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.)
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.
To learn more about programming and analyzing
data in R you may wish to look at:
Bolker, B. 2007. Ecological Models and Data in R. This 430 page book is available for free on the internet from
Bolker's website.
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:
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