Nothing
#This is the main function of MRPC algorithm combine with ModiSkeleton and EdgeOrientation
MRPC <- function (data, suffStat, GV, FDR = 0.05, alpha = 0.05, indepTest = c("gaussCItest","disCItest", "citest"), labels, p,
FDRcontrol = c("LOND", "ADDIS", "NONE"), tau = 0.5, lambda = 0.25, verbose = FALSE)
{
cl <- match.call()
# check FDRcontrol method
if (FDRcontrol == "LOND") {
cat ("Using the LOND method for online FDR control at FDR = ", FDR, "\n")
} else if (FDRcontrol == "ADDIS") {
cat ("Using the ADDIS method for online FDR control at FDR = ", FDR, "\n")
} else if (FDRcontrol == "NONE") {
cat ("Not applying error control. The type I error rate for each test is ", alpha, "\n")
} else {
stop ("Choose one of the following three options for FDRcontrol: LOND, ADDIS, or NONE")
}
# provide either the node labels
# or they are generated based on the number of nodes p
if (!missing(p))
stopifnot(is.numeric(p), length(p <- as.integer(p)) ==
1, p >= 2)
if (missing(labels)) {
if (missing(p))
stop("need to specify 'labels' or 'p'")
labels <- as.character(seq_len(p))
}
else {
stopifnot(is.character(labels))
if (missing(p)) {
p <- length(labels)
}
else if (p != length(labels))
stop("'p' is not needed when 'labels' is specified, and must match length(labels)")
else message("No need to specify 'p', when 'labels' is given")
}
if (verbose)
cat ("Test for independence:", indepTest, "\n")
# Step I: Infer the graph skeleton
skel <- ModiSkeleton(data, suffStat, FDR = FDR, alpha = alpha, indepTest = indepTest,
labels = labels, method = "stable", fixedGaps = NULL,
fixedEdges = NULL, NAdelete = TRUE, m.max = Inf,
FDRcontrol = FDRcontrol, tau = tau, lambda = lambda,
verbose = verbose)
skel@call <- cl
# Step II: Orient the edges
EdgeOrientation(skel, GV = GV, suffStat, FDR, alpha,
FDRcontrol = FDRcontrol, indepTest,
tau = tau, lambda = lambda,
verbose = verbose)
}
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