R/get_file_int.R

In SticsRFiles: Read and Modify 'STICS' Input/Output Files

#' Read STICS observation or simulation file (*.obs or mod_s*)
#'
#' @description Read STICS observation or simulation file(s). This function
#' is not exported because it only reads and pre-formats the file without any
#' clever tests for intercrops or usms.
#'
#' @param workspace  A directory where to read the files
#' @param filename   A vector of file names
#' @param plant_name A vector of plant names. Length of filename, or recycled
#' if one (optional).
#' @param verbose   Logical value (optional), TRUE to display read file name,
#' FALSE otherwise (default)
#'
#' @return A `data.frame` of all observation or simulation files concatenated
#'  by row.
#'
#' @keywords internal
#'
#' @noRd
#'
#' @importFrom rlang .data
#'
#' @examples
#' \dontrun{
#' path <- file.path(get_examples_path(file_type = "obs"))
#' get_file_int(path, "banana.obs")
#' }
get_file_int <- function(workspace,
                         filename,
                         plant_name = NULL,
                         verbose = TRUE) {

  if (verbose) message(filename)

  if (is.list(filename)) filename <- unlist(filename)
  if (is.list(plant_name)) plant_name <- unlist(plant_name)

  if (!is.null(plant_name)) {
    if (length(plant_name) > 1 && length(plant_name) != length(filename)) {
      stop("length(plant_name) should be == 1 or length(filename)")
    }

    if (length(plant_name) == 1) {
      plant_name <- rep(plant_name, length(filename))
    }
  } else {
    plant_name <- filename
  }

  out_table <- mapply(function(x, y) {
    out <- try(data.table::fread(file.path(workspace, x),
                                 data.table = FALSE,
                                 na.strings = c("************", "NA"),
                                 stringsAsFactors = FALSE
    ))

    # Removing empty extra lines (without year)
    out <- dplyr::filter(out, !is.na(.data$ian))


    if (inherits(out, "try-error")) {
      cli::cli_alert_warning(paste0("couldn't find valid file for ",
                                    "{.val {file.path(workspace,x)}}"))
      return(NULL)
    }
    colnames(out) <- var_to_col_names(colnames(out))
    if (nrow(out) == 0) {
      return(NULL)
    }
    out[out <= -999.00] <- NA
    out$Plant <- y
    return(out)
  }, x = filename, y = plant_name, SIMPLIFY = FALSE)

  out_table <- dplyr::bind_rows(out_table)

  if (nrow(out_table) > 0) {

    out_table <- dplyr::mutate(out_table,
                               Date = as.POSIXct(
                                 x = paste(out_table$ian,
                                           out_table$mo,
                                           out_table$jo,
                                           sep = "-"),
                                 format = "%Y-%m-%d",
                                 tz = "UTC"
                               )
    ) %>%
      dplyr::relocate(dplyr::all_of("Date")) %>%
      dplyr::select(-dplyr::all_of(c("ian", "mo", "jo", "jul")))
  }
  out_table
}