R/sample_lcomp.R

In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

#' Sample length compositions from a Stock Synthesis data file
#' 
#' Extract length-composition data from a \code{.ss_new} data file and sample
#' the data. It is assumed that the composition data will be expected values
#' as written by Stock Synthesis in the second section of the data file, but 
#' one can also sample input data. The resulting length-composition
#' data are assumed to represent observed length composition and will overwrite
#' the length data in \code{dat_list}, which is returned invisibly. 
#' The data file can also be written to the disk, if a file path is provided to
#' \code{outfile}, and used as simulated data by an estimation model.
#' If used with \code{\link{run_ss3sim}}, the case file should be named
#' \code{agecomp}. A suggested (default) case letter is \code{D} for data.
#'
#' @author Cole Monnahan and Kotaro Ono
#'
#' @template lcomp-agecomp-index
#' @template lcomp-agecomp
#' @template dat_list
#' @template outfile
#' @template Nsamp
#' @template sampling-return
#' @template casefile-footnote
#' @importFrom r4ss SS_writedat
#'
#' @examples
#' dat_list <- r4ss::SS_readdat(verbose = FALSE,
#'   file = system.file(file.path("extdata", "models", "cod-om", "codOM.dat"), 
#'   package="ss3sim"))
#' ## Generate with constant sample size across years
#' ex1 <- sample_lcomp(dat_list=dat_list, outfile = NULL, 
#'   fleets = 1:2, Nsamp = list(100, 50), 
#'   years=list(seq(26, 100, by = 2), 80:100))
#'
#' @export
#' @family sampling functions
#' @seealso \code{\link{sample_agecomp}} for more examples

sample_lcomp <- function(dat_list, outfile, fleets, Nsamp,
  years, cpar = 1, ESS = NULL){

    check_data(dat_list)
    dat_list$lencomp <- sample_comp(dat_list$lencomp,
      Nsamp = Nsamp, fleets = fleets, years = years,
      cpar = cpar, ESS = ESS)
    dat_list$N_lencomp <- nrow(dat_list$lencomp)

    ## Write the modified file
    if (!is.null(outfile))
        SS_writedat(datlist = dat_list, outfile = outfile, overwrite = TRUE,
                    version = get_ss_ver_dl(dat_list),
                    verbose = FALSE)
    invisible(dat_list)
}