R/change_tail_compression.R

In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

#' Replace tail compression value for length composition data.
#'
#' This function replaces the tail compression value for length composition data
#' in a \code{.dat} file that was read in using \code{\link[r4ss]{SS_readdat}}
#' with those specified in
#' \code{tail_compression}. It then writes a new file with name \code{dat_file_out}
#' into the working directory. If used with \code{\link{run_ss3sim}} the case
#' file should be named \code{tail_compression}. A suggested case letter is
#' \code{T}.
#'
#' @param tail_compression *The new tail_compression value to be used. Must be a
#'   numeric value, as a proportion. For example 0.1 means 10 percent. See the
#'   SS3 manual for further information. A NULL value indicates no action, a
#'   negative value indicates to SS3 to ignore it (not use that feature).
#' @template dat_list
#' @template outfile
#' @return A modified SS3 \code{.dat} file, and that file returned invisibly
#'   (for testing) as a vector of character lines.
#' @template casefile-footnote
#' @author Cole Monnahan
#' @importFrom r4ss SS_writedat
#' @export

change_tail_compression <- function(tail_compression, dat_list,
  outfile = NULL) {

  if(is.null(tail_compression)) return(invisible(NULL))
  stopifnot(is.numeric(tail_compression))

  # The data sections are repeated in the data.ss_new files, so only use first one
  dat_list$comp_tail_compression[1] <- tail_compression
  if (!is.null(outfile)) {
    ss_version <- get_ss_ver_dl(dat_list)
    SS_writedat(dat_list, outfile, overwrite = TRUE,
                version = ss_version, verbose = FALSE)
    }

  invisible(dat_list)
}