Basic Design-Based SAP Data Products

The scripts therein reproducibly produce our typical data products.

This code is always in development. Find code used for various reports in the code releases.

This code is primarally maintained by:

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

Groundfish Assessment Program

NOAA | Alaska Fisheries Science Center

Seattle, WA 98195

Shannon Hennessey (Shannon.Hennessey AT noaa.gov; @ShannonHennessey)

Kodiak Fisheries Research Center

NOAA | Alaska Fisheries Science Center

Kodiak, AK 99615

The code in this repository is regularly being updated and improved. Please refer to releases for finalized products and project milestones.

Table of contents

r toc <- strsplit(x = readtext::readtext(file = here::here("content/README.Rmd"), verbosity = 0)[[2]], split = "\n") toc <- toc[[1]][substr(x = toc[[1]], start = 1, stop = 1) == "#"] toc <- toc[-c(1:3)] toc_list <- toc toc_list <- gsub(pattern = "### ", replacement = "> - [*", x = toc_list, fixed = TRUE) toc_list <- gsub(pattern = "## ", replacement = "> - [*", x = toc_list, fixed = TRUE) toc_list <- gsub(pattern = "# ", replacement = "> - [*", x = toc_list, fixed = TRUE) toc_link <- tolower(gsub(pattern = " ", replacement = "-", x = gsub(pattern = "#", replacement = "", x = gsub(pattern = "# ", replacement = "", x = toc, fixed = TRUE), fixed = TRUE))) toc <- paste0(toc_list, "*](#", toc_link, ")", collapse = "\n")

• User Resources
• Cite this data
  • Access Constraints
• Relevant publications
• Suggestions and Comments
  • R Version Metadata
  • NOAA README
  • NOAA License

User Resources

• Fisheries One Stop Shop (FOSS)

• AFSCs Resource Assessment and Conservation Engineering Division

• Publications and Data Reports

• Research Surveys conducted at AFSC

Cite this data

Use the below bibtext citations, as cited in our groups citation repository for citing the data created and maintained in this repo. Add note = {Accessed: mm/dd/yyyy} to append the day this data was accessed. Included here are AFSC RACE Groundfish and Shellfish Assessment Programs:

• Design-Based Production Data (NOAA Fisheries Alaska Fisheries Science Center, Goundfish Assessment Program, 2024).

• Public Data hosted on the Fisheries One Stop Shop (FOSS) Data Platform (NOAA Fisheries Alaska Fisheries Science Center, 2024).

Access Constraints

There are no legal restrictions on access to the data. They reside in public domain and can be freely distributed.

User Constraints: Users must read and fully comprehend the metadata prior to use. Data should not be used beyond the limits of the source scale. Acknowledgement of AFSC Groundfish Assessment Program, as the source from which these data were obtained, in any publications and/or other representations of these data, is suggested.

General questions and more specific data requests can be sent to nmfs.afsc.gap.metadata@noaa.gov or submitted as an issue on our GitHub Organization. The version of this data used for stock assessments can be found through the Alaska Fisheries Information Network (AKFIN). For questions about the eastern Bering Sea surveys, contact Duane Stevenson (Duane.Stevenson@noaa.gov). For questions about the Gulf of Alaska or Aleutian Islands surveys, contact Ned Laman (Ned.Laman@noaa.gov). For questions specifically about crab data in any region, contact Mike Litzow (Mike.Litzow@noaa.gov), the Shellfish Assessment Program lead.

For questions, comments, and concerns specifically about the Fisheries One Stop Shop (FOSS) platform, please contact us using the Comments page on the FOSS webpage.

Relevant publications

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

srvycite <- srvycite %>% dplyr::filter(SRVY %in% c("EBS", "NBS", "BSS", "CRAB") ) ```

Learn more about these surveys (Hoff, 2016; Markowitz et al., 2024, 2024; Zacher et al., 2024).

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 codes repository.

R Version Metadata

r sessionInfo()

## R version 4.4.1 (2024-06-14 ucrt)
## Platform: x86_64-w64-mingw32/x64
## Running under: Windows 10 x64 (build 19045)
## 
## Matrix products: default
## 
## 
## locale:
## [1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    
## 
## time zone: America/Los_Angeles
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] XML_3.99-0.17      RCurl_1.98-1.16    data.table_1.16.0  akfingapdata_0.1.0 DBI_1.2.3          RODBC_1.3-23       ftExtra_0.6.4     
##  [8] badger_0.2.4       scales_1.3.0       stringr_1.5.1      here_1.0.1         flextable_0.9.6    kableExtra_1.4.0   janitor_2.2.0     
## [15] readxl_1.4.3       tidyr_1.3.1        readr_2.1.5        magrittr_2.0.3     googledrive_2.1.1  akgfmaps_3.5.3     terra_1.7-78      
## [22] stars_0.6-6        abind_1.4-8        sf_1.0-17          gstat_2.1-2        ggplot2_3.5.1      dplyr_1.1.4        classInt_0.4-10   
## [29] gapindex_2.2.0     distill_1.6        devtools_2.4.5     usethis_3.0.0     
## 
## loaded via a namespace (and not attached):
##  [1] RColorBrewer_1.1-3      wk_0.9.3                rstudioapi_0.16.0       dlstats_0.1.7           jsonlite_1.8.9         
##  [6] rmarkdown_2.28          fs_1.6.4                ragg_1.3.3              vctrs_0.6.5             memoise_2.0.1          
## [11] askpass_1.2.1           htmltools_0.5.8.1       cellranger_1.1.0        s2_1.1.7                KernSmooth_2.23-24     
## [16] htmlwidgets_1.6.4       zoo_1.8-12              lubridate_1.9.3         cachem_1.1.0            uuid_1.2-1             
## [21] mime_0.12               lifecycle_1.0.4         pkgconfig_2.0.3         R6_2.5.1                fastmap_1.2.0          
## [26] shiny_1.9.1             snakecase_0.11.1        digest_0.6.37           colorspace_2.1-1        rprojroot_2.0.4        
## [31] pkgload_1.4.0           textshaping_0.4.0       fansi_1.0.6             timechange_0.3.0        httr_1.4.7             
## [36] compiler_4.4.1          gargle_1.5.2            proxy_0.4-27            intervals_0.15.5        remotes_2.5.0          
## [41] fontquiver_0.2.1        withr_3.0.1             pkgbuild_1.4.4          openssl_2.2.1           sessioninfo_1.2.2      
## [46] tools_4.4.1             units_0.8-5             zip_2.3.1               httpuv_1.6.15           glue_1.7.0             
## [51] promises_1.3.0          grid_4.4.1              generics_0.1.3          gtable_0.3.5            tzdb_0.4.0             
## [56] class_7.3-22            hms_1.1.3               sp_2.1-4                xml2_1.3.6              utf8_1.2.4             
## [61] pillar_1.9.0            yulab.utils_0.1.7       later_1.3.2             lattice_0.22-6          FNN_1.1.4.1            
## [66] tidyselect_1.2.1        rvcheck_0.2.1           fontLiberation_0.1.0    miniUI_0.1.1.1          downlit_0.4.4          
## [71] knitr_1.48              fontBitstreamVera_0.1.1 svglite_2.1.3           xfun_0.47               stringi_1.8.4          
## [76] yaml_2.3.10             evaluate_1.0.1          codetools_0.2-20        officer_0.6.7           gdtools_0.4.0          
## [81] tibble_3.2.1            BiocManager_1.30.25     cli_3.6.3               xtable_1.8-4            systemfonts_1.1.0      
## [86] munsell_0.5.1           spacetime_1.3-2         Rcpp_1.0.13             readtext_0.91           parallel_4.4.1         
## [91] ellipsis_0.3.2          profvis_0.4.0           urlchecker_1.0.1        bitops_1.0-9            viridisLite_0.4.2      
## [96] xts_0.14.0              e1071_1.7-14            purrr_1.0.2             rlang_1.1.4

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