R/animal_process.R

In Nature40/Rrt: R radiotracking Rrt

#' Radiotrack an animal
#'
#' @description Does the station processing chain for every station of an animal
#'
#'
#' @param animal list, a list from initAnimal
#'
#'
#'


animal_process = function(animal){

  s = list.files(animal$path$raw, full.names = TRUE)

  # for every station in raw
  for(i in s){

    # subset with awk
    station_subset(animal,
                   station_file = i)


    if(file.info(paste0(animal$path$stations, "/", basename(i)))$size > 1){
      # read subset
      st = station_read(paste0(animal$path$stations, "/", basename(i)))
      # save keepalives
      st_kplv = station_keepalive(st)
      write.csv(st_kplv, paste0(animal$path$keepalive,"/", st_kplv$station[1],"_keep_alives.csv"), row.names = FALSE)

      # cleanup frequency and noise, overwrite awk subset
      st = station_cleanup(st, freq = animal$meta$freq)
      write.csv(st, paste0(animal$path$stations, "/", basename(i)), row.names = FALSE)

    }else{
      file.remove(paste0(animal$path$stations, "/", basename(i)))
    }
  }
}