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Update readme with updated reference and reproducibility steps
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# stpollock | ||
A spatio-temporal CPUE analysis combining bottom and acoustic trawl survey | ||
data for pollock | ||
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This analysis is in development and should not be used. Check back later | ||
for more information and progress. | ||
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# stpollock | ||
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A spatio-temporal CPUE analysis combining bottom and acoustic | ||
trawl survey data for eastern Bering sea pollock | ||
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This repo contains code to reproduce the following paper: | ||
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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 | ||
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A demo of the method is posted at: | ||
https://github.com/James-Thorson-NOAA/VAST/wiki/Combine-acoustic-and-bottom-trawl-data | ||
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Note that this example uses maximum likelihood, while the paper | ||
above uses Bayesian inference via tmbstan. See paper for a | ||
discussion of why. | ||
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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. | ||
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The result files are far too large to save so are | ||
excluded. Otherwise all files necessary to run the analysis are | ||
included. | ||
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