doc: Fix mixed use of Rd and Md doc blocks

DESCRIPTION

@@ -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

@@ -21,6 +21,7 @@
 #' * `adj_i`: adjusted agreement of variable i
 #'
 #' @export
+#' @md
 addSurrogates <- function(RF, trees, s, Xdata, num.threads = parallel::detectCores()) {
   if (!inherits(RF, "ranger")) {
     stop("`RF` must be a ranger object.")
@@ -69,6 +70,7 @@ addSurrogates <- function(RF, trees, s, Xdata, num.threads = parallel::detectCor
 #' 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]]
@@ -92,6 +94,7 @@ 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
@@ -145,6 +148,7 @@ 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)
@@ -155,6 +159,7 @@ 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)

man/var.relations.Rd

@@ -36,7 +36,7 @@ classification mode is used). For survival forests this is the time variable.}
 
 \item{type}{mode of prediction ("regression", "classification" or "survival"). Default is regression.}
 
-\item{s}{predefined number of surrogate splits (it may happen that the actual number of surrogate splits differs in individual nodes). Default is 1 \\% of no. of variables.}
+\item{s}{predefined number of surrogate splits (it may happen that the actual number of surrogate splits differs in individual nodes). Default is 1 \% of no. of variables.}
 
 \item{mtry}{number of variables to possibly split at in each node. Default is no. of variables^(3/4) ("^3/4") as recommended by (Ishwaran 2011). Also possible is "sqrt" and "0.5" to use the square root or half of the no. of variables.}
 
@@ -48,7 +48,7 @@ classification mode is used). For survival forests this is the time variable.}
 
 \item{save.ranger}{set TRUE if ranger object should be saved. Default is that ranger object is not saved (FALSE).}
 
-\item{create.forest}{Default: TRUE if \code{forest} is NULL, FALSE otherwise. Whether to create or use an existing forest.}
+\item{create.forest}{Default: TRUE if `forest` is NULL, FALSE otherwise. Whether to create or use an existing forest.}
 
 \item{forest}{the random forest that should be analyzed}
 

man/var.relations.mfi.Rd

@@ -37,7 +37,7 @@ classification mode is used). For survival forests this is the time variable.}
 
 \item{type}{mode of prediction ("regression", "classification" or "survival"). Default is regression.}
 
-\item{s}{predefined number of surrogate splits (it may happen that the actual number of surrogate splits differs in individual nodes). Default is 1 \\% of no. of variables.}
+\item{s}{predefined number of surrogate splits (it may happen that the actual number of surrogate splits differs in individual nodes). Default is 1 \% of no. of variables.}
 
 \item{mtry}{number of variables to possibly split at in each node. Default is no. of variables^(3/4) ("^3/4") as recommended by (Ishwaran 2011). Also possible is "sqrt" and "0.5" to use the square root or half of the no. of variables.}
 
@@ -49,7 +49,7 @@ classification mode is used). For survival forests this is the time variable.}
 
 \item{save.ranger}{set TRUE if ranger object should be saved. Default is that ranger object is not saved (FALSE).}
 
-\item{create.forest}{Default: TRUE if \code{forest} is NULL, FALSE otherwise. Whether to create or use an existing forest.}
+\item{create.forest}{Default: TRUE if `forest` is NULL, FALSE otherwise. Whether to create or use an existing forest.}
 
 \item{forest}{the random forest that should be analyzed}
 

man/var.select.md.Rd

@@ -41,7 +41,7 @@ classification mode is used). For survival forests this is the time variable.}
 
 \item{save.ranger}{Set TRUE if ranger object should be saved. Default is that ranger object is not saved (FALSE).}
 
-\item{create.forest}{Default: TRUE if \code{forest} is NULL, FALSE otherwise. Whether to create or use an existing forest.}
+\item{create.forest}{Default: TRUE if `forest` is NULL, FALSE otherwise. Whether to create or use an existing forest.}
 
 \item{forest}{the random forest that should be analyzed.}
 

man/var.select.mir.Rd

@@ -40,7 +40,7 @@ classification mode is used). For survival forests this is the time variable.}
 
 \item{type}{mode of prediction ("regression", "classification" or "survival"). Default is regression.}
 
-\item{s}{predefined number of surrogate splits (it may happen that the actual number of surrogate splits differs in individual nodes). Default is 1 \\% of no. of variables.}
+\item{s}{predefined number of surrogate splits (it may happen that the actual number of surrogate splits differs in individual nodes). Default is 1 \% of no. of variables.}
 
 \item{mtry}{number of variables to possibly split at in each node. Default is no. of variables^(3/4) ("^3/4") as recommended by (Ishwaran 2011). Also possible is "sqrt" and "0.5" to use the square root or half of the no. of variables.}
 

man/var.select.smd.Rd

@@ -32,7 +32,7 @@ classification mode is used). For survival forests this is the time variable.}
 
 \item{type}{mode of prediction ("regression", "classification" or "survival"). Default is regression.}
 
-\item{s}{predefined number of surrogate splits (it may happen that the actual number of surrogate splits differs in individual nodes). Default is 1 \\% of no. of variables.}
+\item{s}{predefined number of surrogate splits (it may happen that the actual number of surrogate splits differs in individual nodes). Default is 1 \% of no. of variables.}
 
 \item{mtry}{number of variables to possibly split at in each node. Default is no. of variables^(3/4) ("^3/4") as recommended by (Ishwaran 2011). Also possible is "sqrt" and "0.5" to use the square root or half of the no. of variables.}
 
@@ -44,7 +44,7 @@ classification mode is used). For survival forests this is the time variable.}
 
 \item{save.ranger}{set TRUE if ranger object should be saved. Default is that ranger object is not saved (FALSE).}
 
-\item{create.forest}{Default: TRUE if \code{forest} is NULL, FALSE otherwise. Whether to create or use an existing forest.}
+\item{create.forest}{Default: TRUE if `forest` is NULL, FALSE otherwise. Whether to create or use an existing forest.}
 
 \item{forest}{the random forest that should be analyzed}