README.md

Estimating Precautionary Approach reference points and assessing consequences of harvest control rules for Fraser River Pink salmon

CSAS Research Document for Fraser Pink Salmon. This repository contains all the data, analysis, and csasdown code to fully reproduce the Research Document. We compile available data, fit a state-space spawner-recruit model, estimate biological benchmarks ($S_{MSY}$, $U_{MSY}$ and $S_{GEN}$), use a closed-loop forward simulation conditioned on recent population dynamics to project the stock forward under different harvest control rules (HCRs). Then we evaluate HCRs by how they perform in relation to conservation and fishery objectives.

The root directory contains all files produced when running csasdown's draft("sr") function. In addition to the csasdown files, 📁analysis contains:

• 📁data
  -📁generated data generated from analyses
  -📁raw data used in the analysis or to show the HCR with subfolders: 📁bio containing biological data used to add information in the context section and 📁hatchery with hatchery supplementation data from SEP
• 📁R .R files to fit the model (fir-sr-stan.R), run the forward simulation (fwd-sim.R), create figures/tables (inference-figs.R) and some helper functions
• 📁Stan Stan code to run the state-space spawner-recruit models
• The model validation supplement

To reproduce this document:

• fork or clone this repository
• make sure you have all packages and software (i.e. Stan) installed
• run the analysis (in this order) by:
  • fitting the model,
  • running the forward simulation,
  • generating the figures,
  • and finally knit the index.Rmd file to generate the document.
• Flag problems relating to the analysis and structure of this repo in issues or reach out to dylan.glaser@dfo-mpo.gc.ca for help.