Links to other sites with useful, free software

A website with a search engine specifically for R is called Rseek .

A website with many links to resources for using R (very useful) is Kyle Harms page on R for Ecologists at .

To get the datasets and code to accompany Michael Crawley's opus The R Book, go to his webpage at .

A list of books about R or using R heavily can be found on the r-project website at .

Michael Prager's software. Mike has made several programs available, most notably his package for surplus production modeling (ASPIC)

Russell Millar's software. Russell has made several programs available, most notably for estimating gear selectivity curves, for estimating composition of mixed-stock catches, and for fitting Bayesian state-space models for surplus production modeling and for age-structured sequential population analysis.

R Project. The R Project for Statistical Computing. Links to documentation and download of R. (R is a freeware system and language for manipulating data, performing statistical analysis and graphing.)

RStudio. A fabulous, free editor for R that runs on PCs, Macs, and Linux. Highly recommended.

R mailing lists archive. You can subscribe to the R mailing lists from this site as well as search the archives for messages dealing with topics of interest including questions on statistical methods, availability of R routines for specific purposes and help debugging R code.

The R-Journal. A free, peer-reviewed, online journal devoted to R including new developments, interesting case studies, advice to beginners.

R graphics gallery. A large collection of R language routines for producing almost any kind of graph conceivable is available at the R graphics archive.

Fisheries Library in R (FLR).
According to this webpage, "The FLR library is a collection of tools in R that facilitates the construction of bio-economic simulation models of fisheries and ecological systems… It is a generic toolbox, but is specifically suited for the construction of simulation models for evaluations of fisheries management strategies." The introduction page indicates there are routines for:

Fisheries Methods and Models in R. A series of functions written by Gary Nelson to do a variety of fisheries-related analyses in R.

NMFS Toolbox. Stock assessment programs used by the US National Marine Fisheries Service have been incorporated into a package called the Toolbox.

ICES (International Council for the Exploration of the Sea) Stock Assessment Software. Various stock assessment programs and packages for doing virtual population analysis (VPA), other catch-at-age analyses, Collie-Sissenwine catch-survey-catch models, short-term forecasting, etc.

ICCAT (International Commission for the Conservation of Atlantic Tunas) stock assessment software catalogue: software for production modeling, virtual population analysis (VPA), and more.

AD Model Builder : a now-free programming language for building nonlinear models. This language is now used extensively for stock assessment models. You can download the software, find out about training courses, etc. from the website.

Gary White's program MARK. This authoritative and widely used program fits a very wide variety of models for data on marked-and-released animals.

Other software from Colorado State University. This website has several useful programs you can download to analyze tagging data, analyze distance sampling data to estimate density and abundance of a population, and other things.

Patuxent Wildlife Research Center Software Archive. Another site with a wide variety of downloadable software packages for fitting models to wildlife and fisheries data including software for tagging models, occupancy models, species richness, etc.

CSIRO Poptools Excel Add-in
PopTools is a versatile add-in for PC versions of Microsoft Excel (97, 2000 or XP) that facilitates analysis of matrix population models and simulation of stochastic processes. It is free for non-commercial use.

PopTools was originally written to analyse ecological models, but has much broader application. It has been used for studies of population dynamics, financial modelling, calculation of bootstrap and resampling statistics, and can be used for preparing spreadsheet templates for teaching statistics. It can be used for analysis of population projection matrices and for doing randomisation tests.

When installed, PopTools adds a new menu item to Excel's main menu, and also adds over a hundred new worksheet functions. The routines include array formulas for matrix decompositions (Cholesky, QR, singular values, LU), eigenanalysis (eigenvalues and real eigenvectors of square matrices) and formulas for generation of random variables (eg, Normal, binomial, gamma, exponential, Poisson, logNormal).

Also included in PopTools are routines for iterating spreadsheets. These make it possible to run Monte Carlo simulations, conduct randomisation tests (including the Mantel test) and calculate bootstrap statistics. Some facilities are available for function minimisation and parameter estimation using maximum likelihood techniques, and there are a number of auditing and other tools that the author finds useful in his everyday work.

PopTools requires no programming knowledge, but to fully utilise the package you need some knowledge of matrix algebra, and some understanding of probability and statistics. It is therefore most suitable for those who have done some undergraduate statistics.

FAO Fisheries Management Science Programme software:

A package of four computer programs is described in Hoggarth et al. (2006) and consists of

A CD accompanies the Hoggarth et al. paper. The programs can also be downloaded from the FMSP web site


Hoggarth, D.D., S. Abeyasekera, R.I. Arthur, J.R. Beddington, R.W. Burn, A.S. Halls, G.P. Kirkwood, M. McAllister, P. Medley, C.C. Mees, G.B. Parkes, G.M. Pilling, R.C. Wakeford, R.L. Welcomme. 2006. Stock assessment for fishery management - A framework guide to the stock assessment tools of the Fisheries Management Science Programme (FMSP). FAO Fisheries Technical Paper No. 487, Rome. 261 p., includes CD-ROM.