CASAL 2: NIWA's next generation fisheries population modelling software

CASAL2 is an advanced software package developed by NIWA for modelling the population dynamics of marine species.

CASAL2 is NIWA’s new integrated assessment tool for modelling population dynamics of marine species, including fishery stock assessments. CASAL2 expands functionality and maintainability over its predecessor, CASAL. CASAL2 can be used for quantitative assessments of marine populations, including fish, invertebrates, marine mammals and seabirds.

Introduction

CASAL2 software implements a generalised age-structured marine population model that allows a great deal of choice in specifying the population dynamics, parameter estimation, and model outputs. CASAL2 is designed for flexibility. It can implement an age-structured model for a single population or multiple populations using user-defined categories such as area, sex and maturity. One major change from CASAL is that structural elements are generic and not predefined, but these are easily constructed. CASAL2 models can be used for a single population with a single anthropogenic event (in a fish population model this would be a single fishery), or for multiple species and populations, areas, and/or anthropogenic or exploitation methods.

The time period and annual cycle of CASAL2 is completely defined by the user. Observational data used can be from many different sources, for example removals-at-size or -age from an anthropogenic or exploitation event (e.g. fishery or other human impact), scientific survey and other biomass indices, and mark-recapture data. Model parameters can be estimated using penalised maximum likelihood or Bayesian methods.

As well as generating point estimates of the parameters of interest, CASAL2 can calculate likelihood or posterior profiles and can generate Bayesian posterior distributions using Monte Carlo Markov Chain methods. CASAL2 can project population status into the future using deterministic or stochastic population dynamics, or simulate observations from a set of given model structures.

Technical details

CASAL2 is available for Linux and from the command prompt in Microsoft Windows. The current version of CASAL2 is casal2_v2016-06-06.

The citation for the CASAL2 manual is:
Rasmussen, S., Doonan, I., Dunn, A., Marsh, C., Large, K., Mormede, S. (2016). CASAL2 User Manual V 1.0. NIWA Technical Report 139. 197p.

And a citation for CASAL2 is:
Doonan, I. L., K. Dunn, A. Rasmussen, S. Marsh, C. Mormede, S (In Press). Casal2: New Zealand’s integrated population modelling tool. Fisheries Research.

Several of CASAL2’s tasks are highly computer intensive and a powerful processor is recommended. A minimum of 64 megabytes of free RAM is recommended for running CASAL2 (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.

Getting CASAL2

The CASAL2 software, documentation, example files, and R utility files are freely available at this site. The source code is open source and found at the following git repository. A pre-release version with executable, source code, and examples for windows is provided from:

ftp://ftp.niwa.co.nz/Casal2/windows/Casal2.zip

A linux copy can be downloaded at the following link:

ftp://ftp.niwa.co.nz/Casal2/linux/Casal2.tar.gz

CASAL2 is open source software which gives users the ability to add value and input into the future of this software. Source code can be found at:

https://github.com/NIWAFisheriesModelling/CASAL2

CASAL

CASAL will still be maintained by the development team. For information on CASAL you can download the manual from:

CASAL user manual (PDF 3.9 MB)

CASAL software, documentation, example files, and R utility files are also available on request. A copy of CASAL is freely available on request. Requests for CASAL or more information about CASAL can be made by contacting the CASAL2 Development Team.

Contact

CASAL2 Development Team
email: casal2@niwa.co.nz
NIWA
Private Bag 14901
Kilbirnie, Wellington
New Zealand.