R/read_logger_data_tRackIT.R

In Nature40/tRackIT: Process data recorded with automatic radio-tracking stations

#' join raw logger data per station
#'
#' @description joins all raw logger files in a folder (only for files recorded with tRackit.OS!)
#'
#'
#' @author Jannis Gottwald
#'
#' @param projList list, generatet by initProject function
#'
#' @export
#'
#'


read.logger.data.tRackIT <- function(projList) {
  dirs <- list.dirs(projList$path$raw, recursive = FALSE)

  lapply(dirs, function(d) {
    fls <- list.files(paste0(d, "/radiotracking/"), full.names = TRUE, pattern = ".csv")
    fls <- fls[grep("matched", fls, invert = TRUE)]


    stat_dat <- plyr::ldply(fls, function(f) {
      print(fls)

      tryCatch(
        exp = {
          sig <- data.table::fread(f)
          if (lubridate::is.POSIXct(sig$Time)) {
            return(sig)
          }
        },
        error = function(e) {
          message("file broken")
        }
      )
    })

    colnames(stat_dat)[which(names(stat_dat) == "Device")] <- "receiver"
    colnames(stat_dat)[which(names(stat_dat) == "Time")] <- "timestamp"
    colnames(stat_dat)[which(names(stat_dat) == "Frequency")] <- "frequency"
    colnames(stat_dat)[which(names(stat_dat) == "Duration")] <- "duration"
    colnames(stat_dat)[which(names(stat_dat) == "max (dBW)")] <- "max"
    colnames(stat_dat)[which(names(stat_dat) == "avg (dBW)")] <- "avg"
    colnames(stat_dat)[which(names(stat_dat) == "std (dB)")] <- "std"
    colnames(stat_dat)[which(names(stat_dat) == "noise (dBW)")] <- "noise"
    colnames(stat_dat)[which(names(stat_dat) == "snr (dB)")] <- "snr"

    stat_dat$frequency <- stat_dat$frequency / 1000

    stat_dat$station <- basename(d)


    data.table::fwrite(stat_dat, paste0(projList$path$csv, "/", basename(d), "_FROM_", as.Date(min(stat_dat$timestamp)), "_TO_", as.Date(max(stat_dat$timestamp)), ".csv"))
  })
}