Creates a matrix of length or age composition data WITHOUT expansion

Usage

process_comps_unexpanded(
  dir = NULL,
  datL,
  lgthBins = 1,
  sex = lifecycle::deprecated(),
  partition = 0,
  fleet = "Enter Fleet",
  ageErr = "NA",
  agelow = -1,
  agehigh = -1,
  month = "Enter Month",
  two_sex_model = TRUE,
  printfolder = "forSS",
  verbose = TRUE
)

Arguments

dir: directory this is where the output files will be saved
datL: the read in length comps by the PullBio.fn function
lgthBins: A vector on length bins or age bins to group the data for Stock Synthsis
sex: Deprecated with nwfscSurvey 2.2.1 (February 2023). The function will now output female/male and unsexed compositions if present in the data frame datL
partition: partition for Stock Synthesis
fleet: fleet number
ageErr: Number of ageing error matrix for Stock Synthesis
agelow: age bin for Stock Synthesis (default value of -1)
agehigh: age bin for Stock Synthesis (default value of -1)
month: month the samples were collected used by Stock Synthesis to determine the length/age estimate to compare to.
two_sex_model: Default TRUE. If TRUE and unsexed composition data are present the unsexed comps will be output in the format needed for a two-sex model in Stock Synthesis.
printfolder: folder where the length comps will be saved
verbose: A logical value specifying whether or not to print out message statements to the screen while using this function. The default is to print all messages, i.e., verbose = TRUE.

Author

Chantel Wetzel