GAPsurvey

At-sea data management tools for RACE GAP surveys

This code is always in development

This code is primarally maintained by:

Emily Markowitz (Emily.Markowitz AT noaa.gov; EmilyMarkowitz-NOAA)

Sean Rohan (Sean.Rohan AT noaa.gov; sean-rohan-NOAA)

Margaret Siple (Margaret Siple AT noaa.gov; MargaretSiple-NOAA)

Alaska Fisheries Science Center,

National Marine Fisheries Service,

National Oceanic and Atmospheric Administration,

Seattle, WA 98195

Table of contents

• Make sure the necessary packages are installed
• User Resources
• Updating the Package
  • Step 1: Update the Version Number in DESCRIPTION file
  • Step 2: Once a year: Re-download source data
  • Step 3: If you make needed edits to README.rmd
  • Step 4: If you add or remove functions
  • Step 5: Commit and Push to Main Branch
  • Step 6: Automated Workflows
    • A. R-CMD-check Workflow (.github/workflows/R-CMD-check.yaml)
    • B. pkgdown Workflow (.github/workflows/pkgdown.yml)
  • Cite this data
• Relevant publications
• Suggestions and Comments
  • R Version Metadata
  • NOAA README
  • NOAA License

Make sure the necessary packages are installed

library(devtools)

devtools::install_github("afsc-gap-products/GAPsurvey")
 # Or
remotes::install_github("afsc-gap-products/GAPsurvey@main")

library(GAPsurvey)

or install from local file .tar.gz:

 # example, the user may have a different path
install.packages('C:/Users/User/Downloads/GAPsurvey.tar.gz',
                 repos=NULL, type='source')
library(GAPsurvey)

User Resources

• GitHub repository.

• Access Tips and Documentation for All Production Data

• Fisheries One Stop Shop (FOSS)

• Groundfish Assessment Program Bottom Trawl Surveys

• AFSC’s Resource Assessment and Conservation Engineering Division

• Survey code books

• Publications and Data Reports

• Research Surveys conducted at AFSC

Updating the Package

This repository uses automated GitHub Actions workflows to streamline package updates and documentation builds. Follow these steps to release a new version once you have made your content edits to the package code.

Step 1: Update the Version Number in DESCRIPTION file

The only manual change you need to make is updating the version number in the DESCRIPTION file at the repository root. The version uses a date-based format (YYYY.MM.DD). For example: Version: 2026.04.21

Step 2: Once a year: Re-download source data

Once a year re-download data to go into the package using this data_download.R script.

Step 3: If you make needed edits to README.rmd

Changes should be minimal, but all edits to this README file must be made in the RMD version.

Step 4: If you add or remove functions

If you add or remove functions that are supposed to be used by the user, update the function list in the _pkgdown.yml.

Step 5: Commit and Push to Main Branch

Once you’ve updated the DESCRIPTION file, commit your changes and push to the main branch.

Step 6: Automated Workflows

Two GitHub Actions workflows will automatically trigger on your push to main:

A. R-CMD-check Workflow (.github/workflows/R-CMD-check.yaml)

This workflow:

✅ Runs R package checks on Windows to ensure code quality

✅ Installs all package dependencies (devtools, knitr, rmarkdown, here)

✅ Builds the package into a .tar.gz file with the version number from DESCRIPTION (e.g., GAPsurvey-2026.04.21.tar.gz)

✅ Converts the vignette GAPsurvey-script.Rmd into an R script (inst/r/GAPsurvey-script.R)

✅ Renders inst/r/README.Rmd into README.md

✅ Commits and pushes the updated generated files back to the repository

✅ Uploads the built .tar.gz package as a workflow artifact (available for download in GitHub Actions)

Check status: Visit GitHub Actions to view workflow runs and download built packages.

B. pkgdown Workflow (.github/workflows/pkgdown.yml)

This workflow:

✅ Builds the package documentation site using pkgdown

✅ Deploys the documentation to GitHub Pages

✅ Automatically updates when you push to main

View documentation: https://afsc-gap-products.github.io/GAPsurvey

Cite this data

Use the below bibtext citations for citing the package created and maintained in this repo. Add “note = {Accessed: mm/dd/yyyy}” to append the day this data was accessed.

cat(readLines(con = here::here("inst/CITATION.bib")), sep = "\n") 
#> @misc{GAPsurvey,
#>   author = {{NOAA Fisheries Alaska Fisheries Science Center, Goundfish Assessment Program}},
#>   year = {2024},
#>   title = {AFSC Goundfish Assessment Program at-Sea data management tools for RACE GAP surveys},
#>   howpublished = {https://www.fisheries.noaa.gov/alaska/science-data/groundfish-assessment-program-bottom-trawl-surveys},
#>   publisher = {{U.S. Dep. Commer.}},
#>   copyright = {Public Domain}
#> }

Relevant publications

source("https://raw.githubusercontent.com/afsc-gap-products/citations/main/cite/current_data_tm.r") # srvy_cite 

Learn more about these surveys (Hoff, 2016; Markowitz et al., 2024; Markowitz et al., 2025; Siple et al., 2024; Von Szalay et al., 2023; Zacher et al., 2024).

Hoff, G. R. (2016). Results of the 2016 eastern Bering Sea upper continental slope survey of groundfishes and invertebrate resources (NOAA Tech. Memo. NOAA-AFSC-339). U.S. Dep. Commer. https://doi.org/10.7289/V5/TM-AFSC-339

Markowitz, E. H., Dawson, E. J., Wassermann, S., Anderson, C. B., Rohan, S. K., Charriere, B. K., and Stevenson, D. E. (2024). Results of the 2023 eastern and northern Bering Sea continental shelf bottom trawl survey of groundfish and invertebrate fauna (NOAA Tech. Memo. NMFS-AFSC-487; p. 242). U.S. Dep. Commer. https://doi.org/10.25923/2mry-yx09

Markowitz, E. H., Wassermann, S., Rohan, S. K., Charriere, B. K., Anderson, C. B., and Stevenson, D. E. (2025). Results of the 2024 eastern and northern Bering Sea continental shelf bottom trawl survey of groundfish and invertebrate fauna (NOAA Tech. Memo. NMFS-AFSC-499; p. 203). U.S. Dep. Commer. https://doi.org/10.25923/8qa3-x785

Siple, M. C., Szalay, P. G. von, Raring, N. W., Dowlin, A. N., and Riggle, B. C. (2024). Data report: 2023 gulf of alaska bottom trawl survey (NOAA Tech. Memo. AFSC processed report; 2024-09). U.S. Dep. Commer. https://doi.org/10.25923/gbb1-x748

Von Szalay, P. G., Raring, N. W., Siple, M. C., Dowlin, A. N., Riggle, B. C., and Laman, E. A. and. (2023). Data report: 2022 Aleutian Islands bottom trawl survey (AFSC Processed Rep. 2023-07; p. 230). U.S. Dep. Commer. https://doi.org/10.25923/85cy-g225

Zacher, L. S., Richar, J. I., Fedewa, E. J., Ryznar, E. R., and Litzow, M. A. (2024). The 2024 eastern Bering Sea continental shelf trawl survey: Results for commercial crab species [NOAA Tech. Memo.]. (NFMS-AFSC-491), 237. https://doi.org/10.25923/q0fw-z324

Suggestions and Comments

If you see that the data, product, or metadata can be improved, you are invited to create a pull request, submit an issue to the GitHub organization, or submit an issue to the code’s repository.

R Version Metadata

sessionInfo()
#> R version 4.5.3 (2026-03-11 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> Running under: Windows Server 2022 x64 (build 26100)
#> 
#> Matrix products: default
#>   LAPACK version 3.12.1
#> 
#> locale:
#> [1] LC_COLLATE=English_United States.utf8 
#> [2] LC_CTYPE=English_United States.utf8   
#> [3] LC_MONETARY=English_United States.utf8
#> [4] LC_NUMERIC=C                          
#> [5] LC_TIME=English_United States.utf8    
#> 
#> time zone: UTC
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.39       R6_2.6.1            fastmap_1.2.0      
#>  [4] xfun_0.57           glue_1.8.1          knitr_1.51         
#>  [7] htmltools_0.5.9     rmarkdown_2.31      lifecycle_1.0.5    
#> [10] cli_3.6.6           readtext_0.92.1     vctrs_0.7.3        
#> [13] data.table_1.18.2.1 compiler_4.5.3      rprojroot_2.1.1    
#> [16] here_1.0.2          httr_1.4.8          tools_4.5.3        
#> [19] pillar_1.11.1       evaluate_1.0.5      yaml_2.3.12        
#> [22] otel_0.2.0          rlang_1.2.0         stringi_1.8.7

NOAA README

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.

NOAA License

Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. §105). The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the Software outside of the United States.

U.S. Department of Commerce | National Oceanographic and Atmospheric Administration | NOAA Fisheries