R/change_f_par.r

In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

#' Alter the fishing mortality (\emph{F}) values in an SS3 \code{.par} file.
#'
#' Takes an SS3 \code{.par} file and changes the \emph{F} values for specified years.
#' If used with \code{\link{run_ss3sim}} the case file should be named
#' \code{F}. A suggested (default) case letter is \code{F}.
#'
#' @author Curry James Cunningham
#'
#' @param years *Vector of years for which \emph{F} values are specified,
#' if there is more than one fleet or season the catches must be ordered by
#' season:year:fishery (e.g., season1year1fishery1, season2year1fishery1,
#' season1year2fishery1). The actual vector does not have to correspond to
#' true years but must be the correct length (e.g., instead of
#' \code{2000:2004} you can use \code{1:5}). Use this argument to create
#' an index to old values. \code{years_alter} will use values in this vector.
#' For example, with two seasons and one fishery that operates for 4 years
#' you could use the following: \code{1:8}.
#' @param years_alter *Vector of years for the which \emph{F} values will be altered.
#' If there is more than one fishery or season, use the mapping system
#' created in \code{years} because actual year values cannot be recycled.
#' For example, to change the second season of the second year in the
#' example above, use: \code{4}.
#' @param fvals *Vector of \emph{F} values to be entered into \code{ss.par} file,
#' where \code{length(fvals) == length(years_alter)} must be true.
#' @template par_file_in
#' @template par_file_out
#' @return A modified SS3 \code{.par} file.
#' @family change functions
#' @template casefile-footnote
#' @examples
#' # Create a temporary folder for the output:
#' temp_path <- file.path(tempdir(), "ss3sim-f-example")
#' dir.create(temp_path, showWarnings = FALSE)
#'
#' # Find the example .par file in the package data:
#' d <- system.file("extdata", package = "ss3sim")
#' par_file <- paste0(d, "/change_f/ss3.par")
#'
#' change_f_par(years = 1:49, years_alter = 2, fvals = 9999, par_file_in =
#' par_file, par_file_out = paste0(temp_path, "/test.par"))
#' @export

change_f_par <- function(years, years_alter, fvals, par_file_in = "ss.par",
  par_file_out = "ss.par") {

  n.years_alter <- length(years_alter)

  # Check that sufficient F values are supplied
  if(n.years_alter != length(fvals)) {
    stop(paste('#ERROR: Number of years to alter:', n.years_alter,
        'Does NOT equal length of supplied Fvalues:', length(fvals)))
  }

  # Read in ss.par file
  ss.par <- readLines(par_file_in) # Original
  ss.par.new <- ss.par # New file

  for(y in 1:n.years_alter) {
  	temp.year <- which(years == years_alter[y])
    temp.loc <- which(ss.par == paste('# F_rate[', temp.year, ']:', sep=''))
    ss.par.new[temp.loc+1] <- fvals[y]
  }

  # Write new .par file
  writeLines(ss.par.new, con = par_file_out)
  close(file(par_file_out))
  invisible(ss.par.new)
}