R/SS_splitdat.R

In r4ss: R Code for Stock Synthesis

#' Split apart bootstrap data to make input file.
#'
#' A function to split apart bootstrap data files created in data.ss_new.  To
#' get bootstraps, the input "N bootstrap file to produce" in starter.ss needs
#' to be 3 or greater. The function can either create a file for just the
#' input data (if `inputs=TRUE`), a file for just the MLE values
#' (if `MLE = TRUE`), or separate files for each of the bootstraps
#' (if `inputs=FALSE` and `MLE=FALSE`).
#'
#'
#' @param inpath Directory containing the input file. By default the working
#' directory given by getwd() is used. Default="working_directory".
#' @param outpath Directory into which the output file will be written.
#' Default="working_directory".
#' @param inname File name of input data file to be split.
#' Default="Data.SS_New".
#' @param outpattern File name of output data file. Default="BootData".
#' @param number Append bootstrap number to the file name chosen in
#' `outpattern`? Default=F.
#' @param verbose Provide richer command line info of function progress?
#' Default=TRUE.
#' @param fillblank Replace blank lines with "#". Helps with running on linux.
#' Default=TRUE.
#' @param MLE Grab the maximum likelihood values from the second block in
#' Data.SS_New (instead of bootstrap values or copies of inputs)? Default=TRUE.
#' @param inputs Grab the copy of the input values values from the first block
#' in Data.SS_New (instead of MLE or bootstrap values)? Default=F.
#' @param notes Notes to the top of the new file (comment indicator "#C" will
#' be added). Default="".
#' @author Ian Taylor
#' @export
SS_splitdat <-
  function(inpath = "working_directory",
           outpath = "working_directory",
           inname = "data.ss_new",
           outpattern = "BootData",
           number = FALSE,
           verbose = TRUE,
           fillblank = TRUE,
           MLE = TRUE,
           inputs = FALSE,
           notes = "") {
    # this is a function to split bootstrap aggregated in the data.ss_new file
    # which is output from Stock Synthesis into individual data files.
    if (MLE & inputs) stop("can't have both 'MLE' and 'inputs' = TRUE")

    if (inpath == "working_directory") inpath <- getwd()
    if (outpath == "working_directory") outpath <- getwd()

    infile <- paste(inpath, inname, sep = "/")
    filelines <- readLines(infile)
    if (fillblank) filelines[filelines == ""] <- "#"

    string <- "#_bootstrap file"
    starts <- grep(string, filelines)
    ends <- c(starts[-1] - 1, length(filelines) - 1)

    MLEstring <- "#_expected values with no error added"
    MLEstart <- grep(MLEstring, filelines)
    MLEend <- starts[1] - 1

    if (MLE & length(MLEstart) == 0) stop("no MLE values in ", inname, "\n  change 'N bootstrap datafiles' in starter.ss to 2 or greater")
    inputstring <- "#_observed data"
    inputstart <- grep(inputstring, filelines)
    if (length(MLEstart) == 0) inputend <- length(filelines) else inputend <- MLEstart - 1
    if (length(inputstart) == 0) stop("no values in ", inname, "\n  change 'N bootstrap datafiles' in starter.ss to 1 or greater")


    if (!MLE & !inputs) {
      if (length(starts) == 0) stop("no bootstrap values in ", inname, "\n  change 'N bootstrap datafiles' in starter.ss to 3 or greater")
      for (i in 1:length(starts)) {
        outfile <- paste(outpath, "/", outpattern, ifelse(number, i, ""), ".ss", sep = "")
        outline <- paste("# Data file created from", infile, "to", outfile)
        if (verbose) cat(outline, "\n")
        writeLines(c(outline, filelines[starts[i]:ends[i]]), outfile)
      }
    } else {
      if (MLE) {
        outfile <- paste(outpath, "/", outpattern, ".ss", sep = "")
        if (notes != "") notes <- paste("#C", notes) else notes <- NULL
        notes <- c(notes, paste("#C MLE data file created from", infile, "to", outfile))
        if (verbose) cat("MLE data file created from", infile, "to", outfile, "\n")
        writeLines(c(notes, filelines[MLEstart:MLEend]), outfile)
      }
      if (inputs) {
        outfile <- paste(outpath, "/", outpattern, ".ss", sep = "")
        if (notes != "") notes <- paste("#C", notes) else notes <- NULL
        notes <- c(notes, paste("#C data file created from", infile, "to", outfile))
        if (verbose) cat("file with copies of input data created from", infile, "to", outfile, "\n")
        writeLines(c(notes, filelines[inputstart:inputend]), outfile)
      }
    }
  }