Creates a matrix of unexpanded age compositions

Usage

UnexpandedAFs.fn(
  dir = NULL,
  datA,
  ageBins = 1,
  sex = 3,
  partition = 0,
  fleet = "Enter Fleet",
  ageErr = "NA",
  agelow = -1,
  agehigh = -1,
  month = "Enter Month",
  printfolder = "forSS3",
  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.
datA: A data frame of length-composition data returned from pull_bio().
ageBins: Vector of age bins to create age compositions across. Values above or below the minimum or maximum values, respectively, are grouped into the first age or plus group age.
sex: Options of (0, 1, 2, 3). The integer will be used to define the sex column of the returned input for Stock Synthesis and specifies how the composition are treated with respect to sex. See the Stock Synthesis manual for more information. In short, 0 is for unsexed, 1 is females, 2 is males, and 3 is females and males. The default is 3.
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.
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".
ageErr: Single interget value of ageing error vector to apply to the age data based on Stock Synthesis. Default "Enter".
agelow: Lower age bin for all age composition data based on the expected format for Stock Synthesis. Default value of -1 which translates to the lowest age bin.
agehigh: Upper age bin for all age composition data based on the expected format for Stock Synthesis. Default value of -1 which translates to the highest
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".
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.

Author

Chantel Wetzel