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#' Process Alarms
#'
#' @description Trigger an alarm, if necessary, for incoming multivariate
#' process observations.
#'
#' @param mspMonitor_object An xts matrix returned by the mspMonitor() function
#' @param faultsToTriggerAlarm Specifies how many sequential faults will cause
#' an alarm to trigger. Defaults to 5.
#'
#' @return An xts matrix of the same dimensions as mspMonitor_object, with a
#' recorded negative or positive and type-specific alarm status. Alarm codes
#' are: 0 = no alarm, 1 = Hotelling's T2 alarm, 2 = Squared Prediction Error
#' alarm, and 3 = both alarms.
#'
#' @details This function and the mspMonitor() function are designed to be ran
#' via a scheduled task through Windows "Task Scheduler" or Macintosh OX
#' "launchd" application suites. The file flow is as follows: at each time
#' interval, run the mspMonitor() function on the matrix of daily observations
#' to add a flag status to the most recent incoming observation in the matrix,
#' and return this new xts matrix. Then, pass this updated daily observation
#' matrix to the mspWarning() function, which will check if the process has
#' recorded five or more sequential monitoring statistic flags in a row. Of
#' note, because these functions are expected to be repeatedly called in real
#' time, this function will only check for an alarm within the last row of the
#' xts matrix. To check multiple rows for an alarm state, please use the
#' mspTrain() function, which was designed to check multiple past
#' observations.
#'
#' This function requires an xts matrix returned by the mspMonitor() function.
#'
#' @seealso Pipe flow: \code{\link{mspTrain}} into \code{\link{mspMonitor}}
#' into \code{mspWarning}.
#'
#' @export
#' @importFrom xts lag.xts
#'
#' @examples
#'
#' \dontrun{# cut down on R CMD check time
#'
#' nrml <- mspProcessData(faults = "NOC")
#' n <- nrow(nrml)
#'
#' # Calculate the training summary, but save five observations for monitoring.
#' trainResults_ls <- mspTrain(data = nrml[1:(n - 5), -1],
#' labelVector = nrml[1:(n - 5), 1],
#' trainObs = 4320)
#'
#' # While training, we included 1 lag (the default), so we will also lag the
#' # observations we will test.
#' testObs <- nrml[(n - 6):n, -1]
#' testObs <- xts:::lag.xts(testObs, 0:1)
#' testObs <- testObs[-1,]
#' testObs <- cbind(nrml[(n - 5):n, 1], testObs)
#'
#' # Run the monitoring function.
#' dataAndFlags <- mspMonitor(observations = testObs[, -1],
#' labelVector = testObs[, 1],
#' trainingSummary = trainResults_ls$TrainingSpecs)
#'
#' # Alarm check the last row of the matrix returned by the mspMonitor
#' # function
#' mspWarning(dataAndFlags)
#'
#' }
#'
mspWarning <- function(mspMonitor_object,
faultsToTriggerAlarm = 5){
data_xts <- mspMonitor_object
n <- nrow(data_xts)
# If we see flags on the last row, then we continue
if(data_xts[n, "SPE_Flag"] == 1 || data_xts[n, "T2_Flag"] == 1){
# If we also have enough observations to even trigger an alarm, then we
# continue
if(n >= faultsToTriggerAlarm){
# We create the Alarm Standard
alarmCheck <- rep(1, faultsToTriggerAlarm)
# Now that we are checking the alarm state for observation n, we write a
# 0 over the previous NA value. This shows us that NAs mean the state for
# that specific observation have not been checked.
data_xts[n, "Alarm"] <- 0
# We now check the last few T2 flags
x1 <- as.vector(data_xts[(n - faultsToTriggerAlarm + 1):n, "T2_Flag"])
if(identical(x1, alarmCheck)){
data_xts[n, "Alarm"] <- 1
}
# And we also check the last few SPE flags. We will increment the Alarm
#state based on SPE flag status, T2 flag status, or both
x2 <- as.vector(data_xts[(n - faultsToTriggerAlarm + 1):n, "SPE_Flag"])
if(identical(x2, alarmCheck)){
data_xts[n, "Alarm"] <- data_xts[n, "Alarm"] + 2
}
}
}else{
if(n >= faultsToTriggerAlarm){
# If we didn't see a flag on the last row, then no problem
data_xts[n, "Alarm"] <- 0
}
}
data_xts
}
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