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# Fraser-Pink-ResDoc
DRAFT 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 simulation to project population dynamics forward under different harvest control rules (HCRs), then evaluate these dynamics and HCRs with how they perform in relation to conservation and fishery objectives.
# 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](https://github.com/pbs-assess/csasdown)'s `draft("sr")` function. In addition to the csasdown files, 📁`analysis` contains:
- 📁`data`
-📁`generated` data generated from analyses
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- 📁`Stan` Stan code to run the state-space spawner-recruit model

To reproduce this document, fork or clone this repository, run the analysis, [fit the model](https://github.com/Pacific-salmon-assess/FR-PK-ResDoc/blob/main/analysis/R/fit-sr-stan.R), run the [forward simulation](https://github.com/Pacific-salmon-assess/FR-PK-ResDoc/blob/main/analysis/R/fwd-sim.R), [generate figures](https://github.com/Pacific-salmon-assess/FR-PK-ResDoc/blob/main/analysis/R/inference-figs.R), and finally knit the [csasdown](https://github.com/pbs-assess/csasdown) generated [index](https://github.com/Pacific-salmon-assess/FR-PK-ResDoc/blob/main/index.Rmd) document. Flag problems in [issues](https://github.com/Pacific-salmon-assess/FR-PK-ResDoc/issues) or reach out to dylan.glaser@dfo-mpo.gc.ca for help.

We are currently working on revisions. Main revisions include updating the operating model with time-varying productivity, adding a supplement with posterior distributions of leading parameters and model diagnostics, and some edits to text.

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