This repository stores the code and data used to perform the analysis presented in Staton et al.: Evaluation of methods for spawner-recruit analysis in mixed-stock Pacific salmon fisheries (DOI: 10.1139/cjfas-2019-0281)

The analysis contained two primary phases:

1. Application to the monitored Chinook salmon populations within Kuskokwim River, located in western Alaska (found in the kusko subdirectory)
2. Simulation-testing the methods applied to the Kuskokwim (found in the sim-eval subdirectory)

Dependencies

All code and data to conduct the analysis are found in this repository, though the analyses rely on two other packages written specifically for this analysis: SimSR (handles the simulation of population dynamics and sampling of a system with similar characteristics as the Kuskokwim) and FitSR (handles the fitting of regression and state-space models, regardless of if the data were simulated or empirical). These packages were written by B. Staton, and can be installed using:

devtools::install_github("bstaton1/FitSR")

FitSR installs SimSR automatically, as well as two other dependencies written by B. Staton: postpack (for streamlining posterior summarization from JAGS models) and StatonMisc (a random assortment of shortcut functions).

Program JAGS will also be required to run the code in this repository, and the R package jagsUI (available on CRAN) is used to call JAGS from R, and miscellaneous other packages are used for data formatting and preparations (e.g., dplyr, reshape2, etc.)