CASAL
This advanced software package implements a generalised age- or length-structured fish stock assessment model that allows a great deal of choice in specifying the population dynamics, parameter estimation, and model outputs.
Introduction
CASAL (C++ algorithmic stock assessment laboratory) is an advanced software package developed by NIWA for fish stock assessment. The software implements a generalised age- or length-structured fish stock assessment model that allows a great deal of choice in specifying the population dynamics, parameter estimation, and model outputs.
CASAL is designed for flexibility. It can implement either an age- or length-structured model, optionally also structuring the population by sex, maturity, and/or growth-path. It can be used for a single stock for a single fishery, or for multiple stocks, areas, and/or fishing methods. The user can choose the sequence of events in a model year. The data used can be from many different sources of information, for example catch-at-age or catch-at-size data from commercial fishing, survey and other biomass indices, and survey catch-at-age or catch-at-size data. Estimation can be by least squares, maximum likelihood, or Bayes.
As well as generating point estimates of the parameters of interest, CASAL can calculate likelihood or posterior profiles and can generate Bayesian posterior distributions using Monte Carlo Markov Chain methods. CASAL can project stock status into the future using deterministic or stochastic recruitment and can generate a number of yield measures commonly used in New Zealand stock assessment, including MCY, CAY, Fmax, F0.1, deterministic MSY, and CSP.
Technical details
CASAL is available for Redhat Linux 7.3 and from the command prompt under most Microsoft Windows operating systems. The current version of CASAL is v2.07-2005/08/21.
For a full description of CASAL see:
Bull, B.; Francis, R.I.C.C.; Dunn, A.; McKenzie, A.; Gilbert, D.J.; Smith, M.H. (2005). CASAL (C++ algorithmic stock assessment laboratory): CASAL user manual v2.07-2005/08/21. NIWA Technical Report 127. 272 p.
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Several of CASAL’s tasks are highly computer intensive and a powerful processor is recommended. A minimum of 64 megabytes of free RAM is recommended for running CASAL (although, depending on the scope of the problem, you may need much more). The program itself requires less than 10 megabytes of hard-disk space but output files can consume large amounts of disk space. Depending on number and type of user output requests, the output could range from a few hundred kilobytes to several hundred megabytes.
CASAL is compiled using gcc, a freeware C/C++ compiler developed by the GNU Project. The current version has been compiled on Redhat Linux version 7.3 using gcc version 3.2.3 (20030425) and on Microsoft Windows using MinGW gcc version 3.2.3 (mingw special 20030504-1).
CASAL uses a quasi-Newton optimiser and scalar, vector, and matrix types from the Betadiff automatic differentiation software package. Betadiff is based on a modified version of the program ADOL-C v1.8.4 “A package for automatic differentiation of algorithms written in C/C++” developed by a team including Andreas Griewank at the Technical University of Dresden.
Getting CASAL
The CASAL software, documentation, example files, and S-Plus/R utility files are available on request. CASAL is freely distributed under a restricted license. Requests for CASAL or more information about CASAL can be made by contacting the CASAL development team.
Contact
Alistair Dunn
CASAL Development Team
Phone +64 4 386 0300
Fax +64 4 386 0574
Email: CASAL@niwa.co.nz
NIWA
Private Bag 14901
Kilbirnie, Wellington
New Zealand