jmMSE26

Documentation and implementation guidance for candidate management procedures (CMPs) evaluated for SPRFMO jack mackerel.

This repository is a reporting and specification layer derived primarily from the current jmMSE implementation and outputs. Scientific model development and MSE execution remain in SPRFMO/jmMSE. The site reorganizes the current candidate definitions, workflow, test evidence, and implementation instructions. SCW17 material is retained as historical context.

Render the site

cd doc
quarto render

Rendered files are written to docs/ for GitHub Pages.

Prepare and check the named SC14 release

The current release candidate is SC14-MSE-2026-RC1. Use these commands from the repository root:

Rscript R/render_sc14_release.R
Rscript R/prepare_sc14_release.R
Rscript R/check_sc14_release.R
Rscript R/render_sc14_release.R governance/release-check.qmd

The first command renders the site and PDFs using the release date as a fixed creation time. The second intentionally records the run list and the fingerprints of the files being accepted for the release. The third compares the CMP controls, runs, results, Slick values, public summaries, and recorded files. The final command updates the plain-language agreement report without changing the accepted file list.

Do not rerun prepare_sc14_release.R merely to make a changed-file warning go away. First review why the file changed and whether it belongs in the release.

Repository roles

• doc/cmp/: CMP registry, component inventory, and specification template.
• doc/application/: annual data-update and application procedures.
• doc/workflow/: relationship between assessment, MSE, and management advice.
• doc/evidence/: evidence supporting CMP screening and selection.
• doc/governance/: provenance, versioning, and change-control rules.
• doc/data/cmp-registry.csv: machine-readable registry sourced from jmMSE.
• R/build_candidate_slick.R: validated eight-CMP performance-to-Slick adapter.
• output/jm_candidates_500.slick: the named eight-CMP SC14 review file, combining the om11 reference with the single-stock and two-stock robustness sets (500 posterior iterations, 1970–2050), with Set, OM, and Stock filters and one-click OM presets.

Candidate status is explicit. A test candidate is not an adopted management procedure unless its registry status and decision record say so.

Open the current Slick results

The checked 500-draw file is output/jm_candidates_500.slick. It contains eight CMP comparison cases across the reference and robustness operating models. Northern and Southern stock components retain their source labels. For readable plots, F/FMSY is missing where FMSY is zero and finite F/FMSY values above 4 are displayed at 4; the original jmMSE performance tables are unchanged.

Use the hosted Slick app

1. Download jm_candidates_500.slick.
2. Open the Blue Matter Slick app.
3. If the service says the app has stopped, select Restart app.
4. On the opening page, under Load your MSE Results, select the downloaded .slick file.
5. Wait for the Overview page, then use the MP and OM filters to explore the results.

The hosted app accepts a file upload but does not currently provide a field for loading a Slick file directly from a GitHub URL.

Open it from R

Install Slick once if needed, then download, check, and open the file:

install.packages("Slick")
library(Slick)

url <- paste0(
  "https://raw.githubusercontent.com/SPRFMO/jmMSE26/",
  "main/output/jm_candidates_500.slick"
)
file <- tempfile(fileext = ".slick")
download.file(url, file, mode = "wb")

slick <- readRDS(file)
Check(slick)
App(slick = slick)

Add it to the hosted app's case-study menu

The hosted app obtains its selectable case studies from the Blue-Matter/SlickLibrary repository. To request permanent menu integration:

1. fork or clone Blue-Matter/SlickLibrary;
2. copy this file to Slick_Objects/SPRFMO_Jack_Mackerel.slick in that repository;
3. submit a pull request to Blue Matter; and
4. after it is merged, select SPRFMO Jack Mackerel from the app's case-study menu.

This last step requires approval from the SlickLibrary maintainers. The official Slick developer guide describes the same contribution process.