R/SS_splitdat.R

In r4ss/r4ss: R Code for Stock Synthesis

#' Split apart bootstrap data to make input file.
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#'  `SS_splitdat()` is being deprecated because it is no longer needed in as of
#'  Stock Synthesis 3.30.19, where the files are already split. If needing to
#'  split older version of SS3, this could be done by reading in the file to
#'  `SS_readdat()`, specifying the section argument to grab the desired part of
#'   the file, and then writing out the file using. `SS_writedat()'.
#' @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.
#' @template verbose
#' @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
#' @keywords internal
#' @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 = ""
  ) {
    lifecycle::deprecate_warn(
      "1.45.0",
      "SS_splitdat()",
      details = "Upgrade to SS3.30.19 or see the description in ?SS_splitdat() for a workaround."
    )
    # 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 seq_along(starts)) {
        outfile <- paste(
          outpath,
          "/",
          outpattern,
          ifelse(number, i, ""),
          ".ss",
          sep = ""
        )
        outline <- paste("# Data file created from", infile, "to", outfile)
        if (verbose) {
          message(outline)
        }
        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) {
          message("MLE data file created from", infile, "to", outfile)
        }
        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) {
          message(
            "file with copies of input data created from ",
            infile,
            " to ",
            outfile
          )
        }
        writeLines(c(notes, filelines[inputstart:inputend]), outfile)
      }
    }
  }