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

Usage

get_design_based(
  data,
  strata,
  CI = 0.95,
  dir = NULL,
  month = NA,
  fleet = NA,
  printfolder = "forSS3",
  verbose = TRUE
)

Arguments

data: Data frame of catch data that has been created by the pull_catch().
strata: A data frame that defines the strata and provides the calculated areas for each strata returned from createStrataDF.fn().
CI: A numerical value that specifies the confidence interval to return. Values should be between 0.01 to 0.99.
dir: Directory where output will be saved. The directory where the file should be saved. If dir = NULL no output will be saved.
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".
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".
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 and biomass estimates by year and strata. The biomass estimates are in metric tons.

Details

The design based index is calculated based on the area of the strata with the output estimates representing the adjusted median estimates (e.g., est * exp(0.5*log(var)). 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) { # \dontrun{
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 <- get_design_based(
  data = catch,
  strata = strata
)
} # }