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Calculate stratified mean

Source: R/calc_stratified_mean.R
calc_stratified_mean.Rd

Calculates the stratified mean. This function is actually a wrapper of intermediate functions: strat_prep and strat_mean strat_prep prepares the data set so that the stratified means can be calculated After counting the number of tows and calculating the relative weight of each strata, the resulting output of strat_prep is then passed to the strat_mean function strat_mean calculates 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.

Usage

calc_stratified_mean(
  surveyData,
  areaPolygon = "NEFSC strata",
  areaDescription = "STRATA",
  filterByArea = "all",
  filterBySeason,
  groupDescription = "SVSPP",
  filterByGroup = "all",
  mergesexFlag = T,
  tidy = F,
  returnPrepData = F
)

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

Boolean. Return output in long format (Default = F).

returnPrepData

Boolean. Return both stratmeanData and prepData as a list object. The default (F) returns only the stratmeanData as a data.table.

Value

data frame

See also

Other survdat: calc_swept_area(), 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 stratified mean for specific survey strata for the SPRING season
calc_stratified_mean(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")
# Read in EPU shapefile (loaded as part of the package)
area <- sf::st_read(dsn = system.file("extdata","EPU.shp",package="survdat"),quiet=T)
calc_stratified_mean(surveyData = data$survdat, areaPolygon = area, areaDescription="EPU",
    filterByArea="all",filterBySeason = "all")

} # }