From 56225e5a830e4246823b4c84bc70863fd9e7e766 Mon Sep 17 00:00:00 2001 From: Cole-Monnahan-NOAA Date: Wed, 19 May 2021 09:19:50 -0700 Subject: [PATCH] Update readme with updated reference and reproducibility steps --- README.md | 44 ++++++++++++++++++++++++++++++++++---------- 1 file changed, 34 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index a96e81a..2183566 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,34 @@ -# stpollock -A spatio-temporal CPUE analysis combining bottom and acoustic trawl survey -data for pollock - -This analysis is in development and should not be used. Check back later -for more information and progress. - - - - +# stpollock + +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. + + + + +