This code produces distribution maps of GOA species from DFO synoptic bottom trawl surveys and the sdmTMB package (Anderson et al. 2022), to inform Atlantis GOA initial conditions and seasonal distributions (i.e., S1-S4 parameters).

This is the code that deals with British Columbia.

This code performs 3 tasks:

1. Starting from DFO bottom trawl data and length-weight relationships, it calculates the CPUE of juveniles and adults at each haul location. This is done in catch_to_CPUE_DFO/catch_to_cpue_DFO.Rmd.
2. Loads CPUE data into a knitter file, which subsets to the species of interest. This is done in DFO_sdmTMB_knitter.R.
3. Runs the sdmTMB routine: fits the model, produces figures, output tables and validation metrics by species and stage. This is done in DFO_sdmTMB_template.Rmd.

Utility scripts include DFO_species.R, which maps species names from the DFO data to the Atlantis GOA functional groups. See scripts for details on data sources and methods.

References

Anderson, S.C., E.J. Ward, P.A. English, L.A.K. Barnett. 2022. sdmTMB: an R package for fast, flexible, and user-friendly generalized linear mixed effects models with spatial and spatiotemporal random fields. bioRxiv 2022.03.24.485545; doi: https://doi.org/10.1101/2022.03.24.485545