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 22 Nov 2009).

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 orang utan 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 22 Nov 2009).

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 22 Nov 2009 the current version was MARK 5.1, with the 'mark.exe' file dated 31 Oct 2009 and 'mark_int.exe' dated 8 Nov 2009.

Version 5.1, released in April 08, has additional information in the Project Browser, so you will probably want to update to the new version.

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. WinBUGS is the older and better-known program and more resources are available; for example Gelman & Hill (2007), Bolker (2008) and Royle & Dorazio (2008) all provide code designed for WinBUGS, although it should work in OpenBUGS. In the future, though, OpenBUGS will become the standard version and new functionality will be added to OpenBUGS rather than WinBUGS. More details of the different versions are here.

OpenBUGS

Download and installation: Go to the OpenBUGS page at the University of Helsinki:

http://mathstat.helsinki.fi/openbugs/

In the navigation bar on the left of the page, go to Software, then Binaries. This page has instructions on installing OpenBUGS on Windows and a link to download the software in a .ZIP file, "OpenBUGS.zip".

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. seedsLog.odc, an example file in OpenBUGS.zip) and select Open With. If "winbugs" appears in the next window, select that, otherwise click on Choose Program... You may have to use the Browse... button to navigate to winbugs.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: 3.0.3 (as at 22 Nov 2009).

Documentation: If you press F1 or select Help > WinBUGS User Manual in OpenBUGS, the WinBUGS manual appears. The OpenBUGS manual is available from the OpenBUGS web site (as above). Differences between the two appear to be cosmetic!

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 heading "Installing WinBUGS 1.4 in Windows"; if you are using Windows Vista, be sure to read the note in this section.

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.

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

Current version: 1.4.3 (as at 22 Nov 2009).

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 the file 'setup_presence.zip', which contains the installation file, 'setup_presence.exe'. (As at 22 Nov 2009 the link was still labelled "Download Presence2.0" but the .zip file actually contained v.2.4.)

Current version: (as at 22 Nov 2009) is version 2.4 and the latest build is dated 090925 (25 Sept 2009). 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 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.

Now look for a link to the setup program, called "R-x.x.x-win32.exe" (eg. "R-2.9.2-win32.exe"). 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: see details on CRAN.

Current version: 2.10.0 (dated 26 Oct 2009) and the setup file is called “R-2.10.0-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.