Revert "deleted build_clusters because igraph package is anoying when package is installed "

This reverts commit 66900c16.

DESCRIPTION

@@ -12,6 +12,7 @@ Imports:
 	ranger (>= 0.12.1),
 	Rcpp,
 	randomForestSRC,
+	linkcomm,
   parallel
 RoxygenNote: 7.1.0
 LinkingTo: Rcpp

R/build_clusters.R

+#' Apply cluster analysis to build variable groups
+#'
+#'This function generates variables groups of relation information that was obtained by \link[SurrogateMinimalDepth]{var.relations} function applying
+#'\link[linkcomm]{getLinkCommunities}.
+#'
+#' @param rel a list containing variables, surr.res, threshold, and var. This is the output of \link[SurrogateMinimalDepth]{var.relations} function.
+#' @param hcmethod the hierarchical clustering method that is used. (see \link[linkcomm]{getLinkCommunities})
+#'
+#' @return a data frame containing the variable names and their associated clusters.
+#'
+#' @examples
+#' # read data
+#' data("SMD_example_data")
+#'
+#' \donttest{
+#'  # get trees and variable names
+#'  x = SMD_example_data[,2:ncol(SMD_example_data)]
+#'  y = SMD_example_data[,1]
+#'  allvariables = colnames(x)# extract variables names
+#'  nvar = length(allvariables)   # count number of variables
+#'  set.seed(42)
+#'  RF = ranger::ranger(data = SMD_example_data, dependent.variable.name = "y", num.trees = 10, keep.inbag = TRUE,mtry = floor(nvar^(3/4)), min.node.size = 1)
+#'  trees = getTreeranger(RF = RF, ntree = 10)
+#'  trees.lay = addLayer(trees)
+#'  trees.surr = addSurrogates(RF = RF, trees = trees.lay, s = 10, Xdata = x, num.threads = NULL)
+#'
+#'  # investigate variable relations
+#'  rel=var.relations(forest = list(trees = trees.surr, allvariables = allvariables), variables = allvariables, candidates = allvariables, t = 10)
+#'  groups = build.clusters(rel)
+#' }
+#'
+#' @export
+
+
+build.clusters = function(rel,hcmethod = "ward.D") {
+
+  # create links matrix
+  links = matrix(nrow = length(unlist(rel$var)) ,ncol = 2)
+  links[,1] = unlist(sapply(1:length(rel$variables), function(x) {rep(rel$variables[x],length(rel$var[[x]]))}))
+  links[,2] = unlist(rel$var)
+
+  # cluster analysis to identify clusters
+  link.comm = linkcomm::getLinkCommunities(links,
+                                 hcmethod = hcmethod,
+                                 plot = FALSE)
+  cluster.info = link.comm$nodeclusters
+  return(cluster.info)
+}