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Calculate swept area biomass

Source: R/calc_swept_area.R
calc_swept_area.Rd

This function is a wrapper of intermediate functions calc_stratified_mean and swept_area. The calc_stratified_mean function is used to calculate the stratified mean biomass and abundance for each group (e.g. species) and season, as well as the variance and standard error of the mean. The resulting output of calc_stratified_mean is then passed to the swept_area function which calculates the total biomass/abundance estimates.

Usage

calc_swept_area(
  surveyData,
  areaPolygon = "NEFSC strata",
  areaDescription = "STRATA",
  filterByArea = "all",
  filterBySeason = "all",
  groupDescription = "SVSPP",
  filterByGroup = "all",
  mergesexFlag = TRUE,
  tidy = FALSE,
  q = NULL,
  a = 0.0384
)

Arguments

surveyData

Data table. NEFSC survey data generated by get_survdat_data.R

areaPolygon

sf object or character string. Default = "NEFSC strata". The default option uses the survey strata shapefile bundled with the package. To use any other shapefile for stratification, the shapefile must be read in as an sf object and the areaDescription argument must be specified.

areaDescription

Character String. Column name from areaPolygon that contains the strata designations.

filterByArea

Numeric vector. Set of areas to subset from the areaDescription of the areaPolygon.

filterBySeason

Character string. Which seasons of the surveyData should be included. Choices include "SPRING", "FALL", or "all".

groupDescription

Character string. Column of prepData which contains the groups (e.g. "SVSPP") on which the means are based.

filterByGroup

Character or numeric vector. Set of groups to subset from groupDescription. The default "all" will calculate means for all groups.

mergesexFlag

Boolean. Logical value to merge sexed species such as dogfish.

tidy

[Deprecated] Logical. The tidy argument is deprecated and will be removed in the next version. The function will soon strictly return tidy output. Currently controls whether the output is formatted as a tidy dataset.

q

Data frame. Table of survey catchabilities with a column corresponding to groupDescription and a column of catchabilities. If NULL, assumes a q of 1 for each groupDescription (Minimum swept area estimates).

a

Numeric. The average swept area of the trawl. Default value is the swept area of a standard NOAA Ship Albatross IV tow. (NEFSC, 2006)

Value

data frame

Source

43rd Northeast Regional Stock Assessment Workshop (43rd SAW). 2006. **43rd SAW assessment report.** US Dep. Commer., Northeast Fish. Sci. Cent. Ref. Doc. 06-25; 400 p.

See also

Other survdat: calc_stratified_mean(), get_area(), get_mass_inshore_survey_data(), get_survdat_data(), get_survdat_scallop_data()

Examples

if (FALSE) { # \dontrun{
# Pull data and apply conversion corrections
data <- get_survdat_data(channel)
# Calculate swept area biomass for specific survey strata for the
# SPRING season
calc_swept_area(
  surveyData = data$survdat,
  filterByArea = c(1220, 1240, 1260:1290, 1360:1400),
  filterBySeason = "SPRING"
)

# Calculate stratified mean for area defined by EPU regions, for all
# seasons ("SPRING", "FALL") and return in Tidy format
# Read in EPU shapefile (loaded as part of the package)
area <- sf::st_read(
  dsn = system.file("extdata", "EPU.shp", package = "survdat"),
  quiet = TRUE
)
calc_swept_area(
  surveyData = data$survdat,
  areaPolygon = area,
  areaDescription = "EPU",
  filterByArea = "all",
  filterBySeason = "all",
  tidy = TRUE
)

} # }