NEFSC Transition

[Schiano-NOAA]

This is additional content and updated agenda to incorporate the NEFSC workflow tranistion to asar presented by the NWFSC rep on the steering committee.

I think the plan for this could be to incorporate it into main, then revert at the conclusion of the workshop this week. All the while, this can be maintained in a branch after it gets reverted so the code is there.

[Copilot]

Pull request overview

This PR adds NEFSC workflow transition materials for an upcoming workshop, providing tools and documentation to help migrate from legacy NEFSC assessment workflows to the ASAR (automated stock assessment report) framework. The PR includes conversion utilities, plotting/table generation functions, and updated curriculum content. Per the description, this content is intended to be merged temporarily for the workshop and then reverted, while being maintained in a separate branch.

Changes:

• Added R scripts for converting legacy NEFSC AutoUpdate format to ASAR-compatible structure, including data mapping functions and validation utilities
• Implemented custom plotting and table generation functions (catch, survey indices, projections, biological reference points) that bridge stockplotr functionality with NEFSC-specific formatting requirements
• Updated workshop agenda and Day 2 curriculum to include NEFSC-specific workflow adaptation session with download scripts and step-by-step migration instructions

Reviewed changes

Copilot reviewed 16 out of 21 changed files in this pull request and generated 18 comments.

Show a summary per file

File	Description
testAdditionalStocks.R	Test script demonstrating conversion and visualization for BUTUNIT and SCUNIT stocks with duplicate code blocks
table_projections1.1.R	Function to generate projection summary tables with dynamic F-label mapping and LaTeX/HTML compatibility
table_catch_status1.1.R	Generates catch and status trend tables with configurable display periods and metric labeling
table_brp1.1.R	Creates biological reference point comparison tables with status determination logic
plot_total_catch.R	Plotting function for total catch by fleet with support for line, bar, and histogram visualizations
plot_survey_indices.R	Survey abundance index plotting with adaptive uncertainty visualization (ribbons vs error bars)
create_asar_object.R	Constructor and validator for ASAR stock objects with duplicate add_stock_data function definitions
TestMoreStocksReportOnly.R	Simplified report generation script with undefined report_options variable
MapAutoUpdateToAsar.R	Core conversion function mapping legacy RData to stockplotr structure with LaTeX/HTML cleaning utilities
Example.R	Comprehensive example workflow with undefined update_stock_info function
CheckLatexInstall.R	LaTeX dependency checker with function name mismatch
ASARreportFiles/preamble.R	Report preamble with data extraction and variable calculations for executive summary
ASARreportFiles/in-header.tex	LaTeX header with hardcoded stock name
ASARreportFiles/01_executive_summary.qmd	Executive summary template with dynamic text generation and visualization
agenda.qmd	Workshop agenda with added NEFSC-specific Day 2 schedule
Curriculum/Day_2/day_2.qmd	Updated curriculum with NEFSC adaptation section including file download and migration steps

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[sbreitbart-NOAA]

@Schiano-NOAA Thanks for taking the time to update the workshop with Dan's scripts! I'll test this and add comments based on the workflow next.

In the meantime, I think we should keep this information on the website- not in a branch- because some people will want to refer back to this in the rendered Quarto format. They may confused about how to access the info in a branch, and how to extract the code/steps from the markdown. It would also be helpful for us to refer back to it.

Idea for organizing this info:

• We put this section into a snippet
• Add a section in the sidebar for region-specific info. Under NEFSC, add a mention of this snippet
• Add a mention of this snippet in the Day 2 page, then remove it after the workshop