R/UnexpandedAF.fn.R

In nwfsc-assess/nwfscSurvey: Northwest Fisheries Science Center Survey

#' Creates a matrix of length or age composition data WITHOUT expantion
#' Written by Chantel Wetzel to work with the data warehouse data formatting,
#'
#' @param dir directory this is where the output files will be saved
#' @param datA the read in length comps by the PullBio.fn function
#' @param ageBins length bins
#' @param sex (0 = unsexed, 1 = females, 2 = males, 3 = females then males) sex value for Stock Synthesis
#' @param partition partition for Stock Synthesis
#' @param fleet fleet number
#' @param ageErr Number of ageing error matrix for SS
#' @param agelow age bin for SS (default value of -1)
#' @param agehigh age bin for SS (default value of -1)
#' @param month month the samples were collected
#' @param printfolder folder where the length comps will be saved
#' @template verbose
#'
#' @author Chantel Wetzel
#' @export

UnexpandedAFs.fn <- function(dir = NULL, datA, ageBins = 1, sex = 3, partition = 0, fleet = "Enter Fleet",
                             ageErr = "NA", agelow = -1, agehigh = -1, month = "Enter Month", printfolder = "forSS", verbose = TRUE) {

  # Overwrite inputs to use the same code for lengths as ages
  datL <- datA
  lgthBins <- ageBins
  datL$Length_cm <- datA$Age

  out <- UnexpandedLFs.fn(
    dir = dir,
    datL = datL,
    lgthBins = lgthBins,
    sex = sex,
    partition = partition,
    fleet = fleet,
    month = month,
    ageErr = ageErr,
    agelow = agelow,
    agehigh = agelow,
    printfolder = "forSS",
    verbose = TRUE
  )

  return(out)
}