Calculate unexpanded/raw length or marginal age compositions

Usage

get_raw_caal(
  data,
  len_bins,
  age_bins,
  length_column_name = "length_cm",
  age_column_name = "age",
  dir = NULL,
  month = "Enter Month",
  fleet = "Enter Fleet",
  partition = 0,
  ageerr = "Enter Numeric",
  printfolder = "forSS3",
  verbose = TRUE
)

Arguments

data: A data frame that includes columns of year, sex, and length/ages. The data frame can be survey data pulled using pull_bio from the data warehouse or any data frame that includes column names of sex, year, and the comp_column_name. The sex column is expected to have sexes denoted by F, M, and U.
length_column_name: The length column name to create conditional age-at-length data for. The default is length_cm.
age_column_name: The age column name to create conditional age-at-length data for. The default is age.
dir: Directory where output will be saved. The directory where the file should be saved. If dir = NULL no output will be saved.
month: Month the samples were collected based on the expected format for Stock Synthesis to determine the length/age estimate to compare to. Default "Enter Month".
fleet: A fleet number to assign the composition data to based on the expected format for Stock Synthesis. Default "Enter Fleet".
partition: Partition to assign the composition data based on the expected format for Stock Synthesis. Partition of 0 indicates that the composition data include all composition data, 1 for discarded composition data, and 2 for retained fish only. Default of 0.
ageerr: Number of ageing error vector to apply to the age data based on Stock Synthesis. Default "Enter Numeric".
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

A data frame of conditiona age-at-length compositions for sexed and unsexed fish formatted for Stock Synthesis.

Details

Creates a matrix of unexpanded (or raw) marginal length or age composition data formatted for Stock Synthesis. The code will return composition data for all sexes present in the data frame and no sex assignment is done for unsexed fish. The function will create composition data for either lengths or ages based on the comp_column_name. The function will return a list of composition data based upon the sexes present in the data for a two-sex model or all length/ages for single-sex model.

Author

Chantel Wetzel

Examples

if (FALSE) { # \dontrun{
bio <- pull_bio(
  common_name = "lingcod",
  survey = "NWFSC.Combo"
)

caal_data <- get_raw_comps(
  data = bio,
  len_bins = seq(20, 70, 4),
  age_bins = 1:30,
)
} # }