Datasets, management, and analyses for the Keogh river steelhead and Pacific salmonids projects
This project compiles annual-level population and environmental data relevant to the Keogh River since 1976. We had two phases of analyses:
(1) Preliminary model fits (primarily using maximum likelihood and the 'MARSS' package) applications to see whether the time-series varied. That code can be found in the 'Keogh MARSS AFS.r' file.
and then
(2) integrated Bayesian MARSS model applications for the final set of analyses. The code there can be found in the 'R stan run' and 'Stan' sub-directories.