Merge branch 'main' into fn-rework

DESCRIPTION

 Type: Package
 Package: RFSurrogates
 Title: Surrogate Minimal Depth Variable Importance
-Version: 0.3.3.9008
+Version: 0.3.4
 Authors@R: c(
     person("Stephan", "Seifert", , "stephan.seifert@uni-hamburg.de", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-2567-5728")),
@@ -36,5 +36,4 @@ LinkingTo:
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
-Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3

R/addLayer.R

@@ -18,6 +18,7 @@
 #' * `layer`: Tree layer depth information, starting at 0 (root node) and incremented for each layer.
 #'
 #' @export
+#' @md
 addLayer <- function(trees, num.threads = 1) {
   if (!inherits(trees, "RangerTrees")) {
     stop("`trees` must be a `getTreeranger` `RangerTrees` object.")
@@ -42,6 +43,7 @@ addLayer <- function(trees, num.threads = 1) {
 #' @seealso [addLayer()]
 #'
 #' @keywords internal
+#' @md
 add_layer_to_tree <- function(tree) {
   layer <- rep(NA, nrow(tree))
   layer[1] <- 0

R/addSurrogates.R

@@ -106,6 +106,7 @@ getSurrgate2 <- function(
 #' This is an internal function
 #'
 #' @keywords internal
+#' @md
 getSurrogate <- function(surr.par, k = 1, maxsurr) {
   # weights and trees are extracted
   tree <- surr.par$trees[[k]]
@@ -129,6 +130,7 @@ getSurrogate <- function(surr.par, k = 1, maxsurr) {
 #' @useDynLib RFSurrogates, .registration = TRUE
 #'
 #' @keywords internal
+#' @md
 SurrTree <- function(j, wt, Xdata, controls, column.names, tree, maxsurr, ncat) {
   node <- tree[j, ]
   # for non-terminal nodes get surrogates
@@ -182,6 +184,7 @@ SurrTree <- function(j, wt, Xdata, controls, column.names, tree, maxsurr, ncat)
 #' This is an internal function
 #'
 #' @keywords internal
+#' @md
 name.surr <- function(i, surrogate.names) {
   surrogate.names <- c(surrogate.names, paste0("surrogate_", i))
   return(surrogate.names)
@@ -192,6 +195,7 @@ name.surr <- function(i, surrogate.names) {
 #' This is an internal function
 #'
 #' @keywords internal
+#' @md
 name.adj <- function(i, adj.names) {
   adj.names <- c(adj.names, paste0("adj_", i))
   return(adj.names)

R/getTreeranger.R

@@ -19,6 +19,7 @@
 #' * `layer`: If `add_layer` is `TRUE`, see [addLayer()]
 #'
 #' @export
+#' @md
 getTreeranger <- function(RF, num.trees = RF$num.trees, add_layer = FALSE, num.threads = 1) {
   trees <- parallel::mclapply(1:num.trees, getsingletree,
     mc.cores = num.threads,
@@ -53,6 +54,7 @@ getTreeranger <- function(RF, num.trees = RF$num.trees, add_layer = FALSE, num.t
 #' * `status`: `0` for terminal (`splitpoint` is `NA`) and `1` for non-terminal.
 #'
 #' @keywords internal
+#' @md
 getsingletree <- function(RF, k = 1, add_layer = FALSE) {
   # here we use the treeInfo function of the ranger package to create extract the trees, in an earlier version this was done with a self implemented function
   tree.ranger <- ranger::treeInfo(RF, tree = k)