R/threshold_raster.R

In jscamac/edmaps: Estimate Likelihood of Pest Establishment

#' Threshold raster
#'
#' Threshold raster.
#'
#' @param rast A file path to a raster file.
#' @param threshold A named list giving the minimum and/or maximum values
#'   defining the range of values to retain. Values outside this range will be
#'   replaced with `value`. Can be `list(min = Y, max = Z)` or
#'   `list(min = Y)` or `list(max = Z)`.
#' @param value Numeric. The value supplied to cells beyond the threshold(s).
#' @param outfile Character. Output raster file path. Parent directory will be
#'   created recursively if required. If `outfile` is not provided, the
#'   resulting `RasterLayer` will be returned to R.
#' @return A `RasterLayer` will be written to `outfile` if provided,
#'   and returned to R otherwise.
#' @importFrom raster raster writeRaster
#' @export
threshold_raster <- function(rast, threshold, value = 0, outfile) {
  # Load raster
  if(is.character(rast)) {
    out <- raster::raster(rast)
  } else {
    out <- rast
  }

  if(length(threshold)==2 && all(c("min", "max") %in% names(threshold))) {
    out[out < threshold[['min']] | out > threshold[['max']]]  <- value
  } else if(length(threshold)==1 && names(threshold) == "min") {
    out[out < threshold[['min']]]  <- value
  } else if(length(threshold)==1 && names(threshold) =="max") {
    out[out > threshold[['max']]]  <- value
  } else {
    stop("threshold list can only contain elements named 'min' and/or 'max'.")
  }
  if(!missing(outfile)) {
    # Create directory if it does not exist
    if(!dir.exists(dirname(outfile))) {
      dir.create(dirname(outfile), recursive = TRUE)
    }
    # write out raster
    raster::writeRaster(out, outfile, overwrite=TRUE)
  } else {
    out
  }
}