Spatial distributions for Alaska with sdmTMB

This code produces distribution maps of GOA species from RACE-GAP 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 code performs 3 tasks:

1. Starting from RACE-GAP 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_AKFIN/catch_to_cpue_AKFIN.Rmd.
2. Loads CPUE data into a knitter file, which subsets to the species of interest. This is done in sdmTMB_knitter_AKFIN.R.
3. Runs the sdmTMB routine: fits the model, produces figures, output tables and validation metrics by species and stage. This is done in GOA_sdmTMB_template_AKFIN.Rmd.

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