Sablefish 2025

Code and stock assessment documentation for the 2025 assessment of sablefish off the U.S. West Coast. Files posted should not be considered as finalized products. Below are key dates for the 2025 assessment:

• Pre-assessment data workshop: March 18 or 19, 2025, with the specific date to be selected later
• Final data deadline: April 21, 2025
• STAR panel date: July 14-18, 2025 in Seattle, WA

The pre-assessment data workshop and the STAR panel will each provide virtual participation (workshop) and listening options (STAR Panel). Before the pre-assessment data workshop, materials for the pre-assessment data workshop will be posted online to facilitate participants’ review and robust conversations during the workshop. The finalized stock assessment document and file will be posted to the Pacific Fishery Management Council website in the September 2025 Briefing Book.

Dr. Chantel Wetzel (chantel.wetzel@noaa.gov) at the Northwest Fishery Science Center is the lead assessor for the 2025 assessment.

Installation

You can install {sablefish} from GitHub with

# install.packages("pak")
pak::pkg_install("pfmc-assessments/sablefish_2025")

File structure

This repository is structured like an R package to ease the installation process and increase the ability to easily test code. Please follow the following guidelines for the placement of files.

├───data
├───data-raw
│   └───2023 (git ignored)
│   └───ageing_error (git ignored)
│   └───ashop (git ignored)
│   └───bds (git ignored)
│   └───biology (git ignored)
│   └───discard (git ignored)
│   └───landings (git ignored)
│   └───maturity (git ignored)
│   └───survey (git ignored)
│   └───weight_at_age (git ignored)
├───date-exploration
├───date-processed
├───quarto_website
│   └───figures
├───man
├───model (git ignored)
├───R
└───report
│   └───figures
│   └───SAR_USWC_sablefish_skeleton_files (git ignored)
│   └───shared_text
│   └───support_files
└───scientific_papers (git ignored)

where

• data contains rda file of processed data in its final form that will be included in the assessment or assessment document, only data in its non-confidential form should be saved here;
• data-raw is for data files and .R scripts used to transform these raw files into something that is saved in data or in data-processed; all data files are saved within data-raw, but not saved to github. A list of the files are in .gitignore: 2023, ageing_error, ahsop, biology, bds, discard, landings, maturity, survey, weight_at_age;
• data-processed is for csv or other fully processed and formatted data that will be included in the assessment or assessment document, only data in its non-confidential form should be saved here;
• data-exploration is for exploratory scripts;
• quarto_website contains files for the website;
• report contains file for the creation of the assessment document,
• man stores .Rd files and figures used in the documentation; and
• R stores .R scripts that are loaded when building the package, this means functions only. These scripts are either called within the assessment document or .R scripts in the data-raw folder.

Report

The assessment report is created via quarto files in the report folder. Within the files there are code chunks that load an rda file for the model output containing a list of quantities created by r4ss::SS_output(), tables from the model output created by r4ss::table_all(), plots created via r4ss::SS_plots, and loads needed R packages. To switch the base model for the assessment report users should do the following steps:

1. Confirm that you have the folder structure described above for model files and you have the reference model version in step 2 in your local directory.
2. Run the model_output_objects script in the data-raw folder by updating the model_name object and ensuring the model_dir points to where that model resides.
3. Change the model_name in the ouput_and_quantities code chunk located in the SAR_USWC_sablefish_skeleton.qmd.
4. Required packages for the report document are listed in the 001_load_packages.qmd file. The pacman::p_loadcommand should install any missing packages so no additional steps should be required.
5. If using a specific package within a code chunk in any of the child documents make sure to use the package_name:: option and that the package is included in the list in the 001_load_packages.qmd code chunk.

Disclaimer

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis, and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal laws. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise does not constitute or imply their endorsement, recommendation, or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.