refactor: `getTreeranger()` to use lapply, and include addLayer

DESCRIPTION

 Type: Package
 Package: RFSurrogates
 Title: Surrogate Minimal Depth Variable Importance
-Version: 0.3.3.9001
+Version: 0.3.3.9002
 Authors@R: c(
     person("Stephan", "Seifert", , "stephan.seifert@uni-hamburg.de", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-2567-5728")),

R/getTreeranger.R

@@ -4,6 +4,8 @@
 #'
 #' @param RF A [`ranger::ranger`] object which was created with `keep.inbag = TRUE`.
 #' @param num.trees (Deprecated) Number of trees to convert (Default: `RF$num.trees`).
+#' @param add_layer (Default: `FALSE`) Whether to [addLayer()] in the same loop.
+#' @param num.threads (Default: 1) Number of threads to spawn for parallelization.
 #'
 #' @returns A list of tree data frames of length `RF$num.trees`.
 #' Each row of the tree data frames corresponds to a node of the respective tree and the columns correspond to:
@@ -14,10 +16,15 @@
 #' * `splitpoint`: Split point of the split variable.
 #'    For categorical variables this is a comma separated lists of values, representing the factor levels (in the original order) going to the right.
 #' * `status`: `0` for terminal (`splitpoint` is `NA`) and `1` for non-terminal.
+#' * `layer`: If `add_layer` is `TRUE`, see [addLayer()]
 #'
 #' @export
-getTreeranger <- function(RF, num.trees = RF$num.trees) {
-  lapply(1:num.trees, getsingletree, RF = RF)
+getTreeranger <- function(RF, num.trees = RF$num.trees, add_layer = FALSE, num.threads = 1) {
+  parallel::mclapply(1:num.trees, getsingletree,
+    mc.cores = num.threads,
+    RF = RF,
+    add_layer = add_layer
+  )
 }
 
 #' getsingletree
@@ -26,6 +33,7 @@ getTreeranger <- function(RF, num.trees = RF$num.trees) {
 #'
 #' @param RF A [`ranger::ranger`] object.
 #' @param k Tree index to convert.
+#' @param add_layer
 #'
 #' @returns A tree data frame for the `k`th tree in `RF`.
 #' Each row of the tree data frames corresponds to a node of the respective tree and the columns correspond to:
@@ -38,7 +46,7 @@ getTreeranger <- function(RF, num.trees = RF$num.trees) {
 #' * `status`: `0` for terminal (`splitpoint` is `NA`) and `1` for non-terminal.
 #'
 #' @keywords internal
-getsingletree <- function(RF, k = 1) {
+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)
   ktree <- data.frame(
@@ -55,5 +63,9 @@ getsingletree <- function(RF, k = 1) {
 
   ktree[, 2:4][is.na(ktree[, 2:4])] <- 0
 
+  if (add_layer) {
+    ktree <- add_layer_to_tree(ktree)
+  }
+
   return(ktree)
 }

man/getTreeranger.Rd

@@ -4,12 +4,16 @@
 \alias{getTreeranger}
 \title{Get a list of structured trees from a ranger object.}
 \usage{
-getTreeranger(RF, num.trees = RF$num.trees)
+getTreeranger(RF, num.trees = RF$num.trees, add_layer = FALSE, num.threads = 1)
 }
 \arguments{
 \item{RF}{A \code{\link[ranger:ranger]{ranger::ranger}} object which was created with \code{keep.inbag = TRUE}.}
 
 \item{num.trees}{(Deprecated) Number of trees to convert (Default: \code{RF$num.trees}).}
+
+\item{add_layer}{(Default: \code{FALSE}) Whether to \code{\link[=addLayer]{addLayer()}} in the same loop.}
+
+\item{num.threads}{(Default: 1) Number of threads to spawn for parallelization.}
 }
 \value{
 A list of tree data frames of length \code{RF$num.trees}.
@@ -22,6 +26,7 @@ Each row of the tree data frames corresponds to a node of the respective tree an
 \item \code{splitpoint}: Split point of the split variable.
 For categorical variables this is a comma separated lists of values, representing the factor levels (in the original order) going to the right.
 \item \code{status}: \code{0} for terminal (\code{splitpoint} is \code{NA}) and \code{1} for non-terminal.
+\item \code{layer}: If \code{add_layer} is \code{TRUE}, see \code{\link[=addLayer]{addLayer()}}
 }
 }
 \description{

man/getsingletree.Rd

@@ -4,12 +4,14 @@
 \alias{getsingletree}
 \title{getsingletree}
 \usage{
-getsingletree(RF, k = 1)
+getsingletree(RF, k = 1, add_layer = FALSE)
 }
 \arguments{
 \item{RF}{A \code{\link[ranger:ranger]{ranger::ranger}} object.}
 
 \item{k}{Tree index to convert.}
+
+\item{add_layer}{}
 }
 \value{
 A tree data frame for the \code{k}th tree in \code{RF}.