Nothing
#' 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
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.