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#' Write Stock Synthesis control file
#'
#' Write Stock Synthesis control file from list object in R which was probably
#' created using [SS_readctl()]. This function is a
#' wrapper which calls either SS_writectl_3.24 or SS_writectl_3.30
#' (and potentially additional functions in the future).
#'
#' @param ctllist List object created by [SS_readdat()].
#' @param outfile Filename for where to write new control file.
#' @template version
#' @param overwrite Should existing files be overwritten? Defaults to FALSE.
#' @param verbose Should there be verbose output while running the file?
#' Defaults to FALSE.
#' @author Ian G. Taylor, Yukio Takeuchi, Gwladys I. Lambert, Kathryn Doering
#' @export
#' @seealso [SS_writedat_3.24()], [SS_writedat_3.30()],
#' [SS_readdat()],
#' [SS_readstarter()], [SS_writestarter()],
#' [SS_readforecast()], [SS_writeforecast()]
SS_writectl <- function(ctllist,
outfile,
version = "3.30",
overwrite = FALSE,
verbose = FALSE) {
# function to write Stock Synthesis data files
if (verbose) {
message("Running SS_writectl")
}
# Check user inputs are valid to avoid issues with functions.
# check ctllist
stopifnot(is.list(ctllist))
stopifnot("type" %in% names(ctllist))
if (ctllist[["type"]] != "Stock_Synthesis_control_file") {
stop("Input 'ctllist' should be a list with component type == 'Stock_Synthesis_control_file")
}
if (is.null(version)) {
lifecycle::deprecate_stop(
when = "1.44.1",
what = "SS_readctl(version = 'must be 3.24 or 3.30')"
)
version <- "3.30"
}
if (ifelse(version == "3.3", "3.30", version) != ctllist[["ReadVersion"]]) {
stop(
"Input 'version' does not match ctllist[['ReadVersion']] of ",
"'", ctllist[["ReadVersion"]], "'."
)
}
if (!(version == "3.24" | version == "3.30" | version == 3.3)) {
stop("Input 'version' should be either '3.24' or '3.30'")
}
# Check user inputs and/or prepare the file to be overwitten.
if (file.exists(outfile)) {
if (!overwrite) {
stop(
"Outfile called ", outfile, " exists and input 'overwrite'= FALSE.",
"Please set overwrite = TRUE if you wish to overwrite the file."
)
} else if (overwrite) {
file.remove(outfile)
}
}
# function call depends on user version
if (version == "3.24") {
# Specify nseas, N_areas, and Do_AgeKey as input.
SS_writectl_3.24(ctllist, outfile, overwrite = overwrite, verbose = verbose)
}
if (version == "3.30" | version == 3.3) {
# This function will get nseas, N_areas, and Do_AgeKey from ctllist.
SS_writectl_3.30(
ctllist = ctllist,
outfile = outfile,
overwrite = overwrite,
verbose = verbose
)
}
# because this function is used for its side effects (i.e., writing to disk),
# return its first argument invisibly.
invisible(ctllist)
}
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