q_lls_rpn.Rdlongline database documentation available on akfin
q_lls_rpn(
year,
species,
area = c("goa", "bs", "ai"),
by = "fmpsubarea",
use_historical = FALSE,
db,
print_sql = FALSE,
save = TRUE
)max year to retrieve data from
5 digit afsc/race species code(s) e.g., 20510 for sablefish or c(30576, 30050) for both shortraker and rougheye/blackspotted
options are 'goa', 'bs', 'ai', or a combo. default=c('goa', 'bs', 'ai')
'depth' (stratum-level), 'geoarea' (e.g. Spencer Gully, Kodiak slope), 'councilarea' (e.g., West Yakutat, East Yakutat/Southeast), 'fmpsubarea' (e.g., Eastern Gulf of Alaska), or 'akwide' (only for sablefish). default: 'fmpsubarea' - can only call a single area. note that variances are not available at the depth stratum level (by = 'depth')
T/F include historical Japanese survey data in the results (default: false)
the database to query (akfin)
outputs the sql query instead of calling the data (default: false) - save must be false
save the file in designated folder, if FALSE outputs to global environment
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.
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
if (FALSE) {
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)
}