R/2h4h_second_filter.R

In filteRjsats: Filter Raw JSATS Acoustic Telemetry Files from Lotek, ATS, Teknologic

#' Two or Four Hit Filter for Any Detection File
#'
#' This function takes any acoustic receiver detection dataframe generated from
#' the add_fish() function and filters it a second time to remove any remaining
#' multipath detections. Then depending on the type of receiver file applies an
#' algorithm to assess and filter all remaining detections based on 2 or 4 hits.
#'
#'
#' @param fish_file a dataframe of detections retrieved from add_fish()
#' @returns A dataframe which has been filtered to remove false positives
#' @export
#' @examples
#' # Apply a 2 or 4 hit filter based on the technology
#' second_filter_2h4h(filter_fish_detects)
second_filter_2h4h <- function(fish_file){

  make = fish_file$Make[1]
  final_file = NULL
  if (make == "Lotek") final_file <- second_filter_lotek(fish_file)
  if (make == "Tekno") final_file <- second_filter_tekno(fish_file)
  if (make == "ATS")   final_file <- second_filter_ats(fish_file)
  if (is.null(final_file)) errorCondition("Receiver make should be one of Lotek, Tekno, or ATS")

  message(paste0("Number of Valid Tag IDs: ", length(unique(final_file$Tag_Hex))))
  message(paste0("Number of Valid Detections: ", length(final_file$DateTime_Local)))

  spur <- compare_detects(fish_file, final_file)

  message(paste0("Number of Tags with Spurious Detections: ", length(unique(spur$Tag_Hex))))
  message(paste0("Tags with Only Spurious Detections: "), spur$TagHex[which(!(unique(spur$Tag_Hex) %in% (unique(final_file$Tag_Hex))))])
  message(paste0("Number of Spurious Detections: ", length(spur$DateTime_Local)))

  final_file
}