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Pull AFSC GAP BTS survey data

get_data.Rd

Pulls survey, cruise, haul, catch, size, specimen (age), stratum, subarea, stratum grouping information for the region, years, and species of interest from the RACEBASE, RACE_DATA, and GAP_PRODUCTS schemata in the AFSC Oracle database.

Usage

get_data(
  year_set = c(1996, 1999),
  survey_set = c("GOA", "AI", "EBS", "NBS", "BSS")[1],
  spp_codes = c(21720, 30060, 10110),
  haul_type = 3,
  abundance_haul = c("Y", "N")[1],
  pull_lengths = FALSE,
  taxonomic_source = c("RACEBASE.SPECIES_CLASSIFICATION",
    "GAP_PRODUCTS.TAXONOMIC_CLASSIFICATION")[1],
  remove_na_strata = FALSE,
  na_rm_strata = lifecycle::deprecated(),
  channel = NULL,
  sql_channel = lifecycle::deprecated()
)

Arguments

year_set

numeric or integer vector of years

survey_set

character string. One of c("GOA", "AI", "EBS", "NBS", "BSS").

spp_codes

two-column data.frame of species codes (column name SPECIES_CODE) and GROUP_CODE name (column name GROUP_CODE). For single-species, the GROUP_CODE and species codes can be the same. Examples: 1) For a mixture of individual taxa and taxon groups: data.frame("SPECIES_CODE" = c(21720, 21220, 21230, 21232), "GROUP_CODE" = c(21720, "Grenadiers", "Grenadiers", "Grenadiers")) 2) For single taxa: c(21720, 21740, 10110) 3) FOR PRODUCTION PURPOSES: a NULL value by default uses GAP_PRODUCTS.TAXON_GROUPS from the AFSC Oracle database.

haul_type

integer. Defaults to haul type "3" for "standard bottom sample (preprogrammed station)" used for production purposes.

abundance_haul

character string. "Y" are standardized hauls used in production and "N" are non-standard hauls due to bad performance, different gear, etc.

pull_lengths

boolean T/F. Should length and specimen data be pulled? Defaults to FALSE for speed.

taxonomic_source

character string. Table used to source taxonomic information. One of two options: "RACEBASE.SPECIES" (default) or "GAP_PRODUCTS.TAXONOMIC_CLASSIFICATION". "GAP_PRODUCTS.TAXONOMIC_CLASSIFICATION" is still a provisional table is an option for testing only.

remove_na_strata

boolean. Remove hauls with NA stratum information. Defaults to FALSE.

na_rm_strata

[Deprecated] Use the remove_na_strata argument instead.

channel

connection to Oracle created via gapindex::get_connected() or RODBC::odbcConnect().

sql_channel

[Deprecated] Use the channel argument instead.

Value

a named list containing survey_design, survey, cruise, haul, catch, size (if pull_lengths == TRUE), specimen (if pull_lengths == TRUE), species, stratum, subarea, and stratum_groups information for the survey, years, and species of interest.