Calculates design based estimates from survey data for West Coast surveys.

Usage

Biomass.fn(
  dir = NULL,
  dat,
  strat.vars = c("Depth_m", "Latitude_dd"),
  strat.df,
  printfolder = "forSS3",
  outputMedian = TRUE,
  month = "Enter month",
  fleet = "Enter fleet",
  verbose = TRUE
)

Arguments

dir: Directory where output will be saved. The directory where the file should be saved. If dir = NULL no output will be saved.
dat: Data frame of catch data that has been created by the pull_catch().
strat.vars: Variables in both data frame that are used to define the stratas. Default is bottom depth (m) and latitudes (decimal degrees), i.e., c("Depth_m", "Latitude_dd").
strat.df: A data frame that defines the strata and provides the calculated areas for each strata returned from createStrataDF.fn().
printfolder: A string that will be appended to dir, creating a folder where the output will be saved. If specified as "", the output will just be saved directly in dir. The default is "forSS3".
outputMedian: Logical input to specify whether to output median or the mean biomass estimate. Default TRUE.
month: A single integer value between 1-12. A user input fleet number to assign to the month column based on the expected format for Stock Synthesis. See the Stock Synthesis manual for more information. Default "Enter Month".
fleet: A single integer value. A user input fleet number to assign to the fleet column based on the expected format for Stock Synthesis. Default "Enter Fleet".
verbose: A logical that specifies if you want to print messages and warnings to the console. The default is TRUE.

Value

List of biomass estimates by year, biomass estimates by year and strata, and numbers of fish by year.

Details

The design based index is calculated based on the area of the strata and the mean catch by strata. This function returns a list of design-based estimates by strata and estimates combined across stratas by year. This function is designed to work with data frames pulled from the NWFSC data warehouse using pull_catch(). See: Gunderson, D.R. and Sample, T.M. 1980. Distribution and abundance of rockfish off Washington, Oregon, and California during 1977. Marine Fisheries Review: March - April.

Author

Allan Hicks and Chantel Wetzel

Examples

if (FALSE) {
catch <- pull_catch(
  common_name = "petrale sole",
  survey = "NWFSC.Combo"
)

strata <- CreateStrataDF.fn(
  names = c("shallow_wa", "shallow_or", "shallow_ca", "deep_wa", "deep_or", "deep_ca"),
  depths.shallow = c( 55,   55,   55,  183,  183, 183),
  depths.deep    = c(183,  183,  183,  549,  549, 549),
  lats.south     = c(46.0, 42.0, 32.0, 46.0, 42.0, 32.0),
  lats.north     = c(49.0, 46.0, 42.0, 49.0, 46.0, 42.0))

biommass <- Biomass.fn(
  dat = catch,
  strat.df = strata
)

}