JM_sam

This repository contains State-Space Assessment Model (SAM) analyses for the SPRFMO Chilean jack mackerel (Trachurus murphyi) assessment work.

The SAM model is used here as an independent diagnostic tool for the H1 jack mackerel assessment configuration. It is not intended to replace the Joint Jack Mackerel Model (JJM). Instead, the analyses support review of operating-model conditioning choices for the jack mackerel MSE process, including:

• candidate selectivity block structures;
• productivity and reference point diagnostics;
• index uncertainty, catchability, and fleet-conflict diagnostics;
• retrospective and leave-one-out behavior.

The repository was split from the sam/ directory of JM_SCW_prep and is now the canonical home for the SAM workflow, rendered diagnostics, and supporting data products. The former JM_SCW_prep/sam folder should be treated as retired after migration.

Contents

• 01_run_assessment.R runs the H1 SAM assessment workflow.
• 01_stock.R prepares stock and index inputs.
• 01b_retro_loo_parallel.R runs retrospective and leave-one-out analyses.
• 02_standard_diagnostics.R through 06_selectivity_blocks.R generate the main diagnostic summaries.
• sam_diagnostics.qmd is the Quarto diagnostics report.
• diagnostics/ contains generated diagnostic figures and tables.

Reproducible setup

This repository does not currently ship an renv.lock, so install the runtime dependencies explicitly before running the workflow. The analysis uses R, Quarto, and the FLR/SAM package stack:

install.packages(c(
  "ggplot2",
  "patchwork",
  "RColorBrewer",
  "quarto",
  "R.utils"
))

install.packages("remotes")
remotes::install_github(c(
  "flr/FLCore",
  "flr/FLSAM"
))

Quarto must also be available on PATH for command-line rendering. The active render path is:

Rscript render_from_output.R

To refit the assessment before rendering, run:

Rscript 01_run_assessment.R

Report

The rendered diagnostics report is available through GitHub Pages:

https://sprfmo.github.io/JM_sam/

The source report file is sam_diagnostics.qmd, and the rendered HTML is available as sam_diagnostics.html. The site landing page is generated from index.qmd and links to the active diagnostics report plus a frozen JM_SCW_prep/sam render from commit f5a21f0 for migration provenance.