" and press OK.

Current version: 3.1.1 (as at 14 Aug 2010).

Documentation: The OpenBUGS User Manual is available on the Manuals menu or by pressing F1. Click on the blue arrows next to each main heading to see subheadings.

Citation: Andrew Thomas, Bob O Hara, Uwe Ligges, and Sibylle Sturtz. 2006. Making BUGS Open. R News 6:12-17 (available online at http://www.rni.helsinki.fi/~boh/publications/Rnews2006-1.pdf)

WinBUGS

Download and installation: Go to the WinBUGS page at the MRC Biostatistics Unit, Cambridge:

http://www.mrc-bsu.cam.ac.uk/bugs/winbugs/contents.shtml

Scroll down to the "Quick Start" heading and download and install the various bits: for full functionality, you will need to download and install WinBUGS14.exe and the patch to upgrade to v. 1.4.3 and the key.

If you are using Windows Vista, be sure to read the note in the section "Installing WinBUGS 1.4 in Windows".

Installing the patch and the key require read/write access to Program Files.

Current version: 1.4.3 (as at 20 March 2010).

Documentation: WinBUGS comes with a User Manual (press F1 or select Help > WinBUGS User Manual) which includes a tutorial, and 2 volumes of examples.

Citation: Lunn, D.J., Thomas, A., Best, N., and Spiegelhalter, D. (2000) WinBUGS - a Bayesian modelling framework: concepts, structure, and extensibility. Statistics and Computing, 10:325-337.

Examples on this site: Estimating occupancy of golden cats in Peninsular Malaysia.

PRESENCE

Analyses 'presence/absence' data, estimating and correcting for detection probability.

Download: Go to the PRESENCE page at the USGS Patuxent Wildlife Research Center (USA):

http://www.mbr-pwrc.usgs.gov/software/presence.html

and download one of the versions of the file 'setup_presence.zip', which contains the installation file, 'setup_presence.exe'.

Current versions: as at 14 Aug 2010, version 3.0 was available as a beta test version (latest build 100713). The main difference is the way in which output files are stored: the results for each model are in separate .out files, which you can open in Notepad or other text editor.

If you experience problems with v.3.0 beta, you can download v.2.4.

The Tools menu in PRESENCE has an option 'Check website for new version'.

Documentation:

• The Help facility has a single-page overview plus several useful tutorials based on examples in MacKenzie et al (2006); the data sets for the tutorials are included with the distribution.
• The PRESENCE page has a link to a PDF file with "Worked Examples and Exercises in PRESENCE".
• For detailed background information refer to MacKenzie et al (2006).

Citation: Hines, J. E. (2006). PRESENCE2 - Software to estimate patch occupancy and related parameters. USGS-PWRC. http://www.mbr-pwrc.gov/software/presence.html

Examples on this site: Golden cats in Peninsular Malaysia.

R statistical software

A powerful statistical calculator and programming language, with a huge capacity for customized analysis methods. The 'base distribution' itself has a wide range of functions, and there are numerous add-in packages. You can also readily write your own functions in R.

Download: Go to the R website:

http://www.r-project.org

follow the link to “CRAN”, then select the nearest mirror site (if you are in Malaysia, use one of the sites in Singapore or Thailand). In the box titled "Download and Install R" click on 'Windows', then click on the link to 'base'. This leads to the page for the current release, with the link to the installer in the box at the top of the page. Right-click on this link and select 'Save Target As...'

The page has links to other versions of R, but these have not been comprehensively checked for bugs. The installers have '...pat-win32.exe', '...dev-win32.exe' or '...rc-win32.exe' in the file names. These are not what you want: use the latest official release unless you are already an experienced R user.

Add-in packages can be downloaded and installed from within R: use Packages > Install package(s)... The CRAN website has a link to a list of available packages (look for 'Packages' in the navigation bar on the left). Package descriptions there are cryptic; the "CRAN Task Views" pages group packages by subject with more information on each.

There are some issues with installing R and R packages under Vista and Windows 7: see details on CRAN.

Current version: 2.11.1 (dated 31 May 2010) and the setup file is called “R-2.11.1-win32.exe”. New minor versions (ie. 2.x.0) are released twice a year, in April and October. If bugs are found, patched versions (eg. 2.x.1) may be released at any time.

Updating R: By default, the new version is installed in a new folder; you may then no longer be able to access the contributed packages which you downloaded previously if they were installed in the old version's folder. You can download them all again, but that's tedious. It's easier to install the new version in the same folder as the old version, perhaps first changing the folder name to remove the version number (eg. from "R-2.6.0" to "Rsoftware"). After installation you should open R and select Packages > Update packages... to ensure that your packages are compatible with the new version of R. If you customized the Rprofile.site file, note that this is overwritten by the installation, so you will want to restore this.

Those packages which you have already installed can easily be updated within R with the Packages > Update packages... menu option. It is worth running this from time to time.

Documentation:

• R's own help system and PDF manuals provide thorough descriptions of the functions available. This is good if you know which function you are looking for, but not much use otherwise. (R has a Help > Search help... facility, but again it helps if you know what you are looking for.)
• A growing number of books have been written about R or the use of R in various areas of statistics; a list is here. I found Dalgaard (2002) to be a good starting point and use Venables & Ripley (2002) as a reference.
• There are several R-related discussion groups. A comprehensive search facility is here.

Citation: R Development Core Team (2005). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.

Examples on this site: Randomization tests; Interactive exploration of statistical concepts; Calculation of biodiversity indices.