Calculate numerical CPUE at length by haul — calc_sizecomp

Uses Equation 16 in Wakabayashi et al. 1985 to calculate numbers-catch-per-unit-effort (CPUE, Numbers/km2) at length.

Usage

calc_sizecomp_stratum(
  racebase_tables = deprecated(),
  gapdata = NULL,
  racebase_cpue = deprecated(),
  cpue = NULL,
  racebase_stratum_popn = deprecated(),
  abundance_stratum = NULL,
  spatial_level = c("stratum", "haul")[1],
  fill_NA_method = c("AIGOA", "BS")[1]
)

Arguments

racebase_tables: Use the gapdata argument instead.
gapdata: data object created from gapindex::get_data()
racebase_cpue: Use the cpue argument instead.
cpue: catch per unit effort object created from gapindex::calc_cpue().
racebase_stratum_popn: Use the abundance_stratum argument instead.
abundance_stratum: biomass/abundance by stratum object created from gapindex::calc_biomass_stratum()
spatial_level: string, one of c("stratum", "haul"). Should size compositions be calculated at the level of the "stratum" (used for standard size compositions) or "haul" (used for ModSquad model-based data-inputs).
fill_NA_method: string, one of c("AIGOA", "BS"). This argument changes the way hauls with positive weights but no associated size data are dealt with. In the EBS, NBS, and BSS survey regions ("BS"), these hauls contribute to the dummy length -9 category for their respective strata. In the AI and GOA survey regions ("AIGOA"), an average size distribution is applied to these hauls so the length -9 category does not exist in the AI or GOA versions of the size composition.

Value

Field	Description
LENGTH_MM	Length bin in millimeters. A length of -9 indicates cases where no lengths were collected within a stratum for a species/year, even though catch numbers were recorded.
POPULATION_COUNT	The estimated population caught in the survey for a species, group, or total for a given survey.
SEX	Sex of a specimen where "1" = "Male", "2" = "Female", "3" = Unsexed.
SPECIES_CODE	The species code of the organism associated with the common_name and scientific_name columns. For a complete species list, review the code books.
STRATUM	RACE database statistical area for analyzing data. Strata were designed using bathymetry and other geographic and habitat-related elements. The strata are unique to each survey region. Stratum of value 0 indicates experimental tows.
SURVEY	Name and description of survey. The column survey is associated with the srvy and survey_definition_id columns.
SURVEY_DEFINITION_ID	The survey definition ID key code is an integer that uniquely identifies a survey region/survey design. The column survey_definition_id is associated with the srvy and survey columns. Full list of survey definition IDs are in RACE_DATA.SURVEY_DEFINITIONS and in the code books.
YEAR	Year the observation (survey) was collected.