R/bnlearn_sanitization-graphgen.R

In hmma: Constructs Asymmetric Hidden Markov Models

# sanitize the extra arguments passed to the random graph generation algorithms.
check.graph.generation.args = function(method, nodes, extra.args) {

  if (method == "ordered") {

    if (!is.null(extra.args$prob)) {

      # prob must be numeric.
      if (!is.probability(extra.args$prob))
        stop("the branching probability must be a numeric value in [0,1].")

    }#THEN
    else {

      # this default produces graphs with about the same number of
      # arcs as there are nodes.
      extra.args$prob = 2 / (length(nodes) - 1)

    }#ELSE

  }#THEN
  else if (method %in% c("ic-dag", "melancon")) {

    if (!is.null(extra.args$every)) {

      if (!is.positive(extra.args$every))
        stop("'every' must be a positive integer number.")

    }#THEN
    else {

      extra.args$every = 1

    }#ELSE

    if (!is.null(extra.args$burn.in)) {

      if (!is.positive(extra.args$burn.in))
        stop("the burn in length must be a positive integer number.")

    }#THEN
    else {

      extra.args$burn.in = 6 * length(nodes)^2

    }#ELSE

    if (!is.null(extra.args$max.in.degree)) {

      if (!is.positive.integer(extra.args$max.in.degree))
        stop("the maximum in-degree must be a positive integer number.")

      if (extra.args$max.in.degree >= length(nodes)) {

        warning("a node cannot have an in-degree greater or equal to the number of nodes in the graph.")
        warning("the condition on the in-degree will be ignored.")

      }#THEN

    }#THEN
    else {

      extra.args$max.in.degree = Inf

    }#ELSE

    if (!is.null(extra.args$max.out.degree)) {

      if (!is.positive.integer(extra.args$max.out.degree))
        stop("the maximum out-degree must be a positive integer number.")

      if (extra.args$max.out.degree >= length(nodes)) {

        warning("a node cannot have an out-degree greater or equal to the number of nodes in the graph.")
        warning("the condition on the out-degree will be ignored.")

      }#THEN

    }#THEN
    else {

      extra.args$max.out.degree = Inf

    }#ELSE

    if (!is.null(extra.args$max.degree)) {

      if (!is.positive.integer(extra.args$max.degree))
        stop("the maximum out-degree must be a positive integer number.")

      if (is.finite(extra.args$max.in.degree) &&
          extra.args$max.in.degree > extra.args$max.degree)
        stop("the maximun in-degree must be lesser or equal to the maximum degree.")

      if (is.finite(extra.args$max.out.degree) &&
          extra.args$max.out.degree > extra.args$max.degree)
        stop("the maximun out-degree must be lesser or equal to the maximum degree.")

      if (extra.args$max.degree >= length(nodes)) {

        warning("a node cannot have a degree greater or equal to the number of nodes in the graph.")
        warning("the condition on the degree will be ignored.")

      }#THEN

    }#THEN
    else {

      extra.args$max.degree = Inf

    }#ELSE

  }#THEN

  check.unused.args(extra.args, graph.generation.extra.args[[method]])

  return(extra.args)

}#CHECK.GRAPH.GENERATION.ARGS