R/check.R

In actel: Acoustic Telemetry Data Analysis

#' check.R arguments
#'
#' @param arrays a list containing information for each array.
#' @param bio A table with the tags and biometrics of the studied animals.
#' @param deployments a list of deployments.
#' @param detections The detections data.frame for a specific tag.
#' @param detections.list A list of the detections split by each target tag,
#'  created by \code{\link{splitDetections}}.
#' @param dist.mat A distances matrix.
#' @param discard.orphans Logical: Should actel automatically discard
#'  detections that do not fall within receiver deployment periods, or that
#'  were recorded before the respective animals were released?
#' @param dotmat The matrix of distances between arrays.
#' @param GUI One of "needed", "always" or "never". If "needed", a new window is
#'  opened to inspect the movements only if the movements table is too big to be
#'  displayed in R's console. If "always", a graphical interface is always created
#'  when the possibility to invalidate events emerges. If "never", a graphical
#'  interface is never invoked. In this case, if the table to be displayed does
#'  not fit in R's console, a temporary file will be saved and the user will be
#'  prompted to open and examine that file. Defaults to "needed".
#' @param movements The movements table for a specific tag.
#' @param n A string indicating the overall progress.
#' @param release The release location of the animal.
#' @param secmoves the section movements list.
#' @param spatial A list of spatial objects in the study area.
#' @param tag The tag being analysed.
#' @param unknown.receivers serial number of the receivers to be included.
#' @param valid.movements The valid movements table for a specific tag.
#'
#' @name check_args
#' @keywords internal
#'
NULL

#' Check argument quality
#'
#' @param dp A preloaded datapack (or NULL if no data was preloaded).
#' @inheritParams explore
#' @inheritParams migration
#' @inheritParams residency
#'
#' @keywords internal
#'
#' @return updated parameters
#'
checkArguments <- function(dp, tz, min.total.detections, min.per.event, max.interval, speed.method = c("last to first", "last to last"),
  speed.warning, speed.error, start.time, stop.time, report, auto.open, save.detections, jump.warning, jump.error,
  inactive.warning, inactive.error, exclude.tags, override, print.releases, detections.y.axis = c("auto", "stations", "arrays"),
  if.last.skip.section = NULL, replicates = NULL, section.warning, section.error, section.order = NULL, timestep = c("days", "hours")) {
  appendTo("debug", "Running checkArguments.")

  # Note: Checks only relevant for migration() or residency() are listed at the bottom!

  no.dp.args <- c("tz", "section.order", "start.time", "stop.time", "save.detections", "exclude.tags")
  link <- c(!is.null(tz), 
            !is.null(section.order),
            !is.null(start.time), 
            !is.null(stop.time),
            !(is.logical(save.detections) && !save.detections), !is.null(exclude.tags))

  if (!is.null(dp) & any(link))
    appendTo(c("Screen", "Warning", "Report"), paste0("Argument", ifelse(sum(link) > 1, "s '", " '"), paste(no.dp.args[link], collapse = "', '"),
      ifelse(sum(link) > 1, "' were ", "' was "), "set but a datapack was provided. Disregarding set arguments."))

  if (is.null(dp) & is.null(tz))
    stopAndReport('argument "tz" is missing, with no default')

  if (is.null(dp) && is.na(match(tz, OlsonNames())))
    stopAndReport("'tz' could not be recognized as a timezone. Check available timezones with OlsonNames()")

  if (!is.numeric(min.total.detections))
    stopAndReport("'min.total.detections' must be numeric.")

  if (!is.numeric(min.per.event))
    stopAndReport("'min.per.event' must be numeric.")

  if (min.total.detections <= 0)
    stopAndReport("'min.total.detections' must be positive.")

  if (any(min.per.event <= 0))
    stopAndReport("'min.per.event' must be positive.")

  if (length(min.per.event) == 1)
    min.per.event <- rep(min.per.event, 2)

  if (!is.numeric(max.interval))
    stopAndReport("'max.interval' must be numeric.")

  if (max.interval <= 0)
    stopAndReport("'max.interval' must be positive.")

  if (max.interval < 10)
    appendTo(c("Screen", "Warning"), "Setting 'max.interval' to less than 10 minutes is not recommended!\n         This can lead to the creation of an immense number of movement events,\n         which will be hardly manageable if any quality check is triggered.")

  if (!is.character(speed.method))
    stopAndReport("'speed.method' should be one of 'last to first' or 'last to last'.")
  speed.method <- match.arg(speed.method)

  if (!is.null(speed.warning) && !is.numeric(speed.warning))
    stopAndReport("'speed.warning' must be numeric.")

  if (!is.null(speed.warning) && speed.warning <= 0)
    stopAndReport("'speed.warning' must be positive.")

  if (!is.null(speed.error) && !is.numeric(speed.error))
    stopAndReport("'speed.error' must be numeric.")

  if (!is.null(speed.error) && speed.error <= 0)
    stopAndReport("'speed.error' must be positive.")

  if (!is.null(speed.error) & is.null(speed.warning))
    speed.warning <- speed.error

  if (!is.null(speed.error) && speed.error < speed.warning)
    stopAndReport("'speed.error' must not be lower than 'speed.warning'.")

  if (!is.null(speed.warning) & is.null(speed.error))
    speed.error <- Inf

  if (is.null(dp) && !is.null(start.time) && !grepl("^[1-2][0-9][0-9][0-9]-[0-1][0-9]-[0-3][0-9] [0-2][0-9]:[0-5][0-9]:[0-5][0-9]", start.time))
    stopAndReport("'start.time' must be in 'yyyy-mm-dd hh:mm:ss' format.")

  if (is.null(dp) && !is.null(stop.time) && !grepl("^[1-2][0-9][0-9][0-9]-[0-1][0-9]-[0-3][0-9] [0-2][0-9]:[0-5][0-9]:[0-5][0-9]", stop.time))
    stopAndReport("'stop.time' must be in 'yyyy-mm-dd hh:mm:ss' format.")

  if (!is.logical(report))
    stopAndReport("'report' must be logical.")

  if (!is.logical(auto.open))
    stopAndReport("'auto.open' must be logical.")

  if (is.null(dp) && !is.logical(save.detections))
    stopAndReport("'save.detections' must be logical.")

  if (!is.numeric(jump.warning))
    stopAndReport("'jump.warning' must be numeric.")

  if (jump.warning < 1)
    stopAndReport("'jump.warning' must not be lower than 1.")

  if (!is.numeric(jump.error))
    stopAndReport("'jump.error' must be numeric.")

  if (jump.error < 1)
    stopAndReport("'jump.error' must not be lower than 1.")

  if (jump.error < jump.warning) {
    if (jump.warning == 2) { # this happens if someone changed jump error but didn't set jump warning.
      appendTo(c("screen", "warning"), "Adjusting default 'jump.warning' to match set 'jump.error'.")
      jump.warning <- jump.error
    } else {
      if (jump.error == 3) { # this happens if someone changed jump warning but didn't change jump error.
        appendTo(c("screen", "warning"), "Adjusting default 'jump.error' to match set 'jump.warning'.")
        jump.error <- jump.warning
      } else { # this happens if someone set both jump warning and jump error. In this case, stop and let the user decide.
        stopAndReport("'jump.error' must not be lower than 'jump.warning'.")
      }
    }
  }

  if (!is.null(inactive.warning) && !is.numeric(inactive.warning))
    stopAndReport("'inactive.warning' must be numeric.")

  if (!is.null(inactive.warning) && inactive.warning <= 0)
    stopAndReport("'inactive.warning' must be positive.")

  if (!is.null(inactive.error) && !is.numeric(inactive.error))
    stopAndReport("'inactive.error' must be numeric.")

  if (!is.null(inactive.error) && inactive.error <= 0)
    stopAndReport("'inactive.error' must be positive.")

  if (!is.null(inactive.error) & is.null(inactive.warning))
    inactive.warning <- inactive.error

  if (!is.null(inactive.error) && inactive.error < inactive.warning)
    stopAndReport("'inactive.error' must not be lower than 'inactive.warning'.")

  if (!is.null(inactive.warning) & is.null(inactive.error))
    inactive.error <- Inf

  if (is.null(dp) && !is.null(exclude.tags) && any(!grepl("-", exclude.tags, fixed = TRUE)))
    stopAndReport("Not all contents in 'exclude.tags' could be recognized as tags (i.e. 'codespace-signal'). Valid examples: 'R64K-1234', 'A69-1303-1234'")

  if (!is.null(override) && is.numeric(override)) {
    appendTo(c('report', 'screen', 'warning'), 'Override is numeric (i.e. the code space has not been included). Will attempt to identify tags to be excluded based on signal alone.')
  }

  if (!is.logical(print.releases))
    stopAndReport("'print.releases' must be logical.")

  if (!is.character(detections.y.axis))
    stopAndReport("'detections.y.axis' should be one of 'stations' or 'arrays'")
  detections.y.axis <- match.arg(detections.y.axis)

  if (!is.character(timestep))
    stopAndReport("'timestep' should be one of 'days' or 'hours'")
  timestep <- match.arg(timestep)

  # Check that all the overridden tags are part of the study
  if (!is.null(dp) && !is.null(override)) {
    if (is.numeric(override)) {
      lowest_signals <- sapply(dp$bio$Signal, lowestSignal)
      if (any(link <- is.na(match(override, dp$bio$Signal)))) {
        stopAndReport("Some tags listed in 'override' (", paste0(override[link], collapse = ", "), ") are not listed in the biometrics data.")
      }
    } else {
      if (any(link <- is.na(match(override, dp$bio$Transmitter)))) {
        stopAndReport("Some tags listed in 'override' (", paste0(override[link], collapse = ", "), ") are not listed in the biometrics data.")
      }
    }
  }

  # NON-explore checks
  if (!is.null(section.order) && any(table(section.order) > 1))
    stopAndReport("Some section names are duplicated in the 'section.order' argument. Please include each section only once.")

  if (!is.null(if.last.skip.section) && !is.logical(if.last.skip.section))
    stopAndReport("'if.last.skip.section' must be logical.")

  if (!is.null(replicates) && !is.list(replicates))
    stopAndReport("'replicates' must be a list.")

  if (!is.null(replicates) && length(names(replicates)) != length(replicates))
    stopAndReport("All list elements within 'replicates' must be named (i.e. list(Array = 'St.1') rather than list('St.1')).")

  # only run these in residency calls.
  if (!missing(section.warning)) {
    if (section.error > section.warning) {
      if (section.warning == 1) { # this happens if someone changed section error but didn't set section warning.
        appendTo(c("screen", "warning"), "Adjusting default 'section.warning' to match set 'section.error'.")
        section.warning <- section.error
      } else {
        if (section.error == 1) { # this happens if someone changed section warning but didn't change section error.
          appendTo(c("screen", "warning"), "Adjusting default 'section.error' to match set 'section.warning'.")
          section.error <- section.warning
        } else { # this happens if someone set both section warning and section error. In this case, stop and let the user decide.
          stopAndReport("'section.error' must not be lower than 'section.warning'.")
        }
      }
    }

    if (min.per.event[2] > section.error)
      appendTo(c('screen', 'warning', 'report'), "The minimum number of detections per valid section event is higher than 'section.warning'. Section warnings will never occur.")

    if (min.per.event[2] > section.error)
      appendTo(c('screen', 'warning', 'report'), "The minimum number of detections per valid section event is higher than 'section.error'. Section errors will never occur.")
  } else {
    # placeholder values so that explore and migration don't crash when attempting
    # to export below. These two variables are only used by residency.
    section.error <- 0
    section.warning <- 0
  }

  return(list(min.per.event = min.per.event,
              speed.method = speed.method,
              speed.warning = speed.warning,
              speed.error = speed.error,
              jump.warning = jump.warning,
              jump.error = jump.error,
              inactive.warning = inactive.warning,
              inactive.error = inactive.error,
              detections.y.axis = detections.y.axis,
              section.warning = section.warning,
              section.error = section.error,
              timestep = timestep))
}


#' Verify that the source data has been compiled using actel's preload function
#'
#' @param token The token generated by preload
#' @param timestamp The time when the token was issued
#'
#' @keywords internal
#'
#' @return No return value. Called for side effects.
#'
checkToken <- function(token, timestamp) {
  appendTo("debug", "Running checkToken.")
  if (file.exists(paste0(tempdir(), "/actel_token_list.csv")))
    x <- read.csv(paste0(tempdir(), "/actel_token_list.csv"))
  else
    x <- NULL
  if ((is.null(token) | is.null(timestamp) | is.null(x)) || !any(x$Token == token & x$Timestamp == timestamp))
    stopAndReport("The datapack's token is invalid or missing. Please the function preload() to compile the input data.\nAdditionally, data must to be compiled during the current R session.")
}


#' Check if the dependencies required to open a GUI are installed, and if
#' opening a GUI does not throw an error. Some code adapted from RGtk2's
#' .onLoad function.
#'
#' @inheritParams check_args
#'
#' @keywords internal
#'
#' @return An updated GUI argument (character string)
#'
#'
checkGUI <- function(GUI = c("needed", "always", "never"), save.tables.locally) {
  appendTo("debug", "Running checkGUI.")

  if (!is.character(GUI))
    stopAndReport("'GUI' should be one of 'needed', 'always' or 'never'.")
  
  GUI <- match.arg(GUI)
  
  if (GUI != "never" && length(suppressWarnings(packageDescription("gWidgets2tcltk"))) == 1) {
    appendTo(c("Screen", "Warning"), paste0("GUI is set to '", GUI, "' but package 'gWidgets2tcltk' is not available. Please install it if you intend to run GUI.\n         Disabling GUI (i.e. GUI = 'never') for the current run."))
    GUI <- "never"
  }

  if (GUI == "never" & save.tables.locally & file.exists("actel_inspect_movements.csv"))
    stopAndReport("GUI is set to 'never' and save.tables.locally is set to TRUE, but a file 'actel_inspect_movements.csv' already exists in the current work directory.\n       Stopping to prevent data loss. Delete/rename the existing 'actel_inspect_movements.csv' to be able to run this analysis.")

  if (GUI == "never" & save.tables.locally & file.exists("actel_inspect_detections.csv"))
    stopAndReport("GUI is set to 'never' and save.tables.locally is set to TRUE, but a file 'actel_inspect_detections.csv' already exists in the current work directory.\n       Stopping to prevent data loss. Delete/rename the existing 'actel_inspect_detections.csv' to be able to run this analysis.")

  return(GUI)
}


#' Check if there are duplicated detection in the input data
#'
#' @param input The detections data frame
#'
#' @return The detections data frame, without duplicated detections.
#'
#' @keywords internal
#'
checkDupDetections <- function(input) {
  appendTo("debug", "Running checkDupDetections.")
  paired <- data.frame(
    TimestampA = input$Timestamp[-nrow(input)],
    TimestampB = input$Timestamp[-1],
    ReceiverA = input$Receiver[-nrow(input)],
    ReceiverB = input$Receiver[-1],
    TransmitterA = input$Transmitter[-nrow(input)],
    TransmitterB = input$Transmitter[-1]
    )

  if (any(colnames(input) == "Source.file")) {
    paired$Source.FileA <- input$Source.file[-nrow(input)]
    paired$Source.fileB <- input$Source.file[-1]
  }

  dups <- c(FALSE, paired[,1] == paired[,2] & paired[,3] == paired[,4] & paired[,5] == paired[,6])
  if (any(dups)) {
    appendTo(c("Screen", "Report", "Warning"), paste0(sum(dups), " duplicated detection", ifelse(sum(dups) == 1, " was", "s were"), " found. Could an input file be duplicated?"))
    message("")
    message("Possible options:\n   a) Stop and double-check the data\n   b) Remove duplicated detections\n   c) Continue without changes\n   d) Save duplicated detections to a file and re-open dialogue.")
    message("")
    restart <- TRUE
    while (restart) {
      decision <- userInput("Decision:(a/b/c/d) ", choices = letters[1:4], hash = "# dup. detections")
      if (decision == "a")
        stopAndReport("Function stopped by user command.") # nocov
      if (decision == "b") {
        appendTo(c("Screen", "Report"), "M: Removing duplicated detections from the analysis per user command.")
        output <- input[!dups, ]
        restart <- FALSE
      }
      if (decision == "c") { # nocov start
        appendTo(c("Screen", "Report"), "M: Continuing analysis with duplicated detections per user command.")
        output <- input
        restart <- FALSE
      } # nocov end
      if (decision == "d") { # nocov start
        file.name <- userInput("Please specify a file name (leave empty to abort saving): ", hash = "# save dups to this file")
        # break if empty
        if (file.name == "")
          next()
        # confirm extension
        if (!grepl("\\.csv$", file.name))
          file.name <- paste0(file.name, ".csv")
        # prevent auto-overwrite
        if (file.exists(file.name)) {
          aux <- userInput(paste0("File '", file.name, "' already exists. Overwrite contents?(y/n) "), 
                           choices = c("y", "n"), 
                           hash = "# overwrite file with same name?")
          if (aux == "y")
            overwrite <- TRUE
          else
            overwrite <- FALSE 
        }
        else
          overwrite <- TRUE
        # save
        if (overwrite) {
          success <- TRUE
          # recover if saving fails
          tryCatch(data.table::fwrite(paired[dups[-1], ], file.name, , dateTimeAs = "write.csv"), error = function(e) {
            appendTo(c("Screen", "Report"), paste0("Error: Could not save file (reason: '", sub("\n$", "", e), "').\n       Reopening previous interaction."))
            success <<- FALSE
          })
          if (success)
            appendTo(c("Screen", "Report"), paste0("M: A copy of the duplicated detections has been saved to '", file.name, "'.\n   Reopening previous interaction."))
        }
      } # nocov end
    }
  } else {
    output <- input
  }
  return(output)
}


#' Check the number of detections (total and per event) of a given tag. Works
#' for both array and section movements.
#'
#' @inheritParams check_args
#' @inheritParams explore
#'
#' @return A data frame containing the movements with valid/invalid notes
#'
#' @keywords internal
#'
checkMinimumN <- function(movements, min.total.detections, min.per.event, tag, n) {
  appendTo("debug", "Running checkMinimumN")
  if (sum(movements$Detections) < min.total.detections) {
    appendTo(c("screen", "report", "warning"), paste0("Tag ", tag, " ", n, " has less than ", min.total.detections," detections in total. Discarding this tag."))
    movements$Valid <- FALSE # invalidate the tag
  }
  if (any(movements$Valid) & any(movements$Detections < min.per.event)) {
    if (any(colnames(movements) == 'Array'))
      appendTo(c("screen", "report", "warning"), paste0("Tag ", tag, " ", n, " has ", tolower(colnames(movements)[1]), " movement events with less than ", min.per.event, " detections. Invalidating those events."))
    movements$Valid[movements$Detections < min.per.event] <- FALSE
  }
  return(movements)
}


#' check tag speeds against defined thresholds (in m/s)
#'
#' @inheritParams check_args
#' @inheritParams explore
#'
#' @return A list of movements with updated 'Valid' columns
#'
#' @keywords internal
#'
checkSpeeds <- function(movements, tag, detections, valid.movements, 
  speed.warning, speed.error, GUI, save.tables.locally, n) {
  appendTo("debug", "Running checkSpeeds.")
  the.warning <- NULL
  vm <- valid.movements
  warning.counter <- 0
  if (any(na.as.false(vm$Average.speed.m.s >= speed.warning))) {
    link <- which(vm$Average.speed.m.s >= speed.warning)
    if (link[1] == 1) {
      appendTo(c("Report", "Warning", "Screen"),
        the.warning <- paste0("Tag ", tag, " ", n, " had an average speed of ", round(vm$Average.speed.m.s[1], 2),
          " m/s from release to first valid event (Release -> ", vm$Array[1], ")."))
      the.warning <- paste("Warning:", the.warning)
      link <- link[-1]
      warning.counter <- warning.counter + 1
    }
    if (length(link) > 0) {
      for (i in 1:length(link)) {
        warning.counter <- warning.counter + 1
        if (warning.counter < 5) {
          appendTo(c("Report", "Warning", "Screen"),
            other.warning <- paste0("Tag ", tag, " ", n, " had an average speed of ", round(vm$Average.speed.m.s[link[i]], 2),
              " m/s from valid event ", link[i] - 1, " to ", link[i], " (",vm$Array[link[i] - 1], " -> ", vm$Array[link[i]], ")."))
          other.warning <- paste("Warning:", other.warning)
          the.warning <- paste0(the.warning, "\n", other.warning)
        } else {
          final.warning <- paste0("Warning: Tag ", tag, " ", n, " had an average speed higher than ", speed.warning, " m/s in ", warning.counter, " events (of which the first 4 are displayed above).")
          message(paste0("\r", final.warning), appendLF = FALSE); flush.console()
        }
      }
      if (warning.counter >= 5) {
        message()
        appendTo(c("Report", "Warning"), sub("Warning: ", "", final.warning))
        link <- createEventRanges(link)
        appendTo(c("Screen", "Report"), event.list <- paste0("         Events that raised warnings: ", paste(link, collapse = ", ")))
        the.warning <- paste0(the.warning, "\n", final.warning, "\n", event.list)
      }
    }
  }
  # Trigger user interaction
  if (any(na.as.false(vm$Average.speed.m.s >= speed.error))) { # nocov start
    movements <- tableInteraction(moves = movements, tag = tag, detections = detections, 
                                  trigger = the.warning, GUI = GUI, save.tables.locally = save.tables.locally)
  } # nocov end
  return(movements)
}

#' Find if a tag is standing still in an array
#'
#' @inheritParams check_args
#' @inheritParams explore
#'
#' @return A list of movements with updated 'Valid' columns
#'
#' @keywords internal
#'
checkInactiveness <- function(movements, tag, detections, n,
  inactive.warning, inactive.error, dist.mat, GUI, save.tables.locally) {
  Valid <- NULL
  appendTo("debug", "Running checkInactiveness.")
  if (any(movements$Valid)) {
    valid.moves <- movements[(Valid)]
    # Find first and last potentially inactive movement
    breaks <- rle(valid.moves$Array)
    if(length(breaks$lengths) > 1) {
      Start <- sum(breaks$lengths[1:(length(breaks$lengths) - 1)]) + 1
    } else {
      Start <- 1
    }
    Stop <- nrow(valid.moves)
    # Fetch respective detection rows
    valid.row.list <- lapply(Start:Stop, function(j) {
      Start <- min(which(detections$Timestamp == valid.moves$First.time[j] & detections$Standard.name == valid.moves$First.station[j]))
      Stop <- Start + (valid.moves$Detections[j] - 1)
      return(Start:Stop)
    })
    # Start trimming from the Start to see if a period of inactiveness is present
    continue <- TRUE
    iteration <- 1
    while (continue) {
      the.warning <- NULL
      # count days spent to compare with arguments
      start_i <- Start + iteration - 1
      # Stop if we have reached the end of the possible iterations
      if (start_i > Stop)
        break()
      days.spent <- round(as.numeric(difftime(valid.moves$Last.time[Stop], valid.moves$First.time[start_i], units = "days")), 2)
      # Stop if the days.spent are lesser than enough to trigger a warning
      if (days.spent < inactive.warning)
        break()
      valid.rows <- unlist(valid.row.list[iteration:length(valid.row.list)])
      the.detections <- detections[valid.rows, ]
      # find all stations
      the.stations <- as.character(sort(unique(the.detections$Standard.name)))
      trigger.error <- FALSE
        # Trigger warning
      if (attributes(dist.mat)$valid) {
        aux <- dist.mat[the.stations, the.stations]
        if (all(aux <= 1500)) {
          n.detections <- sum(valid.moves$Detections[start_i:Stop])
          appendTo(c("Report", "Warning", "Screen"),
            the.warning <- paste0("Tag ", tag, " ", n, " was detected ", n.detections,
              " times at stations less than 1.5 km apart in array '", tail(breaks$values, 1),
              "' (", paste(the.stations, collapse = ", "), "), over ", days.spent,
              " days and then disappeared. Could it be inactive?"))
          the.warning <- paste("Warning:", the.warning)
          continue <- FALSE
        }
        if (all(aux <= 1500) & days.spent >= inactive.error)
          trigger.error <- TRUE # nocov
      } else {
        if (length(the.stations) <= 3) {
          n.detections <- sum(valid.moves$Detections[start_i:Stop])
          appendTo(c("Report", "Warning", "Screen"),
            the.warning <- paste0("Tag ", tag, " ", n, " was detected ", n.detections,
              " times at three or less stations of array '", tail(breaks$values, 1),
              "' (", paste(the.stations, collapse = ", "), ") over ", days.spent,
              " days and then disappeared. Could it be inactive?"))
          the.warning <- paste("Warning:", the.warning)
          continue <- FALSE
        }
        if (length(the.stations) <= 3 & days.spent >= inactive.error)
          trigger.error <- TRUE # nocov
      }
      # Trigger user interaction
      if (trigger.error) { # nocov start
        appendTo("Screen", error.message <- paste0("M: Tag ", tag, " ", n, " has been inactive for more than ", inactive.error," days. Inactiveness started on event ", start_i, " (", as.Date(valid.moves$First.time[start_i]),")."))
        movements <- tableInteraction(moves = movements, tag = tag, detections = detections, 
                                      trigger = paste0(the.warning, "\n", error.message), GUI = GUI,
                                      save.tables.locally = save.tables.locally)
      } # nocov end
      iteration <- iteration + 1
    }
  }
  return(movements)
}

#' Find out if a tag moved in an impossible direction
#'
#' @inheritParams check_args
#'
#' @return A list of movements with updated 'Valid' columns
#'
#' @keywords internal
#'
checkImpassables <- function(movements, tag, bio, spatial, detections, dotmat, GUI, save.tables.locally, n){
  appendTo("debug", "Running checkImpassables.")
  Valid <- NULL

  release <- as.character(bio$Release.site[na.as.false(bio$Transmitter == tag)])
  release <- unlist(strsplit(with(spatial, release.sites[release.sites$Standard.name == release, "Array"]), "|", fixed = TRUE))

  restart <- TRUE
  first.time <- TRUE
  while (restart) {
    restart <- FALSE
    warning.counter <- 0
    the.warning <- NULL
    valid.moves <- movements[(Valid)]
    if (!first.time) {
      message("------------------------------------")
      appendTo(c("Screen", "Warning"), "The last interaction did not solve the impassable problem! See remaining problems below.\n         You can also press ESC to abort the current run and alter your spatial.txt file.")
      message("------------------------------------")
    }
    # check release movement
    if (sum(movements$Valid) > 0) {
      if(all(is.na(dotmat[as.character(release), as.character(valid.moves$Array[1])]))) {
        appendTo(c("Screen", "Warning", "Report"), the.warning <- paste0("Tag ", tag, " ", n, " made an impassable jump: It is not possible to go from release site ", as.character(release), " to ", as.character(valid.moves$Array[1]), ".\n         Please resolve this either by invalidating events or by adjusting your 'spatial.txt' file and restarting."))
        the.warning <- paste("Warning:", the.warning)
        warning.counter <- warning.counter + 1
      }
    }
    # check other movements
    if (sum(movements$Valid) > 1) {
      shifts <- data.frame(
        A = valid.moves$Array[-nrow(valid.moves)],
        B = valid.moves$Array[-1])
      distances <- apply(shifts, 1, function(x) dotmat[x[1], x[2]])
      if (any(is.na(distances))) {
        for (i in which(is.na(distances))) {
          warning.counter <- warning.counter + 1
          if (warning.counter < 5) {
            appendTo(c("Screen", "Warning", "Report"), other.warning <- paste0("Tag ", tag, " ", n, " made an impassable jump in events ", i," to ", i + 1, ": It is not possible to go from array ", shifts[i, 1], " to ", shifts[i, 2], "."))
            other.warning <- paste("Warning:", other.warning)
            the.warning <- paste0(the.warning, "\n", other.warning)
          } else {
            final.warning <- paste0("Warning: Tag ", tag, " made ", warning.counter, " impassable jumps (of which the first 4 are displayed above).")
            message(paste0("\r", final.warning), appendLF = FALSE); flush.console()
          }
        }
        if (warning.counter >= 5) {
          message("")
          appendTo(c("Report", "Warning"), sub("Warning: ", "", final.warning))
          link <- createEventRanges(which(is.na(distances)))
          appendTo(c("Screen", "Report"), event.list <- paste0("         Events that raised warnings: ", paste(link, collapse = ", ")))
          the.warning <- paste0(the.warning, "\n", final.warning, "\n", event.list)
        }
      }
    }
    if (!is.null(the.warning)) {
      message("Please resolve this either by invalidating events or by adjusting your 'spatial.txt' file and restarting.")
      if (interactive()) { # nocov start
        the.warning <- paste(the.warning, "\nPlease resolve this either by invalidating events or by adjusting your 'spatial.txt' file and restarting.", collapse = "\n")
        movements <- tableInteraction(moves = movements, tag = tag, detections = detections, 
                                      trigger = the.warning, GUI = GUI, force = TRUE, 
                                      save.tables.locally = save.tables.locally)
        restart <- TRUE
        first.time <- FALSE
      } else { # nocov end
        stop("Preventing analysis from entering interactive mode in a non-interactive session.")
      }
    }
  }
  return(movements)
}

#' Verify number of detections in section movements
#'
#' @inheritParams check_args
#' @inheritParams residency
#'
#' @return A list of section movements with updated 'Valid' columns
#'
#' @keywords internal
#'
checkSMovesN <- function(secmoves, tag, section.warning, section.error, GUI, save.tables.locally, n) {
  appendTo("debug", "Running checkSMovesN.")

  if (any(secmoves$Detections <= section.warning & secmoves$Valid)) {
    the.warning <- paste0("Section movements with ", section.warning, " or less detections are present for tag ", tag, " ", n, ".")
    appendTo(c("Screen", "Report", "Warning"), the.warning)
  }

  if (any(secmoves$Detections <= section.error & secmoves$Valid)) {
    secmoves <- tableInteraction(moves = secmoves, tag = tag, trigger = the.warning, # nocov
                                 GUI = GUI, save.tables.locally = save.tables.locally) # nocov
  }

  return(secmoves)
}

#' Check that the tag linearly moved along the sections
#'
#' @inheritParams check_args
#' @inheritParams migration
#'
#' @return A list of section movements with updated 'Valid' columns
#'
#' @keywords internal
#'
checkLinearity <- function(secmoves, tag, spatial, arrays, GUI, save.tables.locally, n) {
  appendTo("debug", "Running checkLinearity.")

  valid.secmoves <- secmoves[secmoves$Valid, ]

  sections <- names(spatial$array.order)
  back.check <- match(valid.secmoves$Section, sections)
  turn.check <- rev(match(sections, rev(valid.secmoves$Section))) # captures the last event of each section. Note, the values count from the END of the events
  if (is.unsorted(back.check)) {
      if (is.unsorted(turn.check, na.rm = TRUE))
        appendTo(c("Screen", "Report", "Warning"), the.warning <- paste0("Inter-section backwards movements were detected for tag ", tag, " ", n, " and the last events are not ordered!"))
      else
        appendTo(c("Screen", "Report", "Warning"), the.warning <- paste0("Inter-section backwards movements were detected for tag ", tag, " ", n, "."))
    if (interactive()) { # nocov start
      secmoves <- tableInteraction(moves = secmoves, tag = tag, trigger = the.warning, 
                                   GUI = GUI, force = FALSE, save.tables.locally = save.tables.locally)
    } # nocov end
  }
  return(secmoves)
}

#' Check report compatibility
#'
#' Checks if pandoc is up and running and creates a "Report" folder, if necessary
#'
#' @inheritParams explore
#'
#' @return An updated report argument (logical)
#'
#' @keywords internal
#'
checkReport <- function(report){
  appendTo("debug", "Running checkReport.")
  if (report) {
    appendTo("Report", "M: 'report' option has been activated.")
    if (!rmarkdown::pandoc_available()) {
      appendTo(c("Screen", "Report", "Warning"), "'report' can only be activated if pandoc is installed. You can find how to install pandoc at: https://pandoc.org/installing.html\n   You can also check if pandoc is available to R by running rmarkdown::pandoc_available()")
      message("Would you like to:\n\n  a) Stop the analysis and install pandoc.\n  b) Continue with 'report' set to FALSE\n")
      decision <- userInput("Decision:(a/b) ", choices = letters[1:2], hash = "# pandoc warning")
      if (decision == "a")
        stopAndReport("Analysis stopped per user command.")
      if (decision == "b") {
        appendTo(c("Screen", "Report", "Warning"), "Deactivating 'report' to prevent function failure.")
        report <- FALSE
      }
    }
  }
  return(report)
}

#' Check for movements upstream of the release site.
#'
#' @inheritParams check_args
#'
#' @return A data frame with the movements for the target tag with updated 'Valid' column.
#'
#' @keywords internal
#'
checkFirstDetBackFromRelease <- function(movements, tag, bio, detections, arrays, spatial, GUI, save.tables.locally, n) {
  appendTo("debug", "Running checkFirstDetBackFromRelease.")
  # NOTE: The NULL variables below are actually column names used by data.table.
  # This definition is just to prevent the package check from issuing a note due unknown variables.
  Valid <- NULL
  Array <- NULL

  release <- as.character(bio$Release.site[na.as.false(bio$Transmitter == tag)])
  release <- unlist(strsplit(with(spatial, release.sites[release.sites$Standard.name == release, "Array"]), "|", fixed = TRUE))

  the.warning <- NULL
  after.arrays <- unique(c(release, unlist(lapply(release, function(x) arrays[[x]]$all.after.and.par))))

  if (any(movements$Valid))
    vm <- movements[(Valid)]
  else
    return(movements)

  if (any(is.na(match(vm$Array, after.arrays)))) {
    appendTo(c("Screen", "Report", "Warning"), the.warning <- paste0("Tag ", tag, " ", n, " was detected in an array that is not after its release site! Opening relevant data for inspection.\nExpected first array: ", release))
    the.warning <- paste("Warning:", the.warning)
    if (interactive()) { # nocov start
      movements <- tableInteraction(moves = movements, tag = tag, detections = detections, 
                                    trigger = the.warning, GUI = GUI, save.tables.locally = save.tables.locally)
    } # nocov end
  }
  return(movements)
}

#' Check if tags are jumping over arrays
#'
#' @inheritParams check_args
#' @inheritParams explore
#'
#' @return A list of movements with updated 'Valid' columns
#'
#' @keywords internal
#'
checkJumpDistance <- function(movements, tag, bio, detections, spatial, arrays,
  dotmat, paths, jump.warning, jump.error, GUI, save.tables.locally, n) {

  appendTo("debug", "Running checkJumpDistance.")
  # NOTE: The NULL variables below are actually column names used by data.table.
  # This definition is just to prevent the package check from issuing a note due unknown variables.
  Valid <- NULL
  the.warning <- NULL
  warning.counter <- 0
  events.to.complain.about <- NULL
 
  release <- as.character(bio$Release.site[na.as.false(bio$Transmitter == tag)])
  release <- unlist(strsplit(with(spatial, release.sites[release.sites$Standard.name == release, "Array"]), "|", fixed = TRUE))
  release.time <- bio$Release.date[na.as.false(bio$Transmitter == tag)] 

  if (any(movements$Valid)) {
    vm <- movements[(Valid)]
    #########################
    # CHECK RELEASE TO FIRST
    #########################
    # remove any potential first array that is not connected do the first move (this should never happen, but still...)
    release <- release[!is.na(dotmat[as.character(release), as.character(vm$Array[1])])]
    # stop if no arrays are connected to the first move. This should also never happen actually.
    if (length(release) == 0)
        stopAndReport("There are unresolved impassable jumps in the movements (Found at release).")
    # minimum jump size
    release.steps <- min(dotmat[as.character(release), as.character(vm$Array[1])] + 1)
    # Check release-to-first
    if (release.steps > 1) {
      # determine if any arrays were not active during the movement.
      path.dist <- list()
      for (r in release) {
        sub.paths <- paths[[paste0(r, "_to_", vm$Array[1])]]
        if (is.null(sub.paths)) { # failsafe in case step size is 2
          aux <- list(list(n = 2, names = r))
        } else {
          aux <- lapply(sub.paths, function(p) {
            xarrays <- unlist(strsplit(p, " -> "))
            xarrays <- sapply(xarrays, function(a) {
              # if the movement ocurred before the start
              v1 <- arrays[[a]]$live$Start > release.time & 
                    arrays[[a]]$live$Start > vm$First.time[1]
              # or after the stop
              v2 <- arrays[[a]]$live$Stop < release.time & 
                    arrays[[a]]$live$Stop < vm$First.time[1]
              # then that period does not qualify
              v3 <- !(v1 | v2)
              # and if any period qualifies, then the array was up during the movememnt
              any(v3)
            })
            return(list(n = sum(xarrays) + 2, names = names(xarrays)[xarrays])) 
            # +2 because the release site and the array that picked up the animal also
            # count as steps, so the minimal step size is two.
          })
        }
        names(aux) <- sub.paths
        path.dist <- c(path.dist, aux)
        rm(aux)
      }
      new.steps <- sapply(path.dist, function(x) x$n)
      release.steps <- min(new.steps)
      say.at.least <- min(new.steps) != max(new.steps)
      rm(new.steps)
    }
    if (release.steps > jump.warning) {
      # Trigger warning
      appendTo(c("Report", "Warning", "Screen"),
        the.warning <- paste0("Tag ", tag, " ", n, " jumped through ", 
          ifelse(say.at.least, "at least ", ""), release.steps - 1,
          ifelse(release.steps > 2, " arrays ", " array "),
          "from release to first valid event (Release -> ", vm$Array[1], ")."))
      the.warning <- paste("Warning:", the.warning)
      warning.counter <- warning.counter + 1
      events.to.complain.about <- c(events.to.complain.about, 1)
      rm(say.at.least)
    }
    if (release.steps > jump.error)
      trigger.error <- TRUE # nocov
    else
      trigger.error <- FALSE

    #########################
    # CHECK EVENT TO EVENT
    #########################
    if (nrow(vm) > 1) {
      A <- vm$Array[-nrow(vm)]
      B <- vm$Array[-1]
      aux <- cbind(A, B)
      move.steps <- apply(aux, 1, function(x) dotmat[x[1], x[2]])
      names(move.steps) <- paste(A, "->", B)

      if (any(is.na(move.steps)))
        stopAndReport("There are unresolved impassable jumps in the movements (Found during moves).")

      if (any(move.steps > 1)) {
        # isolate troublesome events
        steps.to.check <- which(move.steps > 1)
        # confirm that arrays were active
        for (i in steps.to.check) {
          sub.paths <- paths[[paste0( vm$Array[i], "_to_", vm$Array[i + 1])]]
          path.dist <- lapply(sub.paths, function(p) {
            xarrays <- unlist(strsplit(p, " -> "))
            xarrays <- sapply(xarrays, function(a) {
              # if the movement ocurred before the start
              v1 <- arrays[[a]]$live$Start > vm$Last.time[i] & 
                    arrays[[a]]$live$Start > vm$First.time[i + 1]
              # or after the stop
              v2 <- arrays[[a]]$live$Stop < vm$Last.time[i] & 
                    arrays[[a]]$live$Stop < vm$First.time[i + 1]
              # then that period does not qualify
              v3 <- !(v1 | v2)
              # and if any period qualifies, then the array was up during the movememnt
              any(v3)
            })
            return(list(n = sum(xarrays) + 1, names = names(xarrays)[xarrays]))
            # +1 because the target array also counts as a step
          })
          names(path.dist) <- sub.paths
          new.steps <- sapply(path.dist, function(x) x$n)
          move.steps[i] <- min(new.steps)
          say.at.least <- min(new.steps) != max(new.steps)
          if (move.steps[i] > jump.warning) { # because ">", then if jump.warning = 1, actel only complains if steps = 2.
            warning.counter <- warning.counter + 1
            events.to.complain.about <- c(events.to.complain.about, i + 1)
            if (warning.counter < 5) {
              # Trigger warning
              appendTo(c("Report", "Warning", "Screen"),
                other.warning <- paste0("Tag ", tag, " ", n, " jumped through ",  
                  ifelse(say.at.least, "at least ", ""), move.steps[i] - 1,
                  ifelse(move.steps[i] > 2, " arrays ", " array "),
                  "in valid events ", i, " -> ", i + 1, " (", names(move.steps)[i], ")."))
              other.warning <- paste("Warning:", other.warning)
              the.warning <- paste0(the.warning, "\n", other.warning)
            } else {
              final.warning <- paste0("Warning: Tag ", tag, " ", n, " jumped ", jump.warning, " or more arrays on ", warning.counter, " occasions (of which the first 4 are displayed above).")
              message(paste0("\r", final.warning), appendLF = FALSE); flush.console()
            }
          }
          rm(say.at.least)
          if (move.steps[i] > jump.error) { # same as if above.
            trigger.error <- TRUE # nocov
          }
        }
        if (warning.counter >= 5) {
          message("")
          appendTo(c("Report", "Warning"), sub("Warning: ", "", final.warning))
          link <- createEventRanges(events.to.complain.about)         
          appendTo(c("Screen", "Report"), event.list <- paste0("         Events that raised warnings: ", paste(link, collapse = ", ")))
          the.warning <- paste0(the.warning, "\n", final.warning, "\n", event.list)
        }
      }
    }
    # Trigger user interaction
    if (interactive() && trigger.error) { # nocov start
      movements <- tableInteraction(moves = movements, tag = tag, detections = detections, 
                                    trigger = the.warning, GUI = GUI, save.tables.locally = save.tables.locally)
    } # nocov end
  }
  return(movements)
}

#' Confirm that receivers were not re-deployed before being retrieved
#'
#' @param input The table of deployments
#'
#' @return No return value, called for side effects.
#'
#' @keywords internal
#'
checkDeploymentTimes <- function(input) {
  appendTo("debug", "Running checkDeploymentTimes.")
  aux <- split(input, input$Receiver)
  for (i in 1:length(aux)) {
    if (nrow(aux[[i]]) > 1) {
      A <- aux[[i]]$Start[-1]
      B <- aux[[i]]$Stop[-nrow(aux[[i]])]
      AtoB <- as.numeric(difftime(A, B))
      if (any(AtoB < 0)) {
        appendTo(c("Screen", "Report"), paste0("Error: Receiver ", names(aux)[i], " was re-deployed before being retrieved:\n"))
        aux[[i]][, "Bleh"] <- ""
        aux[[i]][c(FALSE, AtoB < 0), "Bleh"] <- " <- !!!"
        names(aux[[i]])[ncol(aux[[i]])] <- ""
        message(paste0(capture.output(aux[[i]])[-1], collapse = "\n"))
        message("")
        stopAndReport("Fatal exception found. Read lines above for more details.")
      }
    }
  }
}

#' Confirm that the station names in the deployments table match those listed in the spatial file
#'
#' @param input The table of deployments
#' @inheritParams check_args
#'
#' @return A data frame with the deployment locations
#'
#' @keywords internal
#'
checkDeploymentStations <- function(input, spatial) {
  appendTo("debug","Running checkDeploymentStations.")
  aux <- spatial[spatial$Type == "Hydrophone", ]
  link <- match(unique(input$Station.name), aux$Station.name)
  if (any(is.na(link))) {
    appendTo(c("Screen", "Report", "Warning"), 
      paste0("The following station", ifelse(sum(is.na(link)) > 1, "s are", " is"), 
        " listed in the deployments but ",
        ifelse(sum(is.na(link)) > 1, "are", "is"), 
        " not part of the study's stations: '", 
        paste(unique(input$Station.name)[is.na(link)], collapse = "', '"), 
        "'\nDiscarding deployments at unknown stations."))
    to.remove <- match(input$Station.name, unique(input$Station.name)[is.na(link)])
    input <- input[is.na(to.remove), ]
  }
  link <- match(aux$Station.name, unique(input$Station.name))
  if (any(is.na(link))) {
    stopAndReport(paste0("The following station", 
      ifelse(sum(is.na(link)) > 1, "s are", " is"),
      " listed in the spatial file but no receivers were ever deployed there: '",
      paste(aux$Station.name[is.na(link)], collapse = "', '"),
      "'\n"))
  }
  input$Standard.name <- aux$Standard.name[match(input$Station.name, aux$Station.name)]
  input$Array <- aux$Array[match(input$Station.name, aux$Station.name)]

  return(input[, c("Receiver", "Array", "Station.name", "Standard.name", "Start", "Stop")])
}

#' Find detections from unknown receivers
#'
#' @param input The detections data frame
#'
#' @return No return value, called for side effects.
#'
#' @keywords internal
#'
checkUnknownReceivers <- function(input) {
  appendTo("debug", "Running checkUnknownReceivers.")
  unknown <- is.na(input$Standard.name)
  if (any(unknown)) {
    how.many <- length(unique(input$Receiver[unknown]))
    appendTo(c("Screen", "Report", "Warning"), 
      paste0("Detections from receiver", 
        ifelse(how.many > 1, "s ", " "), 
        paste(unique(input$Receiver[unknown]), collapse = ", "), " are present in the data, but ",
        ifelse(how.many > 1, "these receivers are", "this receiver is"),
        " not part of the study's stations. Double-check potential errors."))
  }
}

#' Check for target data in the unknown receivers
#'
#' @inheritParams check_args
#'
#' @return A list containing an updated spatial list and a TRUE/FALSE object indicating whether or not Standard station names must be reprocessed.
#'
#' @return A list containing:
#' \itemize{
#'  \item \code{spatial}: A list containing the spatial elements of the study, with data for the unknown receivers, if relevant.
#'  \item \code{deployments}: A list containing the receiver deployments, with data for the unknown receivers, if relevant.
#'  \item \code{detections.list}: A list containing the detections for each tag, with updated station names.
#' }
#'
#' @keywords internal
#'
checkTagsInUnknownReceivers <- function(detections.list, deployments, spatial) {
  # NOTE: The NULL variables below are actually column names used by data.table.
  # This definition is just to prevent the package check from issuing a note due unknown variables.
  include.all.unknowns <- FALSE
  exclude.all.unknowns <- FALSE
  processed.unknowns <- NULL
  excluded <- NULL
  included <- NULL

  appendTo("debug", "Running tagsInUnknownReceivers")

  deployed.receivers <- unlist(lapply(deployments, function(x) x$Receiver))
  for (i in names(detections.list)) {
    if (any(is.na(detections.list[[i]]$Standard.name))) {
      # If this is not the first iteration, some receivers may have already been processed.
      if (!is.null(processed.unknowns))
        detections.list[[i]] <- detections.list[[i]][!(detections.list[[i]]$Receiver %in% processed.unknowns), ]

      receivers <- detections.list[[i]]$Receiver
      link <- is.na(match(receivers, deployed.receivers))
      new.unknowns <- unique(detections.list[[i]]$Receiver[link])
      
      if (length(new.unknowns) > 0) {
        appendTo(c("Screen", "Report", "Warning"), paste0("Tag ", i, " was detected in one or more receivers that are not listed in the study area (receiver(s): ", paste(new.unknowns, collapse = ", "), ")!"))
        if (!include.all.unknowns & !exclude.all.unknowns) {
          message("Possible options:\n   a) Stop and double-check the data (recommended)\n   b) Temporarily include receiver(s) \n      (Unknown events will be considered invalid, but will be visible in the detection plots)\n   c) Repeat option b for all unknown receivers\n   d) Discard detections for this unknown receiver (not recommended)\n   e) Repeat option d for all unknown receivers (very much not recommended!)")
          decision <- userInput("Which option should be followed?(a/b/c/d/e/comment) ", choices = c("a", "b", "c", "d", "e", "comment"),
                                tag = i, hash = "# unknown receivers")
        } else {
          decision <- "ignore"
        }

        if (decision == "a")
          stopAndReport("Stopping analysis per user command.") # nocov

        if (decision == "c") {
          include.all.unknowns <- TRUE # nocov
        }
        
        if (include.all.unknowns || decision == "b") {
          recipient <- includeUnknownReceiver(spatial = spatial, deployments = deployments, unknown.receivers = new.unknowns)
          spatial <- recipient[[1]]
          deployments <- recipient[[2]]
          link <- is.na(detections.list[[i]]$Standard.name)
          levels(detections.list[[i]]$Standard.name) <- c(levels(detections.list[[i]]$Standard.name), "Ukn.")
          detections.list[[i]]$Standard.name[link] <- "Ukn."
          levels(detections.list[[i]]$Array) <- c(levels(detections.list[[i]]$Array), "Unknown")
          detections.list[[i]]$Array[link] <- "Unknown"
          levels(detections.list[[i]]$Section) <- c(levels(detections.list[[i]]$Section), "Unknown")
          detections.list[[i]]$Section[link] <- "Unknown"
          processed.unknowns <- c(processed.unknowns, as.character(new.unknowns))
          included <- c(included, as.character(new.unknowns))
        }
        
        if (decision == "e") {
          exclude.all.unknowns <- TRUE # nocov
        }
        
        if (exclude.all.unknowns || decision == "d") {
          detections.list[[i]] <- detections.list[[i]][is.na(match(receivers, new.unknowns)), ] # keep the ones that are not unknown
          processed.unknowns <- c(processed.unknowns, as.character(new.unknowns))
          excluded <- c(excluded, as.character(new.unknowns))
        }
        rm(decision)
      }
    }
  }
  # remove empty data frames (for tags detected only at excluded unknown receivers)
  detections.list <- detections.list[sapply(detections.list, nrow) > 0]
  # append summary to spatial
  if (!is.null(included) | !is.null(excluded))
    spatial$unknowns <- list(included = included, excluded = excluded)
  
  return(list(spatial = spatial, deployments = deployments, detections.list = detections.list))
}

#' Temporarily include missing receivers in the spatial object
#'
#' @inheritParams check_args
#'
#' @return A list containing:
#' \itemize{
#'  \item \code{spatial}: A list containing the spatial elements of the study, with data for the unknown receivers, if relevant.
#'  \item \code{deployments}: A list containing the receiver deployments, with data for the unknown receivers, if relevant.
#' }
#'
#' @keywords internal
#'
includeUnknownReceiver <- function(spatial, deployments, unknown.receivers){
  appendTo("debug", "Running includeUnknownReceiver.")
  appendTo(c("Screen", "Report"), "M: Including missing receiver(s) in the deployments and stations. Assigning to array 'Unknown' and standard name 'Ukn.'.")
  if (is.na(match("Unknown", levels(spatial$stations$Station.name)))) {
    levels(spatial$stations$Station.name) <- c(levels(spatial$stations$Station.name), "Unknown")
    levels(spatial$stations$Array) <- c(levels(spatial$stations$Array), "Unknown")
    levels(spatial$stations$Section) <- c(levels(spatial$stations$Section), "Unknown")
    spatial$stations[nrow(spatial$stations) + 1, "Station.name"] <- "Unknown"
    spatial$stations[nrow(spatial$stations), "Array"] <- "Unknown"
    spatial$stations[nrow(spatial$stations), "Section"] <- "Unknown"
    spatial$stations[nrow(spatial$stations), "Standard.name"] <- "Ukn."
  }
  for (i in unknown.receivers) {
    if (is.na(match(i, names(deployments)))) {
      deployments[[length(deployments) + 1]] <- data.frame(
        Receiver = i,
        Array = "Unknown",
        Station.name = "Unknown",
        Standard.name = "Ukn.",
        Start = NA_character_,
        Stop = NA_character_)
      names(deployments)[length(deployments)] <- i
    }
  }
  return(list(spatial = spatial, deployments = deployments))
}

#' Check if there are detections for the target tags before release.
#'
#' @param input The list of detections
#' @inheritParams check_args
#'
#' @keywords internal
#'
#' @return A list containing the detections without invalid data.
#'
checkDetectionsBeforeRelease <- function(input, bio, discard.orphans = FALSE){
  appendTo("debug", "Running checkDetectionsBeforeRelease.")
  remove.tag <- NULL
  link <- match(bio$Transmitter, names(input))
  for(i in seq_len(length(link))) {
    if (!is.na(link[i])) {
      if (any(to.remove <- !(input[[link[i]]]$Timestamp > bio$Release.date[i]))) {
        appendTo(c("Screen", "Warning", "Report"), paste0("Tag ", names(input)[link[i]], " was detected before being released!"))
        if (!discard.orphans) {
          appendTo("Screen", paste0("  Release time: ", bio$Release.date[i]))
          appendTo("Screen", paste0("  First detection time: ", input[[link[i]]]$Timestamp[1]))
          appendTo("Screen", paste0("  Number of detections before release: ", sum(to.remove)))
          appendTo("Screen", "\nPossible options:\n   a) Stop and double-check the data (recommended)\n   b) Discard orphan detections in this instance.\n   c) Discard orphan detections for all instances.\n   d) Save orphan detections to a file and re-open dialogue.")
          
          restart <- TRUE
          while (restart) {
            decision <- userInput("Decision:(a/b/c/d/comment) ", 
                                  choices = c("a", "b", "c", "d", "comment"),
                                  tag = bio$Transmitter[i], 
                                  hash = paste("# detections before release for tag", bio$Transmitter[i]))
            
            if (decision == "a")
              stopAndReport("Function stopped by user command.") # nocov
            
            if (decision == "b")
              restart <- FALSE

            if (decision == "c") {
              discard.orphans <- TRUE # nocov
              restart <- FALSE # nocov
            }

            if (decision == "d") { # nocov start
              file.name <- userInput("Please specify a file name (leave empty to abort saving): ", hash = "# save pre-release orphans to this file")
              # break if empty
              if (file.name == "")
                next()
              # confirm extension
              if (!grepl("\\.csv$", file.name))
                file.name <- paste0(file.name, ".csv")
              # prevent auto-overwrite
              if (file.exists(file.name)) {
                aux <- userInput(paste0("File '", file.name, "' already exists. Overwrite contents?(y/n) "), 
                                 choices = c("y", "n"), 
                                 hash = "# overwrite file with same name?")
                if (aux == "y")
                  overwrite <- TRUE
                else
                  overwrite <- FALSE 
              }
              else
                overwrite <- TRUE
              # save
              if (overwrite) {
                success <- TRUE
                # recover if saving fails
                tryCatch(data.table::fwrite(input[[link[i]]][to.remove, ], file.name, , dateTimeAs = "write.csv"), error = function(e) {
                  appendTo(c("Screen", "Report"), paste0("Error: Could not save file (reason: '", sub("\n$", "", e), "').\n       Reopening previous interaction."))
                  success <<- FALSE
                })
                if (success)
                  appendTo(c("Screen", "Report"), paste0("M: A copy of the orphan detections has been saved to '", file.name, "'.\n   Reopening previous interaction."))
              }
            } # nocov end
          }
        }
        if (all(to.remove)) {
          appendTo(c("Screen", "Report"), paste0("M: ALL detections from tag ", names(input)[link[i]], " removed per user command."))
          remove.tag <- c(remove.tag, link[i])
        } else {
          input[[link[i]]] <- input[[link[i]]][!to.remove, ]
          appendTo(c("Screen", "Report"), paste0("M: ", sum(to.remove), " detection(s) from tag ", names(input)[link[i]], " removed per user command."))
        }
      }
    }
  }
  if (!is.null(remove.tag)) {
    input <- input[-remove.tag]
  }
  return(input)
}

#' Check if there are detections matching the target tags.
#'
#' @param input The list of detections
#' @inheritParams check_args
#'
#' @return No return value, called for side effects.
#'
#' @keywords internal
#'
checkNoDetections <- function(input, bio){
  appendTo("debug", "Running checkNoDetections.")
  if ('Code.space' %in% colnames(bio))
    link <- match(paste0(bio$Code.space, '-', lowestSignal(bio$Signal)), names(input))
  else
    link <- match(lowestSignal(bio$Signal), extractSignals(names(input)))

  if (all(is.na(link)))
    stopAndReport("No detections were found in the input data which matched the target signals.\n")
}

#' Check if there are duplicated signals in the detected tags.
#'
#' @param input list of detections
#' @param bio the biometrics table
#'
#' @return No return value, called for side effects.
#'
#' @keywords internal
#'
checkDupSignals <- function(input, bio){
  appendTo("debug", "Running checkDupSignals.")
  
  if (any(colnames(bio) == "Code.space")) {
    appendTo('debug', 'Debug: Skipping checkDupSignals as there is a codespace column')
  }
  else {  
    signals <- extractSignals(names(input))
    expected <- suppressWarnings(as.numeric(unlist(strsplit(as.character(bio$Signal), "|", fixed = TRUE))))
    to.check <- match(signals, expected)
    if (any(table(to.check) > 1)) {
        bind_list_with_expected <- cbind(names(input), expected[to.check])
        remove_non_detected <- bind_list_with_expected[complete.cases(bind_list_with_expected), ]
        table_the_signals <- table(remove_non_detected[, 1], remove_non_detected[, 2])

        dupsig <- data.frame(Signal = colnames(table_the_signals)[apply(table_the_signals, 
            2, sum) > 1], Tags = NA, stringsAsFactors = FALSE)
        for (i in seq_len(nrow(dupsig))) {
            dupsig$Tags[i] <- paste(row.names(table_the_signals)[table_the_signals[, dupsig$Signal[i]] == 1], collapse = ", ")
        }

        rest.of.message <- NULL
        for (i in seq_len(nrow(dupsig))) {
            rest.of.message <- paste0(rest.of.message, "\n   Signal ", 
                                      dupsig$Signal[i], " was found on tags ", 
                                      dupsig$Tags[i], ".")
        }

        stopAndReport("One or more signals match more than one tag in the detections! Showing relevant signals/tags.", 
            rest.of.message)
    }
  }
}

#' warn users if they are about to run into an unfixed bug.
#' 
#' @return No return value, called for side effects.
#'
#' @keywords internal
#'
checkIssue79 <- function(arrays, spatial) {

  output <- lapply(names(arrays), function(i) {
    link <- match(i, spatial$stations$Array)
    this.section <- as.character(unique(spatial$stations$Section[link]))

    link <- match(arrays[[i]]$before, spatial$stations$Array)
    before <- as.character(unique(spatial$stations$Section[link]))

    if (length(before) > 0) {
      before <- data.frame(
        Section = this.section,
        Neighbour = before,
        type = "Before")
    } else {
      before <- NULL
    }

    link <- match(arrays[[i]]$after, spatial$stations$Array)
    after <- as.character(unique(spatial$stations$Section[link]))

    if (length(after) > 0) {
      after <- data.frame(
        Section = this.section,
        Neighbour = after,
        type = "After")
    } else {
      after <- NULL
    }
    
    return(rbind(before, after))
  })

  x <- do.call(rbind, output)
  x <- x[apply(x, 1, function(i) i[1] != i[2]), ]
  x$tmp <- paste(x[,1], x[,2], x[,3])
  x[!duplicated(x$tmp), ]
  x$tmp <- NULL

  link <- aggregate(x$type, list(x$Section), function(i) any(duplicated(i)))$x

  if (any(link)) {
    if (getOption("actel.bypass_issue_79", default = FALSE)) {
        appendTo(c("Screen", "warning", "report"), "This study area seems to trigger issue 79. However, you have activated the bypass, so the analysis will continue.")     
    } else {
stopAndReport(
"READ CAREFULLY

It seems your study area contains parallel sections. actel is currently incapable of comprehending parallel sections during migration. This bug (issue 79) was brought to light in version 1.2.1, but a fix has not been found yet. This bug is easy to circumvent: you must make sure that the study area sections are sequential. Otherwise, the survival values per section could become compromised. If you wish to read more about this issue (when it appears, what it causes, and how to avoid it), please visit https://hugomflavio.github.io/actel-website/issue_79.html

If you really want to run your analysis as is, or if you think this error came up unnecessarily, you can force the analysis by running the following command and restarting the analysis:

options(actel.bypass_issue_79 = TRUE)

If this issue impacts you and you want to help me fix it, feel free to reach out.

")
    }
  }
}