R/read_alec.R

In gnishihara/gnnlab: Commonly Used Functions for the Lab

#' Read ALEC instruments data
#'
#' This function can read the CEM and CKU data files.
#'
#' For CEM files, when the absolute x- and y- velocities are below 0 or above 200, all data are NA.
#'
#' For CKU files, when the chlorophyll data is below 0 or above 400, the value is set to NA.
#' When turbidity is below 0 or above 1000, the value is set to NA.
#'
#' For both CEM and CKU files, When the temperature is below 0 or above 40, all data are NA.
#'
#' @param filename the name of the file which the data are to be read from. It can be a CSV file or an XLSX file.
#' @param ... further arguments passed to read_csv or read_xlsx
#'
#' @return A tibble containing the data.
#' The contents of the tibble depend on the data file.
#'
#' \strong{Returned variables}
#' \describe{
#'    \item{datetime}{Date-time}
#'    \item{speed}{Current speed (cm / s)}
#'    \item{dir}{Current direction (radians)}
#'    \item{ew}{East-West velocity (cm / s)}
#'    \item{ns}{North-South velocity (cm / s)}
#'    \item{chla}{Chlorophyll-a (μg / L)}
#'    \item{turbidity}{Turbidity (FTU, Formazin Nephelometric Units)}
#'    \item{temperature}{Water temperature (\eqn{^\circ}{degrees}C)}
#' }
#' @export
#'
#' @import dplyr
#' @import tidyselect
#' @importFrom magrittr %>%
#' @importFrom readxl read_xlsx
#' @importFrom readr read_csv
#' @importFrom readr read_lines
#' @importFrom readr locale
#' @importFrom lubridate ymd_hms
#' @importFrom stringr str_extract
#' @importFrom tools file_ext
#' @importFrom stringi stri_detect_regex
#' @examples
#' \dontrun{
#' fnames = dir("~/Lab_Data/kawatea/", full.names=TRUE, recursive=TRUE)
#' df = tibble(fnames = fnames)#'
#' df %>% filter(str_detect(fnames, "CEM")) %>% slice(1) %>% pull(fnames) %>% read_alec()
#' df %>% filter(str_detect(fnames, "CKU")) %>% slice(1) %>% pull(fnames) %>% read_alec()
#' }
#'
read_alec = function(filename, ...) {
  test_file = system(paste("file --brief", filename), intern = TRUE)

  if(!stri_detect_regex(rawToChar(readBin(filename, "raw", 10)), "(Alec)")) {
    stop(paste(filename, "is not an Alec Data file."))
  }

  if(grepl("xlsx", file_ext(filename), ignore.case = TRUE)){
    # If it is xlsx, read as an xlsx file.
    id = read_xlsx(filename, range = "A13")
    out = read_xlsx(filename, skip = 36)
  } else if(grepl("csv", file_ext(filename), ignore.case = TRUE)) {
    # If it is csv, read as a csv file.
    enc = get_encoding(filename)
    id = read_lines(filename, n_max = 40, locale = locale(encoding = enc))
    skip = which(stri_detect_regex(id, "^\\[Item\\]"))
    id = id[stri_detect_regex(id, "^Inst_Type")]

    out = suppressMessages(read_csv(filename, skip = skip, locale = locale(encoding = enc)))
  } else {
    # Exit if not either.
    stop(paste(filename, "is not a readable file."))
  }

  # Add two attributes to the data frame. One for the type of data (CKU or CEM)
  # and one for the filename.
  attributes(out)$loggertype = str_extract(id, "T[GK].*[B]")
  attributes(out)$filename = basename(filename)
  {out = out %>%
      select(ymd = matches("YYYY"),
             hms = matches("hh:mm"),
             speed = matches("Velo"),
             dir = matches("Dir"),
             ew = matches("EW"),
             ns = matches("NS"),
             vx = matches("Vel X\\["),
             vy = matches("Vel Y\\["),
             chla = matches("\\[\\s+\\]"),
             turbidity = matches("Turb\\[ppm\\]"),
             temperature = matches("Temp\\[")) %>%
      mutate(datetime = paste(.data$ymd, .data$hms)) %>%
      mutate(datetime = ymd_hms(.data$datetime)) %>%
      mutate_at(vars(matches("dir")), ~(. / 360 * 2*pi)) %>%
      select(-.data$ymd, -.data$hms) %>%
      select(.data$datetime, everything()) %>%
      mutate_at(vars(matches("chla")), ~(ifelse(((. < 0) | (. > 400)), NA, .))) %>%
      mutate_at(vars(matches("turbidity")), ~(ifelse(((. < 0) | (. > 1000)), NA, .))) %>%
      mutate_at(vars(matches("vx|vy")), ~(ifelse(abs(.) > 200, NA, .))) %>%
      mutate_at(vars(matches("temperature")), ~(ifelse(((. < 0) | (. > 40)), NA, .)))
  }

  chk = colnames(out)
  if("vx" %in% chk) {
    out %>%
      mutate_at(vars(-matches("datetime")), ~(ifelse((is.na(vx)|is.na(vy)|is.na(temperature)), NA, .))) %>%
      select(-matches("vx|vy"))
  } else {
    out
  }
}