Casal2 User and Developer Support
The latest version of Casal2 can be downloaded from Github here.
CASAL2 received a bunch of code cleanup, minor fixes and updates.
Craig Marsh has made extensive changes, additions, and efficiency improvements over the past few months. The main user-facing changes include length-based model functionality, changes to how year class strength (YCS) is defined and used, the generation of simulated observations, additional initialisation types, and the addition of a hybrid fishing mortality process similar to that in Stock Synthesis 3. There is a new length-based Test Case, SCI.
There is a new R package in development for post-processing of Casal2 model input and output, r4Casal2.
This release also updates the MPD reports for 7 Casal2 Test Cases. The Test Cases are now located in a separate repository. The Test Cases are 6 sets of age-based stock assessment models (labeled BCO, HAK, HOK, LIN, ORH, and SBW) and one length-based stock assessment model (labeled SCI) that were constructed to validate a commonly used subset of the existing functionality. The functionality for the MCMC mode and the projection mode is being validated with the Test Cases.
The User Manuals and other documentation are not complete.
Craig Marsh, Scott Rasmussen, and Alistair Dunn have made extensive changes, additions, and efficiency improvements over the past few months. The main user-facing changes are that tag-release by length and tag-recapture by length have been reviewed and tested, as has time-varying growth.
This release also updates the MPD reports for the Casal2 Test Cases. The Test Cases are 6 sets of age-based stock assessment models (labeled BCO, HAK, HOK, LIN, ORH, and SBW) that were constructed to validate a commonly used subset of the existing functionality. The functionality for the MCMC mode and the projection mode is being validated with the Test Cases.
The simulation functionality has been reviewed and tested.
The Windows installation package for CASAL and the executables for Windows and Linux are in the TestCases/CASAL subdirectory.
The documentation in this release is not complete.
This release is from the proportions_at_weight_202101 branch. This is an interim release, as the new observation class was used in the 2021 bluenose (BNS) stock assessment which used Casal2 and followed from this document.
This release contains a new observation class, ProcessRemovalsByWeight. The technical specification for this new observation class is in the Documentation/Enhancements subdirectory. The unit test and the R code that produced the values in the unit test are also in the repository.
Casal2 now outputs the covariance matrix from CppAD minimisation.
This release also updates the MPD reports for the Casal2 Test Cases. The Test Cases are 6 sets of age-based stock assessment models (labeled BCO, HAK, HOK, LIN, ORH, and SBW) that were constructed to include a commonly used subset of the existing functionality.
The Windows installation package for CASAL and the executables for Windows and Linux are in the TestCases/CASAL subdirectory.
The executables in this release have known efficiency issues.
The documentation in this release is not complete.
The simulation functionality has not been reviewed or tested.
The CASAL and Casal2 R packages have been tested with R versions 3.6.X only.
This release tests and validates the functionality used in the Casal2 Test Cases. The Test Cases are 6 sets of age-based stock assessment models (labeled BCO, HAK, HOK, LIN, ORH, and SBW) that were constructed to include a commonly used subset of the existing functionality.
All of the Test Case Casal2 models were compared with their CASAL counterparts for MPD and MCMC results. The reports of the MPD and MCMC results are in the repository. The projection functionality has been reviewed and tested.
The executables in this release have known efficiency issues and require a review with respect to code optimisation and memory usage. The focus for this release was on testing and validating functionality.
The documentation in this release is not complete.
The simulation functionality has not been reviewed or tested.
Casal2 does not output the covariance matrix from CppAD minimisation.
The CASAL and Casal2 R packages have been tested with R versions 3.6.X only.