Report: Assessing rebuilding potential for Gulf of St. Lawrence shrimp stocks, Pandalus borealis, in the critical zone

Authors: Sophie Mormede, Daniel Duplisea, Marie-Julie Roux, Hugo Bourdages
Date: December 2024
Contact: Sophie Mormede [email protected]

Description

These are the Casal2 inputs (.csl2) and main output files for the base case models.

• estimate.log contains the MPD outputs.
• objectives.x and samples.x contain the main MCMC outputs, one file per MCMC chain.

The final MCMC outputs of all quantities are excluded due to the size of the files.

Recreating Final MCMC Outputs

To recreate the final MCMC outputs using the Casal2 software, run the following commands in the folder where objectives.x are located:

casal2 -c config-tab.csl2 -r -i samples.1 -t > quantities.1
casal2 -c config-tab.csl2 -r -i samples.2 -t > quantities.2
casal2 -c config-tab.csl2 -r -i samples.3 -t > quantities.3

Software and Tools

A version of Casal2 is available at https://github.com/alistairdunn1/CASAL2.

R extractor functions for Casal2 outputs are also provided on the above GitHub page.