This R project contains the code used to create data, figures, and tables for the 2026 Longfin Squid Snapshot Ecosystem and Socioeconomic Profile document. Methods are further documented in 'docs/2026_readme.txt'. This R project is intended to allow a user to recreate the 2026 Longfin Squid Snapshot Ecosystem and Socioeconomic Profile data and analyses; however, due to local differences in R packages, file paths, and R versions, it is likely that a user will need to complete (hopefully minimal) troubleshooting in order to successfully execute the entire codebase. We hope that the documentation here and the readme in the docs folder will help users complete any needed troubleshooting.

Folders and files in this repository:

• .github folder: Contains GitHub actions
• inputs folder: Contains indicator time series data (bottom temperature and commercial indicators)
  • GLORYS_monthly_BottomT_ECOMON6_1993_2024.csv: Raw data for bottom temperature indicator
  • NES_5REGIONS.shp: Shape file for bottom temperature indicator
  • SOCIEOECONOMIC_COMMERCIAL_INDICATORS_FINAL.csv: Raw data for commercial indicators (landings, vessels, revenue)
• intermediates folder: Contains raw or intermediate data files (currently empty for 2026 Snapshot)
• outputs folder: Contains final data files (currently empty for 2026 Snapshot)
• docs folder: Contains Quarto document and associated helper files to generate the Snapshot pdf report
  • archive folder: Contains data and scripts not used in final Snapshot ESP
  • 2026_readme.txt: Contains etails on each section in 2026 Snapshot
  • bg_pg1.jpg: JPG file for page 1 background. Need to add to PDF in Adobe
  • bg_pg2.jpg: JPG file for page 2 background. Need to add to PDF in Adobe
  • snapshot_template.qmd: Code to render Snapshot ESP
  • snapshot_template.pdf: Output of rendered quarto doc
  • snapshot_template.tex: Necessary helper file to render Snapshot
  • template.tex: Necessary helper file to render Snapshot
  • table_template.xlsx: Excel file to produce indicator table
• images folder: Contains images of indicator time series and png files for Snaphot
• scripts folder: Contains scripts used to create indicators, plot indicators, and other functions needed to create the snapshot pdf report
  • plot_bottomT_indicator.R: Code to produce and plot bottom temperature indicator
  • plot_com_indicators.R: Code to produce and plot commercial indicators
  • plot_gsi_indicator.R: Code to produce and plot Western GSI indicator
  • plot_indicator_ts.R: Generic indicator plotting function. Base code for other plot_xxx_indicator.R scripts
  • plot_risk_longfin.R: Code to produce risk assessment bar plot
  • script_template.R: Contains a metadata template for scripts

Legal 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 law. 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.