R/print.sequencecheck.r

In gobbios/EloRating: Animal Dominance Hierarchies by Elo Rating

# print.sequencecheck 14_11_19

#' prints its argument
#'
#' prints its argument
#'
#' @param x result from \code{\link{seqcheck}}
#' @param ... further arguments passed to or from other methods (ignored here)
#'
#' @author Christof Neumann
#'
#' @export
#'
#' @examples
#' data(adv)
#' data(advpres)
#' print(seqcheck(winner = adv$winner, loser = adv$loser, Date = adv$Date,
#'                  presence = advpres))

print.sequencecheck <- function(x, ...) {
  cat("Presence data supplied, see below for details\n")
  # purely interaction sequence
  if (x$checksum["IDcheck"] == 1) cat("IDs occur in the data with inconsistent capitalization (ignore if on purpose)...WARNING\n")
  if (x$checksum["selfinteractions"] == 1) cat(x$selfinteractions, "\n", sep = "")
  if (x$checksum["length"] == 1) cat("Your data vectors do not match in length\n")
  if (x$checksum["singledayobs"] == 1) cat("The following individuals were observed only on one day: ", paste(x$singledaycases, collapse = ", "), " ...WARNING\n", sep = "" )
  if (x$checksum["seqdateorder"] == 1) cat("Date column is not ordered...WARNING\n")

  if (x$checksum["selfinteractions"] + x$checksum["IDcheck"] + x$checksum["length"] + x$checksum["singledayobs"] + x$checksum["seqdateorder"] == 0) cat("Everything seems to be fine with the interaction sequence...OK\n")

  # presence related

  if (x$checksum["presence"] == 0) cat("\n#####################################\n\n")

  if (x$checksum["datecol"] == 1) cat("No 'Date' column found in presence...ERROR\n")

  if (x$checksum["startpresence1"] == 1) cat("Presence starts earlier than data...WARNING\n")
  if (x$checksum["startpresence2"] == 1) cat("Presence starts AFTER data...ERROR\n")
  if (x$checksum["endpresence1"] == 1) cat("Presence stops BEFORE data...ERROR\n")
  if (x$checksum["endpresence2"] == 1) cat("Presence continues beyond data...WARNING\n")

  if (x$checksum["IDmatch"] == 1) {
    cat("IDs in datasequence and presence do not match!\n")
    if (x$IDmatch1[1] != "none") {
      cat("The following IDs occur in the presence data but NOT in the data sequence:...WARNING\n")
      cat("   ", paste(x$IDmatch1, collapse = ", "), "\n")
    }
    if (x$IDmatch2[1] != "none") {
      cat("The following IDs occur in the data sequence but NOT in the presence data:...ERROR\n")
      cat("   ", paste(x$IDmatch2, collapse = ", "), "\n")
    }
  }

  if (x$checksum["IA_presencematch"] == 1) {
    cat("During the following interactions, IDs were absent according to the presence data:...ERROR\n")
    cat("   ", paste(x$IA_presencematchN, collapse = ", "), "\n")
  }

  if (x$checksum["IA_presencematch"] == 2) {
    cat("Your presence data does not match the interaction data and therefore no check could be performed as to whether IDs were actually present on interaction dates...WARNING\n")
  }
  
  if (x$checksum["zeropresencerow"] == 1) {
    cat(x$zeropresencerow, "...ERROR\n")
  }
  

  if (x$checksum["presenceentries"] == 1) cat("At least one presence entry is not 1 or 0...ERROR\n")

  if (x$checksum["continouspres"] == 1) cat("There appear to be gaps in your presence (days missing?)...ERROR\n")

  if (sum(x$checksum[c("startpresence1", "startpresence2", "endpresence1", "endpresence2", "IDmatch", "IA_presencematch", "presenceentries", "datecol", "continouspres", "zeropresencerow")]) == 0) cat("Presence data seems to be fine and matches interaction sequence...OK\n")

  if (x$checksum["presence"] == 0) cat("\n#####################################\n")
}