Package 'afscdata'

Description

copy of all base model files, adds a "README.md" file that identifies the model used (or appends the current README), predicated on using the 'afscdata::setup_folders()' function, though has an option for other folder structures. Note, this function copies everything over (e.g., retrospectives) and may take a few minutes to complete

Usage

accepted_model(base_year, base_model, year, folder = NULL)

Arguments

Value

a 'base' model folder with all of the prior years inputs/outputs

Examples

## Not run: 
accepted_model(base_year = 2020, base_model = "m18.2b", year = 2021)

## End(Not run)

Description

raw data query for the BSAI Atka mackerel assessment

Usage

bsai_amak(year, off_yr = FALSE)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
bsai_amak(year = 2023, off_yr = TRUE)

## End(Not run)

Description

A dataset containing historical catch data by year for 1977-1990, pulled from 2022 stock assessment data file.

Usage

bsai_amak_catch_1977_1990

Format

A data frame with 14 observations and 2 variables:

year

1977-1990

catch

catch in tons

Description

raw data query for BSAI arrowtooth flounder

Usage

bsai_atf(year, off_yr = FALSE)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
bsai_atf(year = 2022, off_yr = FALSE)

## End(Not run)

Description

raw data query for BSAI flathead sole

Usage

bsai_fhs(year, off_yr = FALSE)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
bsai_fhs(year = 2022, off_yr = FALSE)

## End(Not run)

Description

A dataset containing trawl gear catch by year for 1964-1994

Usage

bsai_fhs_catch_1964_1994

Format

A data frame with 30 observations and 2 variables:

year

year of catch

catch

weight of catch in 1,000 t

Description

raw data query for BSAI northern rocksole

Usage

bsai_nrs(year, off_yr = FALSE)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
bsai_atf(year = 2022, off_yr = FALSE)

## End(Not run)

Description

raw data query for BSAI octopus

Usage

bsai_octopus(year)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
bsai_octopus(year = 2023)

## End(Not run)

Description

raw data query for BSAI other rockfish

Usage

bsai_orox(year, off_yr = FALSE, catch_report = FALSE)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
bsai_orox(year = 2022, off_yr = FALSE)

## End(Not run)

Description

Reformat Catch to SS3 structure currently only handles a single fleet, values in t

Usage

catch_to_ss3(year, se = 0.01, season = 7, fleet = 1, yld_rat = NULL)

Arguments

Value

saves a csv in output/ with the correct format

Description

adds correct quotes for sql queries, nested within sql_filter

Usage

collapse_filters(x)

Arguments

Description

utility function to connect to server

Usage

connect(db = "akfin")

Arguments

Description

utility function to disconnect from server

Usage

disconnect(db)

Arguments

Description

A dataset containing area definitions

Usage

fmp_key

Format

A data frame with 923 observations and 2 variables:

loc

long_lat

FMP_SUBAREA

defined area for location

Description

compare GAP updated survey biomass to (now) retired design-based biomass estimates

Usage

gap_check_bio(year, species, area, type)

Arguments

Value

a list with orig values, gap values, and a basic report

Examples

## Not run: 
out <- gap_check_bio(year = 2024, species = 30420, type = 'total', area = 'AI' )
out$report

## End(Not run)

Description

raw data query for the GOA Atka mackerel assessment

Usage

goa_amak(year)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
goa_amak(year = 2023)

## End(Not run)

Description

raw data query for GOA arrowtooth founder

Usage

goa_atf(year, off_yr = FALSE)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
goa_atf(year = 2022, off_yr = FALSE)

## End(Not run)

Description

A dataset containing trawl gear catch by year for 1961-1990

Usage

goa_atf_catch_1961_1990

Format

A data frame with 30 observations and 2 variables:

Year

year of catch

Catch

weight of catch in 1,000 t

Description

raw data query for GOA dusky rockfish

Usage

goa_dusk(year, off_yr = FALSE)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
goa_dusk(year = 2022, off_yr = FALSE)

## End(Not run)

Description

A dataset containing trawl gear catch by year for 1977-1990

Usage

goa_dusk_catch_1977_1990

Format

A data frame with 14 observations and 2 variables:

year

year of catch

catch

weight of catch in 1,000 t

Description

raw data query for GOA flathead sole

Usage

goa_fhs(year, off_yr = FALSE)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
goa_fhs(year = 2022, off_yr = FALSE)

## End(Not run)

Description

A dataset containing historical catch data by year for 1978-1990

Usage

goa_fhs_catch_1978_1990

Format

A data frame with 13 observations and 2 variables:

year

1978-1990

catch

catch in tons

Description

raw data query for GOA northern rockfish

Usage

goa_nork(year, off_yr = FALSE)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
goa_nork(year = 2022, off_yr = FALSE)

## End(Not run)

Description

A dataset containing trawl gear catch by year for 1961-1992

Usage

goa_nork_catch_1961_1992

Format

A data frame with 32 observations and 2 variables:

Year

year of catch

Catch

weight of catch in 1,000 t

Description

raw data query for GOA octopus

Usage

goa_octopus(year)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
goa_octopus(year = 2023)

## End(Not run)

Description

A dataset containing historical catch data by year for 1977-1990

Usage

goa_pcod_catch_1977_1990

Format

A data frame with 280 observations and 4 variables:

tons

catch in tons

gear

fishery gear type

year

1977-1990

season

quarterly fishery season

Description

A dataset containing larval index collections year for 1977-2022

Usage

goa_pcod_larval_indices

Format

A data frame with 92 observations and 5 variables:

year

1977-2022

seas

season?

index

index id

obs

observation

se_log

log standard error of obs

Description

raw data query for GOA POP

Usage

goa_pop(year, off_yr = FALSE)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
goa_pop(year = 2022, off_yr = FALSE)

## End(Not run)

Description

A dataset containing trawl gear catch by year for 1961-1990

Usage

goa_pop_catch_1960_1990

Format

A data frame with 30 observations and 2 variables:

year

year of catch

catch

weight of catch in 1,000 t

Description

A dataset containing length comp collection data by year for 1963-1977

Usage

goa_pop_fixed_fish_length_comp

Format

A data frame with 765 observations and 4 variables:

Length

length in cm

value

number of lengths collected

year

1963-1977

hauls_sampled

number of hauls sampled

Description

raw data query for GOA rougheye/blackspotted rockfish

Usage

goa_rebs(year, off_yr = FALSE)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
goa_rebs(year = 2021, off_yr = FALSE)

## End(Not run)

Description

A dataset containing trawl and longline gear catch by year for 1977-2004

Usage

goa_rebs_catch_1977_2004

Format

A data frame with 28 observations and 2 variables:

year

year of catch

catch

weight of catch in t

Details

The catches from 1977-1992 were from Soh (1998), which reconstructs the catch history using an information weighting factor (λ) to combine catch histories from both survey and fishery information. The catches from 1993-2004 were constructed used observer catch data from the FMA Observer Program (Clausen et al. 2004, Appendix A). Observed catches were available from the FMA database by area, gear, and species for hauls sampled by observers. This information was used to calculate proportions of RE/BS catch by gear type. These proportions were then applied to the combined shortraker/rougheye catch from the NMFS Alaska Regional Office to yield estimates of total catch for RE/BS rockfish.

Clausen, D. M., D.H. Hanselman, J.T. Fujioka, and J. Heifetz. 2004. Gulf of Alaska shortraker/rougheye and other slope rockfish. In Stock assessment and fishery evaluation report for the groundfish resources of the Gulf of Alaska, p. 413 – 463. North Pacific Fishery Management Council, 605 W 4th Ave, Suite 306, Anchorage AK 99501. https://apps-afsc.fisheries.noaa.gov/refm/docs/2004/GOAsloperf.pdf

Soh, Sung Kwon. 1998. The use of harvest refugia in the management of shortraker and rougheye rockfish (Sebastes borealis/Sebastes aleutianus) in the Gulf of Alaska. Ph.D. Thesis – University of Washington. 194 pp.

Description

raw data query for GOA shallow-water flatfish

Usage

goa_shal_flats(year, off_yr = FALSE, catch_report = FALSE)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
goa_shal_flats(year = 2022, off_yr = FALSE)

## End(Not run)

Description

raw data query for GOA thorynhead rockfish

Usage

goa_thornyhead(year, off_yr = FALSE, catch_report = FALSE)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
goa_thornyhead(year = 2022, off_yr = FALSE)

## End(Not run)

Description

currently only available for goa and ai total age comps (not strata)

Usage

q_bts_agecomp(year, species, area, db, print_sql = FALSE, save = TRUE)

Arguments

Details

for the goa and ai there is a "type" switch that queries by stratum, or total - !!stratum should not be used at the moment !!. only one of these can be used at a time.

Value

saves bts agecomp data as data/raw/area_bts_age_data.csv and area_bts_age_specimen_data.csv or outputs to the global environment, also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect("afsc")
q_bts_agecomp(year=2022, species=21921, area = "goa", db = db)

## End(Not run)

Description

probably need to beef up the documentation on the "by" switch

Usage

q_bts_biomass(
  year,
  species,
  area,
  type = "total",
  db,
  print_sql = FALSE,
  save = TRUE
)

Arguments

Details

six areas are available to query from bs = bering sea + northwest 1987-present (includes nw stations) - recommended bsslope = bering sea slope nbs = northern bering sea ai = aleutian islands goa = gulf of alaska old_bs = bering sea standard 1982-present (minus ~20 stations in nw) - not recommended

for the goa and ai there is a "type" switch that queries by depth, stratum, area, total, or uses the inpfc table or inpfc by depth table only one of these can be used at a time.

Value

saves bts biomass data as data/raw/area_(type)_bts_biomass_data.csv or outputs to the global environment, also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect("akfin")
q_bts_biomass(year=2022, species=21921, area = "goa", type = "depth", db = db)

## End(Not run)

Description

query GAP bottom trawl survey agecomps

Usage

q_bts_gap_agecomp(year, species, area, db, print_sql = FALSE, save = TRUE)

Arguments

Value

saves bts length data as data/raw/bts_gap_agecomp_data.csv or outputs to the global environment, also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect()
q_bts_gap_agecomp(year=2022, species=21921, area = "goa", db = db)

## End(Not run)

Description

query bottom trawl survey length data from GAP on the AKFIN server

Usage

q_bts_gap_length(year, species, area, db, print_sql = FALSE, save = TRUE)

Arguments

Value

saves bts length data as data/raw/bts_length_data.csv or outputs to the global environment, also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect()
q_bts_gap_length(year=2022, species=10110, area = "goa", db = db)

## End(Not run)

Description

query GAP bottom trawl survey sizecomps

Usage

q_bts_gap_sizecomp(year, species, area, db, print_sql = FALSE, save = TRUE)

Arguments

Value

saves bts sizecomp data as data/raw/area_bts_gap_sizecomp_data.csv or outputs to the global environment, also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect()
q_bts_gap_sizecomp(year=2022, species=21921, area = "goa", db = db)

## End(Not run)

Description

query GAP bottom trawl survey specimen data from the AKFIN server

Usage

q_bts_gap_specimen(year, species, area, db, print_sql = FALSE, save = TRUE)

Arguments

Value

saves bts length data as data/raw/bts_length_data.csv or outputs to the global environment, also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect()
q_bts_gap_specimen(year=2022, species=21921, area = "goa", db = db)

## End(Not run)

Description

query bottom trawl survey length data from the AFSC server

Usage

q_bts_length(year, species, area, db, print_sql = FALSE, save = TRUE)

Arguments

Value

saves bts length data as data/raw/bts_length_data.csv or outputs to the global environment, also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect("afsc")
q_bts_length(year=2022, species=10110, area = "goa", db = db)

## End(Not run)

Description

currently only available for goa and ai total size comps

Usage

q_bts_sizecomp(year, species, area, db, print_sql = FALSE, save = TRUE)

Arguments

Value

saves bts sizecomp data as data/raw/area_bts_sizecomp_data.csv or outputs to the global environment, also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect("afsc")
q_bts_sizecomp(year=2022, species=21921, area = "goa", db = db)

## End(Not run)

Description

query bottom trawl survey specimen data from the AFSC server

Usage

q_bts_specimen(year, species, area, db, print_sql = FALSE, save = TRUE)

Arguments

Value

saves bts length data as data/raw/bts_length_data.csv or outputs to the global environment, also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect("afsc")
q_bts_length(year=2022, species=21921, area = "goa", db = db)

## End(Not run)

Description

Note that this function produces results that may be confidential. They can be hidden from git/GitHub by adding fish_catch_data.csv to your .gitignore file

Usage

q_catch(
  year,
  species,
  area,
  db,
  add_fields = NULL,
  print_sql = FALSE,
  save = TRUE
)

Arguments

Value

saves catch data as data/raw/fish_catch_data.csv or outputs to the global environment, save also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect()
q_catch(year=2022, species="NORK", area="goa", db=db)

## End(Not run)

Description

something about the species names and area codes, since they are so different from everything else? pulls data from AKFIN pre1991.foreign_blend table

Usage

q_catch_foreign(year, species, area, db, print_sql = FALSE, save = TRUE)

Arguments

Value

saves catch data as data/raw/for_catch_data.csv or outputs to the global environment, also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect()
q_catch_foreign(year=2022, species="sablefish", area = 54:57, db = db)

## End(Not run)

Description

utility function for date of data query

Usage

q_date(year, loc = NULL)

Arguments

Value

a query date file saved as year/data/raw/data_called.txt

Description

currently setup for pulling haul level detail for age or length compositions

Usage

q_fish_obs(year, species, area, db, print_sql = FALSE, save = TRUE)

Arguments

Value

saves observer data as data/raw/fish_obs_data.csv or outputs to the global environment, save also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect()
q_fish_obs(year=2022, species=301, area="goa", db=db)

## End(Not run)

Description

query fish ticket data

Usage

q_fish_ticket(
  year,
  species,
  area,
  db,
  add_fields = NULL,
  print_sql = FALSE,
  save = TRUE
)

Arguments

Value

saves fish ticket data as data/raw/fishticket_data.csv or outputs to the global environment, save also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
q_fish_ticket(year=2022, species="NORK", area="goa", db=db)

## End(Not run)

Description

query fishery length data from the AKFIN server

Usage

q_fsh_length(
  year,
  species,
  area,
  db,
  add_fields = NULL,
  print_sql = FALSE,
  save = TRUE
)

Arguments

Value

saves fishery length data as data/raw/fish_length_data.csv or outputs to the global environment, also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect("akfin")
q_fsh_length(year=2022, species=301, area="goa", db=db)

## End(Not run)

Description

query fishery specimen data from the AKFIN server

Usage

q_fsh_specimen(
  year,
  species,
  area,
  db,
  add_fields = NULL,
  print_sql = FALSE,
  save = TRUE
)

Arguments

Value

saves fishery specimen data as data/raw/fish_specimen_data.csv or outputs to the global environment, also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect("akfin")
q_fsh_specimen(year=2022, species=301, area = "goa", db = db)

## End(Not run)

Description

six areas are available to query from bs = bering sea + northwest 1987-present (includes nw stations) - recommended bsslope = bering sea slope nbs = northern bering sea ai = aleutian islands goa = gulf of alaska old_bs = bering sea standard 1982-present (minus ~20 stations in nw) - not recommended

Usage

q_gap_biomass(
  year = 2024,
  species = 10110,
  area = "goa",
  type = "region",
  design_yr = 2025,
  db,
  print_sql = FALSE,
  save = TRUE
)

Arguments

Value

saves bts biomass data as data/raw/(area)_(type)_bts_biomass_data.csv or outputs to the global environment, also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect()
q_gap_biomass(year=2024, species=10110, area="bs", type="region", db=db)

## End(Not run)

Description

longline database documentation available on akfin

Usage

q_lls_length(
  year,
  species,
  area = c("goa", "bs", "ai"),
  use_historical = FALSE,
  db,
  print_sql = FALSE,
  save = TRUE
)

Arguments

Details

primarily used in stock assessments for calculating sample size tables

sex-specific lengths are collected for sablefish, giant grenadier, spiny dogfish, pacific cod, and greenland turbot (starting in 2021!). sex codes: 1=male, 2=female, 3=unknown

source table on akfin: lls_length_summary_view

Value

saves lls length data as data/raw/lls_length_data.csv or outputs to the global environment. also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
# raw sablefish length frequencies in 1988 (year when the domestic survey started) 
# in the gulf of alaska

db <- connect("akfin")
q_lls_length(year=1988, species=20510, area="goa", db=db)

## End(Not run)

Description

longline database documentation available on akfin

Usage

q_lls_rpn(
  year,
  species,
  area = c("goa", "bs", "ai"),
  by = "fmpsubarea",
  use_historical = FALSE,
  db,
  print_sql = FALSE,
  save = TRUE
)

Arguments

Details

variables of interest: cpue = numbers per skate (1 skate = 45 hooks); relative population numbers (rpns) = area-weighted cpue (area estimates are defined by depth strata and geographic area), relative population weights (rpw) = rpn multiplied by mean fish weight, which is calculated using an allometric relationship and the mean length of fish collected in a given strata and geographic area.

methods for variance estimation of these indices are documented on p 26 the 2016 sablefish safe pdf (p 350 of the goa safe).

the time series starts for the domestic longline survey in the bs and ai starts in 1996, and there are historical data available in the bs/ai from the cooperative Japanese/U.S. survey. in the modern/domestic survey, the eastern ai are surveyed in even years, and the bs is surveyed in odd years. the longline survey does not sample the western ai. estimates in nw and sw ai are based on fixed ratios in the ne and se ai, respectively, from historical cooperative Japanese/U.S. surveys in 1979-1994.

sablefish: includes data from strata 3-7 (depths 201-1000 m) and rpns are adjusted for sperm whale depredation

all other species: includes data from all strata (depths 151-1000 m)

source tables on akfin: lls_area_stratum_rpn lls_area_stratum_rpn_depred lls_area_rpn_all_strata lls_area_rpn_3_to_7 lls_area_rpn_3_to_7_depred lls_council_sablefish_area_all_strata lls_council_sablefish_area_3_to_7_depred lls_fmp_subarea_all_strata lls_fmp_subarea_3_to_7_depred lls_ak_wide_3_to_7_depred

Value

saves lls rpn/rpw data as data/raw/lls_rpn_(by)_data.csv or outputs to the global environment. also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- connect("akfin")
# sablefish domestic survey rpn/rpw time series (1990-2022) by goa fmp subarea (wgoa,
# cgoa, egoa). note that sablefish rpns are corrected for sperm whale
# depredation and only include data from strata 3-7

q_lls_rpn(year=2022, species=20510, area='goa', by='fmpsubarea', db=db, save = FALSE)

# pcod domestic survey rpn/rpw time series by bering sea geographic area and
# depth stratum. note that the domestic bs time series is odd years starting in
# 1997 (ai starts in 1996).

q_lls_rpn(year=2022, species=21720, area='bs', by='depth', db=db, save=FALSE) 

## End(Not run)

Description

longline database documentation available on akfin

Usage

q_lls_rpn_length(
  year,
  species,
  area = c("goa", "bs", "ai"),
  by = "fmpsubarea",
  use_historical = FALSE,
  db,
  print_sql = FALSE,
  save = TRUE
)

Arguments

Details

sablefish: includes data from strata 3-7 (depths 201-1000 m) and rpns are adjusted for sperm whale depredation

all other species: includes data from all strata (depths 151-1000 m)

sex-specific lengths are collected for sablefish, giant grenadier, spiny dogfish, pacific cod, and greenland turbot (starting in 2021!). sex codes: 1=male, 2=female, 3=unknown

results only include geographic/stratum areas that are used for rpns calc (i.e., exploitable == 1). also ' records with length = 999 have been removed. these records are present in the database to account for instances when there ' was catch in a stratum/station but no lengths collected. the ' 999 lengths ensure rpns sum properly to the area-level but should not be included in the length compositions.

available source tables on akfin: lls_length_area_3_to_7_depred lls_length_area_all_strata

Value

saves lls rpn-weighted length frequency data as data/raw/lls_rpn_length_data.csv or outputs to the global environment. also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
db <- afscdata::connect("akfin")
# sablefish domestic longline survey rpn-weighted length frequencies (1990-2022) for
# goa and bsai. note that sablefish rpns are corrected for sperm whale 
# depredation and only include data from strata 3-7

q_lls_rpn_length(year=2022, species=20510, area=c('bsai','goa'), db=db, save=FALSE)

# pcod domestic longline survey rpn-weighted length frequencies (1997-2022,
# odd years only) for the bering sea

q_lls_rpn_length(year=2022, species=21720, area='bs', db=db, save=FALSE) 

## End(Not run)

Description

longline database documentation available on akfin

Usage

q_lls_sable_specimen(
  year,
  area = c("goa", "bs", "ai"),
  use_historical = FALSE,
  db = akfin,
  print_sql = FALSE,
  save = TRUE
)

Arguments

Details

source table on akfin: afsc.lls_age_view

Value

saves lls sablefish specimen data as data/raw/lls_specimen_data.csv or outputs to the global environment. also saves a copy of the SQL code used for the query and stores it in the data/sql folder.

Examples

## Not run: 
# sablefish specimen data in 1996 (first year ages were collected in the goa domestic survey) 
# in the gulf of alaska

q_lls_specimen(year=2000, area="goa", db=db)

## End(Not run)

Description

non-target catch estimates by weight (or numbers)

Usage

q_nontarget(year, target, area, db, save = TRUE)

Arguments

Value

a csv of non-target species catch by trip target group, saved in the data/output folder

Examples

## Not run: 
akfin = afscdaya::connect()
q_nontarget(year=2022, target="k", area="goa", db=akfin, save=FALSE)
disconnect(akfin)

## End(Not run)

Description

prohibited species catch (PSC) estimates reported in tons for halibut and herring, counts for salmon, crabs and other fish. Note that you can combine trip target codes c("k", "x") and regions - though results will be lumped together

Usage

q_psc(year, target, area, db, save = TRUE)

Arguments

Value

a csv of prohibited species catch by trip target group, saved in the data/output folder

Examples

## Not run: 
akfin = connect()
q_psc(year=2022, target="k", area="goa", db=akfin, save=FALSE)
disconnect(akfin)

## End(Not run)

Description

Query specs

Usage

q_specs(year, species, area, db, print_sql = FALSE, save = TRUE)

Arguments

Examples

## Not run: 
db = connect()
q_specs(year=2024, species='PCOD', area='BSAI', db=db, save=F)

## End(Not run)

Description

A dataset containing size at age parameters for POP <= 1960

Usage

saa_pop_60

Format

A data frame with 1 observations and 5 variables:

linf

von B parameter

k

von B parameter

t0

von B parameter

a

a parameter

b

b parameter

Description

A dataset containing both fixed gear and trawl gear catch, cpue, rpn & rpw data by year

Usage

sabl_fixed_abundance

Format

A data frame with 121 observations and 5 variables:

year

year

value

weight of catch in 1,000 t, or relative abundance

variable

rpw, rpn, cpue, or catch

fleet

japan or domestic

gear

lls = longline survey, llf = longline fishery, tf = trawl fishery

Description

A dataset containing both age and length composition data for multiple fisheries and surveys

Usage

sabl_fixed_comps

Format

A data frame with 2010 observations and 7 variables:

year

year

fleet

japan or domestic

type

age or length

gear

lls = longline survey, tf = trawl fishery, ts = trawl survey

age

if relevant, otherwise NA

length

length cm if relevant, otherwise NA

comp

age or length

sex

male, female or NA

Description

A dataset containing area definitions

Usage

sabl_new_areas

Format

A data frame with 15 observations and 2 variables:

NMFS_AREA

area number

AREA_NAME

assignment for area number

Description

Vessel lengths for calculating whale depredation rates in the sablefish fishery

Usage

sabl_vessel_lengths

Format

A data frame with 7558 observations and 2 variables:

VESSEL_CODE

vessel id

LENGTH

length of the vessel

Description

A dataset containing weights at age for two time blocks, by sex

Usage

sabl_waa

Format

A data frame with 90 observations and 3 variables:

waa

weight at age

sex

male or female

timeblock

current or old

Description

Creates a common folder structure for assessment data

Usage

setup_folders(
  year,
  dirs = c("raw", "user_input", "output", "sara", "sql"),
  tier = NULL
)

Arguments

Value

creates a designated/named folder structure

Examples

## Not run: 
setup(2022)

## End(Not run)

Description

raw data query for GOA/BSAI sharks

Usage

sharks(year, area)

Arguments

Value

a suite of raw data .csv files and a time stamp of when the query was done

Examples

## Not run: 
sharks(year = 2023, area = "goa")

## End(Not run)

Description

utility function to filter sql files

Usage

sql_filter(sql_precode = "IN", x, sql_code, flag = "-- insert species")

Arguments

Examples

## Not run: 
.d = sql_filter(sql_precode = "<=", 2011, sql_code = .d, flag = "-- insert year")

## End(Not run)

Description

utility function to read sql file

Usage

sql_read(x)

Arguments

Examples

## Not run: 
.d = sql_read("fsh_catch.sql")

## End(Not run)

Description

utility function to run sql query

Usage

sql_run(database, query)

Arguments

Examples

## Not run: 
.d = sql_read("fsh_catch.sql")
.d = sql_filter(sql_precode = "<=", 2011, sql_code = .d, flag = "-- insert year")
.d = sql_filter(x = area, sql_code = .d, flag = "-- insert region")
.d = sql_filter(sql_precode = "IN", x = c("PEL7", "PELS"), 
                   sql_code = .d, flag = "-- insert species")

afsc = DBI::dbConnect(odbc::odbc(), "afsc", UID = "afsc_user", PWD = "afsc_pwd") 
 
sql_run(afsc, query) %>%
         vroom::vroom_write(here::here(year, 'data', 'raw', 'fsh_catch_data.csv'))
DBI::dbDisconnect(afsc)

## End(Not run)