A spatio-temporal CPUE analysis combining bottom and acoustic trawl survey data for eastern Bering sea pollock
This repo contains code to reproduce the following paper:
Cole C Monnahan, James T Thorson, Stan Kotwicki, Nathan Lauffenburger, James N Ianelli, Andre E Punt, Incorporating vertical distribution in index standardization accounts for spatiotemporal availability to acoustic and bottom trawl gear for semi-pelagic species, ICES Journal of Marine Science, 2021;, fsab085, https://doi.org/10.1093/icesjms/fsab085
A demo of the method is posted at: https://github.com/James-Thorson-NOAA/VAST/wiki/Combine-acoustic-and-bottom-trawl-data
Note that this example uses maximum likelihood, while the paper above uses Bayesian inference via tmbstan. See paper for a discussion of why.
To reproduce the analysis, clone the repo, open the script "run_analysis.R" and step through calculations. The whole thing may take a month or so to run.
The result files are far too large to save so are excluded. Otherwise all files necessary to run the analysis are included.