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R/sanitization-scores.R
In bnlearn: Bayesian Network Structure Learning, Parameter Learning and Inference
Defines functions
check.custom.score.arguments
check.custom.score.function
check.newdata
check.l
check.graph.hyperparameters
check.graph.prior
check.extended.penalty
check.penalty
check.experimental
check.iss.w
check.iss.mu
check.nu
check.iss
check.score.args
is.score.decomposable
is.score.equivalent
check.score
# check score labels.
check.score = function(score, data, allowed = available.scores) {
metadata = attr(data, "metadata")
if (!is.null(score)) {
# check the score label.
check.label(score, choices = allowed, labels = score.labels,
argname = "score", see = "bnlearn-package")
# check if it's the right score for the data (discrete, continuous, mixed).
if ((metadata$type %!in% discrete.data.types) &&
(score %in% available.discrete.scores))
stop("score '", score, "' may only be used with discrete data.")
if ((metadata$type != "continuous") &&
(score %in% available.continuous.scores))
stop("score '", score, "' may only be used with continuous data.")
if ((metadata$type != "mixed-cg") &&
(score %in% available.mixedcg.scores))
stop("score '", score, "' may only be used with a mixture of continuous and discrete data.")
# if the data are incomplete, check whether the score can be used at all.
if (any(!metadata$complete.nodes) &&
(score %!in% scores.for.incomplete.data))
stop("score '", score, "' cannot be used with incomplete data.")
return(score)
}#THEN
else {
# warn about ordinal data modelled as unordered categorical ones.
if (metadata$type %in% c("ordered", "mixed-do"))
warning("no score is available for ordinal data, disregarding the ordering of the levels.")
if (all(metadata$complete.nodes)) {
if (metadata$type %in% discrete.data.types)
return("bic")
else if (metadata$type == "continuous")
return("bic-g")
else if (metadata$type == "mixed-cg")
return("bic-cg")
}#THEN
else {
if (metadata$type %in% discrete.data.types)
return("pnal")
else if (metadata$type == "continuous")
return("pnal-g")
else if (metadata$type == "mixed-cg")
return("pnal-cg")
}#ELSE
}#ELSE
}#CHECK.SCORE
# check whether a score is score equivalent.
is.score.equivalent = function(score, nodes, extra) {
# log-likelihood for discrete and Gaussian data is always score equivalent.
if (score %in% c("loglik", "loglik-g", "pred-loglik", "pred-loglik-g"))
return(TRUE)
# same with AIC and BIC.
if (score %in% c("aic", "aic-g", "bic", "bic-g", "ebic", "ebic-g"))
return(TRUE)
# the quotient NML is score equivalent, but the factorized NML is not.
if (score %in% c("qnml"))
return(TRUE)
# BDe and BGe can be score equivalent depending on the graph prior.
if ((score %in% c("bde", "bge")) &&
(extra$prior %in% c("uniform", "marginal", "vsp")))
return(TRUE)
# all the node-average likelihood scores are score equivalent.
if (score %in% c("nal", "nal-g", "pnal", "pnal-g"))
return(TRUE)
# a conservative default (BDla, BDs, BDj, all *-cg scores).
return(FALSE)
}#IS.SCORE.EQUIVALENT
# check whether a score is decomposable.
is.score.decomposable = function(score, extra) {
# Castelo & Siebes prior is not decomposable.
if ((score %in% c("bde", "bds", "bdj", "mbde", "bdla", "bge")) &&
(extra$prior %in% c("cs", "marginal")))
return(FALSE)
# a sensible default.
return(TRUE)
}#IS.SCORE.DECOMPOSABLE
# sanitize the extra arguments passed to the network scores.
check.score.args = function(score, network, data, extra.args, learning = FALSE) {
# check the imaginary sample size.
if (has.argument(score, "iss", score.extra.args))
extra.args[["iss"]] =
check.iss(iss = extra.args[["iss"]], network = network)
# check the graph prior distribution.
if (has.argument(score, "prior", score.extra.args))
extra.args[["prior"]] =
check.graph.prior(prior = extra.args[["prior"]], network = network)
# check the sparsity parameter of the graph prior distribution.
if (has.argument(score, "beta", score.extra.args))
extra.args[["beta"]] =
check.graph.hyperparameters(beta = extra.args[["beta"]],
prior = extra.args[["prior"]], network = network, data = data,
learning = learning)
# check the list of the experimental observations in the data set.
if (has.argument(score, "exp", score.extra.args))
extra.args[["exp"]] =
check.experimental(exp = extra.args[["exp"]], network = network,
data = data)
# check the likelihood penalty.
if (has.argument(score, "k", score.extra.args))
extra.args[["k"]] =
check.penalty(k = extra.args[["k"]], network = network, data = data,
score = score)
# check the additional penalty in the extended BIC.
if (has.argument(score, "gamma", score.extra.args))
extra.args[["gamma"]] =
check.extended.penalty(gamma = extra.args[["gamma"]], network = network)
# check the number of scores to average.
if (has.argument(score, "l", score.extra.args))
extra.args[["l"]] = check.l(l = extra.args[["l"]], network = network)
# check the normal-Wishart prior arguments.
if (has.argument(score, "nu", score.extra.args))
extra.args$nu =
check.nu(nu = extra.args[["nu"]], network = network, data = data)
if (has.argument(score, "iss.mu", score.extra.args))
extra.args[["iss.mu"]] =
check.iss.mu(iss.mu = extra.args[["iss.mu"]], network = network)
if (has.argument(score, "iss.w", score.extra.args))
extra.args[["iss.w"]] =
check.iss.w(iss.w = extra.args[["iss.w"]], network = network, data = data)
# check the test data for predictive scores.
if (has.argument(score, "newdata", score.extra.args))
extra.args[["newdata"]] =
check.newdata(newdata = extra.args[["newdata"]], network = network,
data = data)
# check the R function implementing a custom score.
if (has.argument(score, "fun", score.extra.args))
extra.args[["fun"]] =
check.custom.score.function(fun = extra.args[["fun"]], network = network)
if (has.argument(score, "args", score.extra.args))
extra.args[["args"]] =
check.custom.score.arguments(args = extra.args[["args"]], network = network)
# warn about and remove unused arguments.
extra.args = check.unused.args(extra.args, score.extra.args[[score]])
return(extra.args)
}#CHECK.SCORE.ARGS
# check the imaginary sample size of the Dirichlet prior.
check.iss = function(iss, network) {
if (!is.null(iss)) {
# validate the imaginary sample size.
if (!is.positive(iss))
stop("the imaginary sample size must be a positive number.")
if (iss < 1)
warning("very small imaginary sample size, the results may be affected by numeric problems.")
}#THEN
else {
# check whether there is an imaginary sample size stored in the bn object;
# otherwise use a the de facto standard value of 1.
if (!is.null(network$learning$args$iss))
iss = network$learning$args$iss
else
iss = 1
}#ELSE
# coerce iss to integer.
return(as.numeric(iss))
}#CHECK.ISS
# check the prior mean in the BGe score.
check.nu = function(nu, network, data) {
if (!is.null(nu)) {
# check type and length.
if (!is.real.vector(nu))
stop("the prior mean vector must contain real numbers.")
if (length(nu) != ncol(data))
stop("the length of the prior mean vector does not match the number of variables in the data.")
# check the names.
if (is.null(names(nu)))
names(nu) = names(data)
else if (!setequal(names(nu), names(data)))
stop("the prior mean vector and the data contain variables with different names.")
}#THEN
else {
if (!is.null(network$learning$args$nu))
nu = network$learning$args$nu
else
nu = structure(colMeans(data), names = names(data))
}#ELSE
return(nu)
}#CHECK.NU
# check the imaginary sample size for the normal prior over the mean.
check.iss.mu = function(iss.mu, network) {
if (!is.null(iss.mu)) {
# validate the imaginary sample size.
if (!is.positive(iss.mu))
stop("the imaginary sample size must be a positive number.")
if (iss.mu < 1)
warning("very small imaginary sample size, the results may be affected by numeric problems.")
}#THEN
else {
# check whether there is an imaginary sample size stored in the bn object;
# otherwise use a the de facto standard value of 1.
if (!is.null(network$learning$args$iss.mu))
iss.mu = network$learning$args$iss.mu
else
iss.mu = 1
}#ELSE
# coerce iss to integer.
return(as.numeric(iss.mu))
}#CHECK.ISS.MU
# check the imaginary sample size for the Wishart prior over the covariance.
check.iss.w = function(iss.w, network, data) {
if (!is.null(iss.w)) {
if (!is.positive.integer(iss.w))
stop("the imaginary sample size for the Wishart prior component must be a positive integer number.")
}#THEN
else {
if (!is.null(network$learning$args$iss.w))
iss.w = network$learning$args$iss.w
else
iss.w = ncol(data) + 2
}#ELSE
return(iss.w)
}#CHECK.ISS.W
# check the experimental data list.
check.experimental = function(exp, network, data) {
if (!is.null(exp)) {
if (!is.list(exp))
stop("experimental data must be specified via a list of indexes.")
if (any(names(exp) %!in% names(data)) || (length(names(exp)) == 0))
stop("unkown variables specified in the experimental data list.")
for (var in names(exp)) {
if (!is.positive.vector(exp[[var]]))
stop("indexes of experimental data must be positive integer numbers.")
if (any(duplicated(exp[[var]])))
stop("duplicated indexes for experimental data.")
if (any(exp[[var]] > length(data[, var])))
stop("out of bounds indexes for experimental data.")
# just kill empty elements.
if (length(exp[[var]]) == 0)
exp[[var]] = NULL
# also, convert everything to integers to make things simpler at the
# C level.
exp[[var]] = as.integer(exp[[var]])
}#FOR
}#THEN
else {
# check whether there is a list stored in the bn object; if no experimental
# data is specified, return an empty list (which is the same as using the
# plain BDe score).
if (!is.null(network$learning$args$exp))
exp = network$learning$args$exp
else
exp = structure(vector(ncol(data), mode = "list"), names = names(data))
}#ELSE
return(exp)
}#CHECK.EXPERIMENTAL
# check the penalty used in AIC and BIC.
check.penalty = function(k, network, data, score) {
if (!is.null(k)) {
# validate the penalty weight.
if (!is.positive(k))
stop("the penalty weight must be a positive numeric value.")
# warn if using a non-standard penalty.
if (grepl("^aic", score) && (k != 1))
warning("using AIC with a non-standard penalty k = ", k, ".")
if (grepl("^[e]*bic", score) && (k != log(nrow(data)) / 2))
warning("using BIC with a non-standard penalty k = ", k, ".")
}#THEN
else {
# check whether there is a penalization coefficient stored in the bn object,
# use the default for the score function otherwise.
if (!is.null(network$learning$args$k) && (score == network$learning$test))
k = network$learning$args$k
else {
if (grepl("^aic", score))
k = 1
else if (grepl("^[e]*bic", score))
k = log(nrow(data)) / 2
else if (grepl("^[p]*nal", score))
k = 1 / length(network$nodes) * nrow(data) ^ -0.25
}#ELSE
}#ELSE
return(as.numeric(k))
}#CHECK.PENALTY
# check the additional penalty used in the extended BIC.
check.extended.penalty = function(gamma, network) {
if (!is.null(gamma)) {
if (!is.probability(gamma))
stop("'gamma' must be a number between 0 and 1.")
}#THEN
else {
if (!is.null(network$learning$args$gamma))
gamma = network$learning$args$gamma
else
gamma = 0.5
}#ELSE
return(as.numeric(gamma))
}#CHECK.EXTENDED.PENALTY
# sanitize prior distributions over the graph space.
check.graph.prior = function(prior, network) {
if (is.null(prior)) {
# check whether there is a graph prior stored in the bn object, use the
# uniform one otherwise.
if (!is.null(network$learning$args$prior))
prior = network$learning$args$prior
else
prior = "uniform"
}#THEN
else {
# check whether prior is a string, and whether the label matches a known prior.
check.label(prior, choices = prior.distributions, labels = prior.labels,
argname = "prior distribution", see = score)
}#ELSE
return(prior)
}#CHECK.GRAPH.PRIOR
# check the sparsity parameter of the prior distribution over the graph space.
check.graph.hyperparameters = function(beta, prior, network, data,
learning = FALSE) {
default.beta =
list("uniform" = NULL, "vsp" = 1/(ncol(data) - 1),
"marginal" = structure(0.5, nodes = names(network$nodes)),
"cs" = cs.completed.prior(data.frame(character(0), character(0),
numeric(0)), names(data)))
if (is.null(beta)) {
# check whether there is a graph prior stored in the bn object, use the
# uniform one otherwise.
if (!is.null(network$learning$args$prior))
beta = network$learning$args$beta
else
beta = default.beta[[prior]]
}#THEN
else {
if (prior %in% c("uniform")) {
warning("unused argument beta.")
beta = NULL
}#THEN
else if (prior == "marginal") {
if (!is.probability(beta) || (beta >= 1))
stop("beta must be a probability smaller than 1.")
beta = structure(noattr(beta, ok = character(0)), nodes = names(network$nodes))
}#THEN
else if (prior == "vsp") {
if (!is.probability(beta) || (beta >= 1))
stop("beta must be a probability smaller than 1.")
}#THEN
else if (prior == "cs") {
# arcs' prior probabilities should be provided in a data frame.
if (!is.data.frame(beta) || (ncol(beta) != 3) ||
!identical(colnames(beta), c("from", "to", "prob")))
stop("beta must be a data frame with three colums: 'from', 'to' and 'prob'.")
# the probs cloumns must contain only probabilities.
if (!is.probability.vector(beta$prob, zero = TRUE))
stop("arcs prior must contain only probabilities.")
# check that the first two columns contain only valid arcs.
check.arcs(beta[, c("from", "to")], nodes = names(data))
# complete the user-specified prior.
beta = cs.completed.prior(beta, names(data), learning)
}#THEN
}#ELSE
return(beta)
}#CHECK.GRAPH.SPARSITY
# check the number of scores to average.
check.l = function(l, network) {
if (is.null(l)) {
if (!is.null(network$learning$args$l))
l = network$learning$args$l
else
l = 5
}#THEN
else {
if (!is.positive.integer(l))
stop("l must be a positive integer, the number of scores to average.")
}#ELSE
return(as.numeric(l))
}#CHECK.L
# check the test data for predictive scores.
check.newdata = function(newdata, network, data, required = TRUE,
allow.missing = FALSE) {
if (is.null(newdata)) {
if (!is.null(network$learning$args$newdata))
return(network$learning$args$newdata)
else if (required)
stop("predictive scores require a test set passed as 'newdata'.")
else
return(NULL)
}#THEN
# newdata must be a data frame.
if (!is.data.frame(newdata))
stop("newdata must be in a data frame.")
# check whether data and newdata have the same columns.
names.data = names(data)
names.newdata = names(newdata)
if (length(names.data) < length(names.newdata)) {
if (all(names.newdata %in% names(data))) {
warning("extra variables in newdata will be ignored.")
newdata = .data.frame.column(newdata, names.data, drop = FALSE)
}#THEN
else {
stop("some variables in the data are missing in newdata.")
}#ELSE
}#THEN
else if (length(names.data) > length(names.newdata)) {
stop("some variables in the data are missing in newdata.")
}#THEN
# reorder the columns of newdata to match data.
newdata = .data.frame.column(newdata, names.data, drop = FALSE)
# check whether data and newdata have the same data types.
types.data = lapply(data, class)
types.newdata = lapply(newdata, class)
for (i in seq_along(types.data))
if (!isTRUE(all.equal(types.data[[i]], types.newdata[[i]])))
stop("variable ", names.data[i], " has a different class in newdata.")
# for discrete variables, also check that the levels match.
levels.data = lapply(data, levels)
levels.newdata = lapply(newdata, levels)
for (i in seq_along(types.data))
if (any(types.data[i] %in% "factor"))
if (!isTRUE(all.equal(levels.data[[i]], levels.newdata[[i]]))) {
if (setequal(levels.data[[i]], levels.newdata[[i]]))
levels(newdata[[i]]) = levels(data[[i]])
else
stop("variable ", names.data[i], " has a different levels in newdata.")
}#THEN
# make sure to return a data frame with column names.
newdata = .data.frame(newdata)
names(newdata) = names.data
# sanitize the reworked data frame and add the metadata.
newdata = check.data(newdata, label = "newdata", allow.levels = TRUE,
allow.missing = allow.missing)
return(newdata)
}#CHECK.NEWDATA
# check the R function implementing a custom score.
check.custom.score.function = function(fun, network) {
# there is no possible default value.
if (is.null(fun)) {
if (!is.null(network$learning$args$fun))
fun = network$learning$args$fun
else
stop("missing the custom score function.")
}#THEN
else {
# check the argument list.
fun.arguments = names(formals(fun))
if (!identical(fun.arguments, c("node", "parents", "data", "args")))
stop("the custom score function must have signature function(node, parents, data, args).")
}#ELSE
return(fun)
}#CHECK.CUSTOM.SCORE.FUNCTION
# check the additional argument list passed to a custom test.
check.custom.score.arguments = function(args, network) {
# default to an empty argument list.
if (is.null(args)) {
if (!is.null(network$learning$args$args))
args = network$learning$args$args
else
args = list()
}#THEN
else {
if (!is.list(args))
stop("the arguments for the custom score must be passed as a list.")
}#ELSE
return(args)
}#CHECK.CUSTOM.SCORE.ARGUMENTS
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Defines functions check.custom.score.arguments check.custom.score.function check.newdata check.l check.graph.hyperparameters check.graph.prior check.extended.penalty check.penalty check.experimental check.iss.w check.iss.mu check.nu check.iss check.score.args is.score.decomposable is.score.equivalent check.score
# check score labels.
check.score = function(score, data, allowed = available.scores) {
metadata = attr(data, "metadata")
if (!is.null(score)) {
# check the score label.
check.label(score, choices = allowed, labels = score.labels,
argname = "score", see = "bnlearn-package")
# check if it's the right score for the data (discrete, continuous, mixed).
if ((metadata$type %!in% discrete.data.types) &&
(score %in% available.discrete.scores))
stop("score '", score, "' may only be used with discrete data.")
if ((metadata$type != "continuous") &&
(score %in% available.continuous.scores))
stop("score '", score, "' may only be used with continuous data.")
if ((metadata$type != "mixed-cg") &&
(score %in% available.mixedcg.scores))
stop("score '", score, "' may only be used with a mixture of continuous and discrete data.")
# if the data are incomplete, check whether the score can be used at all.
if (any(!metadata$complete.nodes) &&
(score %!in% scores.for.incomplete.data))
stop("score '", score, "' cannot be used with incomplete data.")
return(score)
}#THEN
else {
# warn about ordinal data modelled as unordered categorical ones.
if (metadata$type %in% c("ordered", "mixed-do"))
warning("no score is available for ordinal data, disregarding the ordering of the levels.")
if (all(metadata$complete.nodes)) {
if (metadata$type %in% discrete.data.types)
return("bic")
else if (metadata$type == "continuous")
return("bic-g")
else if (metadata$type == "mixed-cg")
return("bic-cg")
}#THEN
else {
if (metadata$type %in% discrete.data.types)
return("pnal")
else if (metadata$type == "continuous")
return("pnal-g")
else if (metadata$type == "mixed-cg")
return("pnal-cg")
}#ELSE
}#ELSE
}#CHECK.SCORE
# check whether a score is score equivalent.
is.score.equivalent = function(score, nodes, extra) {
# log-likelihood for discrete and Gaussian data is always score equivalent.
if (score %in% c("loglik", "loglik-g", "pred-loglik", "pred-loglik-g"))
return(TRUE)
# same with AIC and BIC.
if (score %in% c("aic", "aic-g", "bic", "bic-g", "ebic", "ebic-g"))
return(TRUE)
# the quotient NML is score equivalent, but the factorized NML is not.
if (score %in% c("qnml"))
return(TRUE)
# BDe and BGe can be score equivalent depending on the graph prior.
if ((score %in% c("bde", "bge")) &&
(extra$prior %in% c("uniform", "marginal", "vsp")))
return(TRUE)
# all the node-average likelihood scores are score equivalent.
if (score %in% c("nal", "nal-g", "pnal", "pnal-g"))
return(TRUE)
# a conservative default (BDla, BDs, BDj, all *-cg scores).
return(FALSE)
}#IS.SCORE.EQUIVALENT
# check whether a score is decomposable.
is.score.decomposable = function(score, extra) {
# Castelo & Siebes prior is not decomposable.
if ((score %in% c("bde", "bds", "bdj", "mbde", "bdla", "bge")) &&
(extra$prior %in% c("cs", "marginal")))
return(FALSE)
# a sensible default.
return(TRUE)
}#IS.SCORE.DECOMPOSABLE
# sanitize the extra arguments passed to the network scores.
check.score.args = function(score, network, data, extra.args, learning = FALSE) {
# check the imaginary sample size.
if (has.argument(score, "iss", score.extra.args))
extra.args[["iss"]] =
check.iss(iss = extra.args[["iss"]], network = network)
# check the graph prior distribution.
if (has.argument(score, "prior", score.extra.args))
extra.args[["prior"]] =
check.graph.prior(prior = extra.args[["prior"]], network = network)
# check the sparsity parameter of the graph prior distribution.
if (has.argument(score, "beta", score.extra.args))
extra.args[["beta"]] =
check.graph.hyperparameters(beta = extra.args[["beta"]],
prior = extra.args[["prior"]], network = network, data = data,
learning = learning)
# check the list of the experimental observations in the data set.
if (has.argument(score, "exp", score.extra.args))
extra.args[["exp"]] =
check.experimental(exp = extra.args[["exp"]], network = network,
data = data)
# check the likelihood penalty.
if (has.argument(score, "k", score.extra.args))
extra.args[["k"]] =
check.penalty(k = extra.args[["k"]], network = network, data = data,
score = score)
# check the additional penalty in the extended BIC.
if (has.argument(score, "gamma", score.extra.args))
extra.args[["gamma"]] =
check.extended.penalty(gamma = extra.args[["gamma"]], network = network)
# check the number of scores to average.
if (has.argument(score, "l", score.extra.args))
extra.args[["l"]] = check.l(l = extra.args[["l"]], network = network)
# check the normal-Wishart prior arguments.
if (has.argument(score, "nu", score.extra.args))
extra.args$nu =
check.nu(nu = extra.args[["nu"]], network = network, data = data)
if (has.argument(score, "iss.mu", score.extra.args))
extra.args[["iss.mu"]] =
check.iss.mu(iss.mu = extra.args[["iss.mu"]], network = network)
if (has.argument(score, "iss.w", score.extra.args))
extra.args[["iss.w"]] =
check.iss.w(iss.w = extra.args[["iss.w"]], network = network, data = data)
# check the test data for predictive scores.
if (has.argument(score, "newdata", score.extra.args))
extra.args[["newdata"]] =
check.newdata(newdata = extra.args[["newdata"]], network = network,
data = data)
# check the R function implementing a custom score.
if (has.argument(score, "fun", score.extra.args))
extra.args[["fun"]] =
check.custom.score.function(fun = extra.args[["fun"]], network = network)
if (has.argument(score, "args", score.extra.args))
extra.args[["args"]] =
check.custom.score.arguments(args = extra.args[["args"]], network = network)
# warn about and remove unused arguments.
extra.args = check.unused.args(extra.args, score.extra.args[[score]])
return(extra.args)
}#CHECK.SCORE.ARGS
# check the imaginary sample size of the Dirichlet prior.
check.iss = function(iss, network) {
if (!is.null(iss)) {
# validate the imaginary sample size.
if (!is.positive(iss))
stop("the imaginary sample size must be a positive number.")
if (iss < 1)
warning("very small imaginary sample size, the results may be affected by numeric problems.")
}#THEN
else {
# check whether there is an imaginary sample size stored in the bn object;
# otherwise use a the de facto standard value of 1.
if (!is.null(network$learning$args$iss))
iss = network$learning$args$iss
else
iss = 1
}#ELSE
# coerce iss to integer.
return(as.numeric(iss))
}#CHECK.ISS
# check the prior mean in the BGe score.
check.nu = function(nu, network, data) {
if (!is.null(nu)) {
# check type and length.
if (!is.real.vector(nu))
stop("the prior mean vector must contain real numbers.")
if (length(nu) != ncol(data))
stop("the length of the prior mean vector does not match the number of variables in the data.")
# check the names.
if (is.null(names(nu)))
names(nu) = names(data)
else if (!setequal(names(nu), names(data)))
stop("the prior mean vector and the data contain variables with different names.")
}#THEN
else {
if (!is.null(network$learning$args$nu))
nu = network$learning$args$nu
else
nu = structure(colMeans(data), names = names(data))
}#ELSE
return(nu)
}#CHECK.NU
# check the imaginary sample size for the normal prior over the mean.
check.iss.mu = function(iss.mu, network) {
if (!is.null(iss.mu)) {
# validate the imaginary sample size.
if (!is.positive(iss.mu))
stop("the imaginary sample size must be a positive number.")
if (iss.mu < 1)
warning("very small imaginary sample size, the results may be affected by numeric problems.")
}#THEN
else {
# check whether there is an imaginary sample size stored in the bn object;
# otherwise use a the de facto standard value of 1.
if (!is.null(network$learning$args$iss.mu))
iss.mu = network$learning$args$iss.mu
else
iss.mu = 1
}#ELSE
# coerce iss to integer.
return(as.numeric(iss.mu))
}#CHECK.ISS.MU
# check the imaginary sample size for the Wishart prior over the covariance.
check.iss.w = function(iss.w, network, data) {
if (!is.null(iss.w)) {
if (!is.positive.integer(iss.w))
stop("the imaginary sample size for the Wishart prior component must be a positive integer number.")
}#THEN
else {
if (!is.null(network$learning$args$iss.w))
iss.w = network$learning$args$iss.w
else
iss.w = ncol(data) + 2
}#ELSE
return(iss.w)
}#CHECK.ISS.W
# check the experimental data list.
check.experimental = function(exp, network, data) {
if (!is.null(exp)) {
if (!is.list(exp))
stop("experimental data must be specified via a list of indexes.")
if (any(names(exp) %!in% names(data)) || (length(names(exp)) == 0))
stop("unkown variables specified in the experimental data list.")
for (var in names(exp)) {
if (!is.positive.vector(exp[[var]]))
stop("indexes of experimental data must be positive integer numbers.")
if (any(duplicated(exp[[var]])))
stop("duplicated indexes for experimental data.")
if (any(exp[[var]] > length(data[, var])))
stop("out of bounds indexes for experimental data.")
# just kill empty elements.
if (length(exp[[var]]) == 0)
exp[[var]] = NULL
# also, convert everything to integers to make things simpler at the
# C level.
exp[[var]] = as.integer(exp[[var]])
}#FOR
}#THEN
else {
# check whether there is a list stored in the bn object; if no experimental
# data is specified, return an empty list (which is the same as using the
# plain BDe score).
if (!is.null(network$learning$args$exp))
exp = network$learning$args$exp
else
exp = structure(vector(ncol(data), mode = "list"), names = names(data))
}#ELSE
return(exp)
}#CHECK.EXPERIMENTAL
# check the penalty used in AIC and BIC.
check.penalty = function(k, network, data, score) {
if (!is.null(k)) {
# validate the penalty weight.
if (!is.positive(k))
stop("the penalty weight must be a positive numeric value.")
# warn if using a non-standard penalty.
if (grepl("^aic", score) && (k != 1))
warning("using AIC with a non-standard penalty k = ", k, ".")
if (grepl("^[e]*bic", score) && (k != log(nrow(data)) / 2))
warning("using BIC with a non-standard penalty k = ", k, ".")
}#THEN
else {
# check whether there is a penalization coefficient stored in the bn object,
# use the default for the score function otherwise.
if (!is.null(network$learning$args$k) && (score == network$learning$test))
k = network$learning$args$k
else {
if (grepl("^aic", score))
k = 1
else if (grepl("^[e]*bic", score))
k = log(nrow(data)) / 2
else if (grepl("^[p]*nal", score))
k = 1 / length(network$nodes) * nrow(data) ^ -0.25
}#ELSE
}#ELSE
return(as.numeric(k))
}#CHECK.PENALTY
# check the additional penalty used in the extended BIC.
check.extended.penalty = function(gamma, network) {
if (!is.null(gamma)) {
if (!is.probability(gamma))
stop("'gamma' must be a number between 0 and 1.")
}#THEN
else {
if (!is.null(network$learning$args$gamma))
gamma = network$learning$args$gamma
else
gamma = 0.5
}#ELSE
return(as.numeric(gamma))
}#CHECK.EXTENDED.PENALTY
# sanitize prior distributions over the graph space.
check.graph.prior = function(prior, network) {
if (is.null(prior)) {
# check whether there is a graph prior stored in the bn object, use the
# uniform one otherwise.
if (!is.null(network$learning$args$prior))
prior = network$learning$args$prior
else
prior = "uniform"
}#THEN
else {
# check whether prior is a string, and whether the label matches a known prior.
check.label(prior, choices = prior.distributions, labels = prior.labels,
argname = "prior distribution", see = score)
}#ELSE
return(prior)
}#CHECK.GRAPH.PRIOR
# check the sparsity parameter of the prior distribution over the graph space.
check.graph.hyperparameters = function(beta, prior, network, data,
learning = FALSE) {
default.beta =
list("uniform" = NULL, "vsp" = 1/(ncol(data) - 1),
"marginal" = structure(0.5, nodes = names(network$nodes)),
"cs" = cs.completed.prior(data.frame(character(0), character(0),
numeric(0)), names(data)))
if (is.null(beta)) {
# check whether there is a graph prior stored in the bn object, use the
# uniform one otherwise.
if (!is.null(network$learning$args$prior))
beta = network$learning$args$beta
else
beta = default.beta[[prior]]
}#THEN
else {
if (prior %in% c("uniform")) {
warning("unused argument beta.")
beta = NULL
}#THEN
else if (prior == "marginal") {
if (!is.probability(beta) || (beta >= 1))
stop("beta must be a probability smaller than 1.")
beta = structure(noattr(beta, ok = character(0)), nodes = names(network$nodes))
}#THEN
else if (prior == "vsp") {
if (!is.probability(beta) || (beta >= 1))
stop("beta must be a probability smaller than 1.")
}#THEN
else if (prior == "cs") {
# arcs' prior probabilities should be provided in a data frame.
if (!is.data.frame(beta) || (ncol(beta) != 3) ||
!identical(colnames(beta), c("from", "to", "prob")))
stop("beta must be a data frame with three colums: 'from', 'to' and 'prob'.")
# the probs cloumns must contain only probabilities.
if (!is.probability.vector(beta$prob, zero = TRUE))
stop("arcs prior must contain only probabilities.")
# check that the first two columns contain only valid arcs.
check.arcs(beta[, c("from", "to")], nodes = names(data))
# complete the user-specified prior.
beta = cs.completed.prior(beta, names(data), learning)
}#THEN
}#ELSE
return(beta)
}#CHECK.GRAPH.SPARSITY
# check the number of scores to average.
check.l = function(l, network) {
if (is.null(l)) {
if (!is.null(network$learning$args$l))
l = network$learning$args$l
else
l = 5
}#THEN
else {
if (!is.positive.integer(l))
stop("l must be a positive integer, the number of scores to average.")
}#ELSE
return(as.numeric(l))
}#CHECK.L
# check the test data for predictive scores.
check.newdata = function(newdata, network, data, required = TRUE,
allow.missing = FALSE) {
if (is.null(newdata)) {
if (!is.null(network$learning$args$newdata))
return(network$learning$args$newdata)
else if (required)
stop("predictive scores require a test set passed as 'newdata'.")
else
return(NULL)
}#THEN
# newdata must be a data frame.
if (!is.data.frame(newdata))
stop("newdata must be in a data frame.")
# check whether data and newdata have the same columns.
names.data = names(data)
names.newdata = names(newdata)
if (length(names.data) < length(names.newdata)) {
if (all(names.newdata %in% names(data))) {
warning("extra variables in newdata will be ignored.")
newdata = .data.frame.column(newdata, names.data, drop = FALSE)
}#THEN
else {
stop("some variables in the data are missing in newdata.")
}#ELSE
}#THEN
else if (length(names.data) > length(names.newdata)) {
stop("some variables in the data are missing in newdata.")
}#THEN
# reorder the columns of newdata to match data.
newdata = .data.frame.column(newdata, names.data, drop = FALSE)
# check whether data and newdata have the same data types.
types.data = lapply(data, class)
types.newdata = lapply(newdata, class)
for (i in seq_along(types.data))
if (!isTRUE(all.equal(types.data[[i]], types.newdata[[i]])))
stop("variable ", names.data[i], " has a different class in newdata.")
# for discrete variables, also check that the levels match.
levels.data = lapply(data, levels)
levels.newdata = lapply(newdata, levels)
for (i in seq_along(types.data))
if (any(types.data[i] %in% "factor"))
if (!isTRUE(all.equal(levels.data[[i]], levels.newdata[[i]]))) {
if (setequal(levels.data[[i]], levels.newdata[[i]]))
levels(newdata[[i]]) = levels(data[[i]])
else
stop("variable ", names.data[i], " has a different levels in newdata.")
}#THEN
# make sure to return a data frame with column names.
newdata = .data.frame(newdata)
names(newdata) = names.data
# sanitize the reworked data frame and add the metadata.
newdata = check.data(newdata, label = "newdata", allow.levels = TRUE,
allow.missing = allow.missing)
return(newdata)
}#CHECK.NEWDATA
# check the R function implementing a custom score.
check.custom.score.function = function(fun, network) {
# there is no possible default value.
if (is.null(fun)) {
if (!is.null(network$learning$args$fun))
fun = network$learning$args$fun
else
stop("missing the custom score function.")
}#THEN
else {
# check the argument list.
fun.arguments = names(formals(fun))
if (!identical(fun.arguments, c("node", "parents", "data", "args")))
stop("the custom score function must have signature function(node, parents, data, args).")
}#ELSE
return(fun)
}#CHECK.CUSTOM.SCORE.FUNCTION
# check the additional argument list passed to a custom test.
check.custom.score.arguments = function(args, network) {
# default to an empty argument list.
if (is.null(args)) {
if (!is.null(network$learning$args$args))
args = network$learning$args$args
else
args = list()
}#THEN
else {
if (!is.list(args))
stop("the arguments for the custom score must be passed as a list.")
}#ELSE
return(args)
}#CHECK.CUSTOM.SCORE.ARGUMENTS
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