Package: afscdata 1.0.0

The package maintainer

afscdata: An R Package for Extraction of AFSC Fishery Data

This package provides a folder structure and SQL queries for accessing the AKFIN and AFSC databases in support of fishery stock assessments. Additionally, archived data are held/provided to maintain consistency across assessments/assessment authors.

Authors:Benjamin Williams [aut, cre], Jane Sullivan [ctb], Steve Barbeaux [ctb], Pete Hulson [ctb], Jim Ianelli [ctb], Matt Callahan [ctb], Meaghan Bryan [ctb], Kalei Shotwell [ctb], Margaret Siple [ctb]

afscdata_1.0.0.tar.gz
afscdata_1.0.0.zip(r-4.7)afscdata_1.0.0.zip(r-4.6)afscdata_1.0.0.zip(r-4.5)
afscdata_1.0.0.tgz(r-4.6-any)afscdata_1.0.0.tgz(r-4.5-any)
afscdata_1.0.0.tar.gz(r-4.7-any)afscdata_1.0.0.tar.gz(r-4.6-any)
afscdata_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
afscdata/json (API)

# Install 'afscdata' in R:
install.packages('afscdata', repos = c('https://jimianelli.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/afsc-assessments/afscdata/issues

Pkgdown/docs site:https://afsc-assessments.github.io

Datasets:

On CRAN:

Conda:

5.05 score 2 stars 25 scripts 52 exports 43 dependencies

Last updated from:96ed9cea60. Checks:7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE139
source / vignettesOK255
linux-release-x86_64NOTE126
macos-release-arm64NOTE77
macos-oldrel-arm64NOTE94
windows-develNOTE112
windows-releaseNOTE76
windows-oldrelNOTE104
wasm-releaseOK117

Exports:%>%accepted_modelbsai_amakbsai_atfbsai_fhsbsai_nrsbsai_octopusbsai_oroxcatch_to_ss3collapse_filtersconnectdisconnectgap_check_biogoa_amakgoa_atfgoa_duskgoa_fhsgoa_norkgoa_octopusgoa_popgoa_rebsgoa_shal_flatsgoa_thornyheadq_bts_agecompq_bts_biomassq_bts_gap_agecompq_bts_gap_lengthq_bts_gap_sizecompq_bts_gap_specimenq_bts_lengthq_bts_sizecompq_bts_specimenq_catchq_catch_foreignq_dateq_fish_obsq_fish_ticketq_fsh_lengthq_fsh_specimenq_gap_biomassq_lls_lengthq_lls_rpnq_lls_rpn_lengthq_lls_sable_specimenq_nontargetq_pscq_specssetup_folderssharkssql_filtersql_readsql_run

Dependencies:askpassbitbit64blobclicpp11crayondata.tableDBIdplyrfilelockgenericsgetPassglueherehmskeyringlifecyclelubridatemagrittrodbcpillarpkgconfigprettyunitsprogressR6Rcpprlangrprojrootrstudioapistringistringrsystibbletidyselecttidytabletimechangetzdbutf8vctrsvroomwithryaml

Development

Rendered fromdevelopment.Rmdusingknitr::rmarkdownon May 24 2026.

Last update: 2026-04-03
Started: 2026-04-03

gap_check

Rendered fromgap_check.Rmdusingknitr::rmarkdownon May 24 2026.

Last update: 2026-04-03
Started: 2026-04-03

Getting started

Rendered fromgetting-started.Rmdusingknitr::rmarkdownon May 24 2026.

Last update: 2026-04-03
Started: 2026-04-03

Readme and manuals

Help Manual

Help pageTopics
copy the previous SSC accepted model as the new "base" modelaccepted_model
raw data query for the BSAI Atka mackerel assessmentbsai_amak
BSAI Atka mackerel historical catchbsai_amak_catch_1977_1990
raw data query for BSAI arrowtooth flounderbsai_atf
raw data query for BSAI flathead solebsai_fhs
BSAI flathead sole historical catch data 1964-1994bsai_fhs_catch_1964_1994
raw data query for BSAI northern rocksolebsai_nrs
raw data query for BSAI octopusbsai_octopus
raw data query for BSAI other rockfishbsai_orox
Reformat Catch to SS3 structure currently only handles a single fleet, values in tcatch_to_ss3
utility function for sql queriescollapse_filters
utility function to connect to serverconnect
utility function to disconnect from serverdisconnect
Sablefish fmp area key by locationfmp_key
compare GAP updated survey biomass to (now) retired design-based biomass estimatesgap_check_bio
raw data query for the GOA Atka mackerel assessmentgoa_amak
raw data query for GOA arrowtooth foundergoa_atf
GOA arrowtooth flounder historical catch datagoa_atf_catch_1961_1990
raw data query for GOA dusky rockfishgoa_dusk
GOA dusky rockfish historical catch datagoa_dusk_catch_1977_1990
raw data query for GOA flathead solegoa_fhs
GOA flathead sole historical catchgoa_fhs_catch_1978_1990
raw data query for GOA northern rockfishgoa_nork
GOA northern rockfish historical catch datagoa_nork_catch_1961_1992
raw data query for GOA octopusgoa_octopus
GOA Pacific cod historical catchgoa_pcod_catch_1977_1990
GOA Pacific cod historical larval index datagoa_pcod_larval_indices
raw data query for GOA POPgoa_pop
GOA POP historical catch datagoa_pop_catch_1960_1990
GOA POP historical fishery length comp datagoa_pop_fixed_fish_length_comp
raw data query for GOA rougheye/blackspotted rockfishgoa_rebs
GOA rougheye/blackspotted rockfish historical catch datagoa_rebs_catch_1977_2004
raw data query for GOA shallow-water flatfishgoa_shal_flats
raw data query for GOA thorynhead rockfishgoa_thornyhead
query bottom trawl survey agecompsq_bts_agecomp
query bottom trawl survey biomassq_bts_biomass
query GAP bottom trawl survey agecompsq_bts_gap_agecomp
query bottom trawl survey length data from GAP on the AKFIN serverq_bts_gap_length
query GAP bottom trawl survey sizecompsq_bts_gap_sizecomp
query GAP bottom trawl survey specimen data from the AKFIN serverq_bts_gap_specimen
query bottom trawl survey length data from the AFSC serverq_bts_length
query bottom trawl survey sizecompsq_bts_sizecomp
query bottom trawl survey specimen data from the AFSC serverq_bts_specimen
query fishery catch data from AKFIN serverq_catch
query foreign catch data from the AKFIN serverq_catch_foreign
utility function for date of data queryq_date
fishery observer data queryq_fish_obs
query fish ticket dataq_fish_ticket
query fishery length data from the AKFIN serverq_fsh_length
query fishery specimen data from the AKFIN serverq_fsh_specimen
query GAP products bottom trawl survey biomass note: pay attention to the 'design_year' column, particularly for region or depth queries as there may be data duplicatesq_gap_biomass
query nmfs longline survey raw length frequencies at the depth stratum and station levelq_lls_length
query nfms longline survey relative population numbers or weightsq_lls_rpn
query nfms longline survey rpn-weighted length frequenciesq_lls_rpn_length
query nmfs longine survey specimen data (age, length, weight, sex, maturity). only available for sablefish!q_lls_sable_specimen
query non-target species catch estimateq_nontarget
query prohibited species catch (psc) estimateq_psc
Query specsq_specs
GOA POP historical size at age parameters datasaa_pop_60
Sablefish historical abundance datasabl_fixed_abundance
Sablefish age and length comp datasabl_fixed_comps
Sablefish defining areas for age samplessabl_new_areas
vessel lengthssabl_vessel_lengths
Sablefish fixed weights at agesabl_waa
Setup folder structuresetup_folders
raw data query for GOA/BSAI sharkssharks
utility function to filter sql filessql_filter
utility function to read sql filesql_read
utility function to run sql querysql_run