R/read_mow_data.R

In inbo/inborutils: Collection of Useful R Utilities

#' Read MOW data
#'
#' Coordinate data is contained in the header of the file
#'
#' @param filename path/filename of the `RWS` datafile
#' @param n_max integer; shortcut for testing, loading just a section of the
#' data
#'
#' @return `data.frame` with the headers `location_name`, `datetime` (UTC),
#' value, `unit`, `variable_name`, `latitude`, `longitude` and `source_filename`
#'
#' @export
#' @importFrom readr read_delim cols col_character col_double
#' @importFrom dplyr select mutate %>%
#' @importFrom iterators ireadLines nextElem
#' @importFrom sf st_crs
#' @importFrom lubridate dmy_hms
#' @importFrom rlang .data
#'
#' @family download_functions
#'
#' @examples
#' \dontrun{
#' # see vignettes for more examples
#' file_path <- "mow_file.txt"
#' mow_data <- read_mow_data(file_path)
#' }
read_mow_data <- function(filename, n_max = Inf) {
  mow_con <- file(filename, "r", encoding = "UTF-8")
  header_it <- ireadLines(mow_con)
  line <- nextElem(header_it)
  cnt <- 1
  while (!startsWith(line, "Date")) {
    # extract station coordinate info
    if (startsWith(line, "Station Name")) {
      station_name <- mow_header_split(line)
    }
    if (startsWith(line, "Easting")) {
      longitude <- as.numeric(mow_header_split(line))
    }
    if (startsWith(line, "Northing")) {
      latitude <- as.numeric(mow_header_split(line))
    }
    if (startsWith(line, "Parameter Name")) {
      variable_name <- mow_header_split(line)
    }
    if (startsWith(line, "Time series Unit")) {
      variable_unit <- mow_header_split(line)
    }
    line <- nextElem(header_it)
    cnt <- cnt + 1
  }
  header <- strsplit(line, "\t")[[1]]
  close(mow_con)

  # Handle coordinate information
  crs_lambert <- st_crs(31370)
  crs_wgs84 <- st_crs(4326)
  coordinates <- as.data.frame(list(
    latitude = latitude,
    longitude = longitude
  ))
  coordinates_wgs <- transform_coordinates(
    coordinates, "longitude",
    "latitude", crs_lambert, crs_wgs84
  )

  # Define mapping for mow supported values
  wt <- "T\u00B0"
  Encoding(wt) <- "UTF8"
  variable_mapping <- list(
    "DO" = "dissolved_oxygen",
    "Turb_YSI" = "turbidity_ySI",
    "Turb_SG5" = "turbidity_SG5",
    "Turb_SG25" = "turbidity_SG25",
    "Cond" = "conductivity",
    "water_temperature"
  )
  names(variable_mapping)[[length(variable_mapping)]] <- wt
  variable_name_mapped <- variable_mapping[[variable_name]]
  if (is.null(variable_name_mapped)) {
    variable_name_mapped <- variable_name
    print(sprintf(
      "Variable name is not mapped, using %s as variable name",
      variable_name_mapped
    ))
  }

  # Read data.frame from the file itself
  col_types <- cols(
    X1 = col_character(),
    X2 = col_character(),
    X3 = col_double(),
    X4 = col_character(),
    X5 = col_character()
  )
  mow_data <- read_delim(filename,
    delim = "\t", skip = cnt,
    n_max = n_max, col_names = FALSE,
    col_types = col_types
  )
  colnames(mow_data) <- header
  mow_data %>%
    mutate(datetime = dmy_hms(paste(
      .data$Date,
      .data$Time
    ))) %>% # UTC by default
    select(.data$datetime,
      value = header[[3]],
      quality_code = .data$`Quality flag`,
      quality_comments = .data$Comments
    ) %>%
    mutate(location_name = station_name) %>%
    mutate(variable_name = variable_name_mapped) %>%
    mutate(unit = variable_unit) %>%
    mutate(longitude = coordinates_wgs$longitude) %>%
    mutate(latitude = coordinates_wgs$latitude) %>%
    mutate(source_filename = basename(filename))
}


#' Get data entry from MOW header data file
#'
#' @param inputline character string coming from MOW data file
#' @keywords internal
#' @return char string with the entry
mow_header_split <- function(inputline) {
  trimws(strsplit(inputline, ":")[[1]][[2]])
}