Defines functions check.criterion check.cutpoints check.threshold check.bn.strength.vs.bn check.bn.strength check.customlist

# check the list of networks passed to custom.strength().
check.customlist = function(custom, nodes) {

  objname = deparse(substitute(custom))

  # check that input is a list.
  if (!is(custom, "list"))
    stop(objname, " must be a list of objects of class 'bn', 'bn.fit' or of arc sets.")

  for (i in seq_along(custom)) {

    if (is(custom[[i]], c("bn", "bn.fit"))) {

      check.nodes(.nodes(custom[[i]]), graph = nodes,
        min.nodes = length(nodes), max.nodes = length(nodes))

    else if (is(custom[[i]], "matrix")) {

      check.arcs(arcs = custom[[i]], nodes = nodes)

    else {

      stop(objname, "[[", i, "]] is not an object of class 'bn', 'bn.fit' or an arc set.")




# check an object of class bn.strength.
check.bn.strength = function(strength, nodes, valid = available.strength.methods) {

  # check that the object is there and with the right class.
  if (missing(strength))
    stop("an object of class 'bn.strength' is required.")
  if (!is(strength, "bn.strength"))
    stop(sprintf("%s must be an object of class 'bn.strength'.",
  # check the object structure.
  if (ncol(strength) %!in% 3:4)
    stop("objects of class 'bn.strength' must have 3 or 4 columns.")
  if (!identical(names(strength), c("from", "to", "strength")) &&
      !identical(names(strength), c("from", "to", "strength", "direction")))
    stop("objects of class 'bn.strength' must be data frames with column names ",
         "'from', 'to', 'strength' and (optionally) 'direction'.")
  if (any(c("method", "threshold") %!in% names(attributes(strength))))
    stop("objects of class 'bn.strength' must have a 'method' and a 'strength' attributes.")
  # check the estimation method.
  if (attr(strength, "method") %!in% valid)
    check.label(attr(strength, "method"), choices = valid,
      argname = "strength estimation methods")


# check that a bn.strength object is consistent with a bn object or node set.
check.bn.strength.vs.bn = function(strength, reference) {

  strength.nodes = attr(strength, "nodes")
  if (is(reference, "bn"))
    reference.nodes = names(reference$nodes)
  else if (is(reference, "character"))
    reference.nodes = reference

  # check the consistency with the network's node set.
  check.nodes(strength.nodes, graph = reference.nodes)


# sanitize the threshold value.
check.threshold = function(threshold, strength) {

  if (missing(threshold))
    return(attr(strength, "threshold"))

  method = attr(strength, "method")

  if (method %in% c("test", "bootstrap", "bayes-factor")) {

    if (!is.probability(threshold))
      stop("the threshold must be a numeric value between 0 and 1.")

  else if (method == "score"){

    if (!is.real.number(threshold) && !is.infinite(threshold))
      stop("the threshold must be numeric value.")




# check the cutpoints used to bin arc strengths.
check.cutpoints = function(cutpoints, strength, threshold, method) {

  if (!missing(cutpoints)) {

    if (method %in% c("test", "bootstrap", "bayes-factor")) {

      # make sure the cutpoints are in the [0, 1] interval.
      if (!is.probability.vector(cutpoints))
        stop("the cutpoints must be numeric values between 0 and 1.")
      # make sure that zero and one are included if needed, so that all strength
      # values fall into an interval.
      if (any(strength < min(cutpoints)) && all(cutpoints != 0))
        cutpoints = c(0, cutpoints)
      if (any(strength > max(cutpoints)) && all(cutpoints != 1))
        cutpoints = c(cutpoints, 1)

    else if (method == "score"){

      # score differences are defined on the whole real axis.
      if (!is.real.vector(cutpoints))
        stop("the cutpoints must be numeric values.")
      # make sure to include +Inf and -Inf are included if needed, so that all
      # strength values fall into an interval.
      if (any(strength < min(cutpoints)) && all(cutpoints != -Inf))
        cutpoints = c(-Inf, cutpoints)
      if (any(strength > max(cutpoints)) && all(cutpoints != +Inf))
        cutpoints = c(cutpoints, +Inf)


    # make sure the cutpoints are unique.
    if (anyDuplicated(cutpoints)) {

      warning("removing duplicated cutpoints.")
      cutpoints = unique(cutpoints)


  else {

    if (method == "test")
      cutpoints = unique(c(0, threshold/c(10, 5, 2, 1.5, 1), 1))
    else if (method %in% c("bootstrap", "bayes-factor"))
      cutpoints = unique(c(0, (1 - threshold)/c(10, 5, 2, 1.5, 1), 1))
    else if (method == "score") {

      # define a set of cut points using the quantiles from the empirical
      # distribution of the score deltas corresponding to significant arcs.
      significant = strength[strength < threshold]
      q = quantile(significant, 1 - c(0.50, 0.75, 0.90, 0.95, 1), names = FALSE)
      cutpoints = c(-Inf, threshold, unique(q), Inf)





# check a string that may be a score or a test label.
check.criterion = function(criterion, data) {

  if (!missing(criterion) && !is.null(criterion)) {

    # check and return errors from minimal.check.labels().
    check.label(criterion, choices = c(available.tests, available.scores),
      labels = c(test.labels, score.labels), argname = "criterion",
      see = "bnlearn-package")

  else {

    # set the defaults using check.score() and check.test().
    if (criterion %in% available.tests)
      criterion = check.test(criterion, data)
    else if (criterion %in% available.scores)
      criterion = check.score(criterion, data)




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bnlearn documentation built on Sept. 7, 2021, 1:07 a.m.