[R] Finalizes switch to markdown doc (dmlc#10733)

---------

Co-authored-by: Jiaming Yuan <[email protected]>

Author: mayer79

R-package/R/callbacks.R

@@ -56,7 +56,7 @@
 #'   It should match with argument `nrounds` passed to [xgb.train()] or [xgb.cv()].
 #'
 #'   Note that boosting might be interrupted before reaching this last iteration, for
-#'   example by using the early stopping callback \link{xgb.cb.early.stop}.
+#'   example by using the early stopping callback [xgb.cb.early.stop()].
 #' - iteration Index of the iteration number that is being executed (first iteration
 #'   will be the same as parameter `begin_iteration`, then next one will add +1, and so on).
 #'

R-package/R/xgb.Booster.R

@@ -222,12 +222,11 @@ xgb.get.handle <- function(object) {
 #' For multi-class and multi-target, will be a 4D array with dimensions `[nrows, ngroups, nfeats+1, nfeats+1]`
 #' }
 #'
-#' If passing `strict_shape=FALSE`, the result is always an array:\itemize{
-#' \item For normal predictions, the dimension is `[nrows, ngroups]`.
-#' \item For `predcontrib=TRUE`, the dimension is `[nrows, ngroups, nfeats+1]`.
-#' \item For `predinteraction=TRUE`, the dimension is `[nrows, ngroups, nfeats+1, nfeats+1]`.
-#' \item For `predleaf=TRUE`, the dimension is `[nrows, niter, ngroups, num_parallel_tree]`.
-#' }
+#' If passing `strict_shape=FALSE`, the result is always an array:
+#' - For normal predictions, the dimension is `[nrows, ngroups]`.
+#' - For `predcontrib=TRUE`, the dimension is `[nrows, ngroups, nfeats+1]`.
+#' - For `predinteraction=TRUE`, the dimension is `[nrows, ngroups, nfeats+1, nfeats+1]`.
+#' - For `predleaf=TRUE`, the dimension is `[nrows, niter, ngroups, num_parallel_tree]`.
 #'
 #' If passing `avoid_transpose=TRUE`, then the dimensions in all cases will be in reverse order - for
 #' example, for `predinteraction`, they will be `[nfeats+1, nfeats+1, ngroups, nrows]`
@@ -623,7 +622,7 @@ validate.features <- function(bst, newdata) {
 #' change the value of that parameter for a model.
 #' Use [xgb.parameters<-()] to set or change model parameters.
 #'
-#' The [xgb.attributes<-()] setter either updates the existing or adds one or several attributes,
+#' The `xgb.attributes<-` setter either updates the existing or adds one or several attributes,
 #' but it doesn't delete the other existing attributes.
 #'
 #' Important: since this modifies the booster's C object, semantics for assignment here
@@ -635,11 +634,11 @@ validate.features <- function(bst, newdata) {
 #' @param object Object of class `xgb.Booster`. **Will be modified in-place** when assigning to it.
 #' @param name A non-empty character string specifying which attribute is to be accessed.
 #' @param value For `xgb.attr<-`, a value of an attribute; for `xgb.attributes<-`,
-#'        it is a list (or an object coercible to a list) with the names of attributes to set
-#'        and the elements corresponding to attribute values.
-#'        Non-character values are converted to character.
-#'        When an attribute value is not a scalar, only the first index is used.
-#'        Use `NULL` to remove an attribute.
+#'   it is a list (or an object coercible to a list) with the names of attributes to set
+#'   and the elements corresponding to attribute values.
+#'   Non-character values are converted to character.
+#'   When an attribute value is not a scalar, only the first index is used.
+#'   Use `NULL` to remove an attribute.
 #' @return
 #' - `xgb.attr()` returns either a string value of an attribute
 #'   or `NULL` if an attribute wasn't stored in a model.

R-package/R/xgb.DMatrix.R

@@ -2,12 +2,13 @@
 #'
 #' Save xgb.DMatrix object to binary file
 #'
-#' @param dmatrix the \code{xgb.DMatrix} object
+#' @param dmatrix the `xgb.DMatrix` object
 #' @param fname the name of the file to write.
 #'
 #' @examples
 #' \dontshow{RhpcBLASctl::omp_set_num_threads(1)}
-#' data(agaricus.train, package='xgboost')
+#' data(agaricus.train, package = "xgboost")
+#'
 #' dtrain <- with(agaricus.train, xgb.DMatrix(data, label = label, nthread = 2))
 #' fname <- file.path(tempdir(), "xgb.DMatrix.data")
 #' xgb.DMatrix.save(dtrain, fname)

R-package/R/xgb.DMatrix.save.R

@@ -1,24 +1,26 @@
+#' Set and get global configuration
+#'
 #' Global configuration consists of a collection of parameters that can be applied in the global
 #' scope. See \url{https://xgboost.readthedocs.io/en/stable/parameter.html} for the full list of
-#' parameters supported in the global configuration. Use \code{xgb.set.config} to update the
-#' values of one or more global-scope parameters. Use \code{xgb.get.config} to fetch the current
+#' parameters supported in the global configuration. Use `xgb.set.config()` to update the
+#' values of one or more global-scope parameters. Use `xgb.get.config()` to fetch the current
 #' values of all global-scope parameters (listed in
 #' \url{https://xgboost.readthedocs.io/en/stable/parameter.html}).
+#'
 #' @details
 #' Note that serialization-related functions might use a globally-configured number of threads,
 #' which is managed by the system's OpenMP (OMP) configuration instead. Typically, XGBoost methods
-#' accept an `nthreads` parameter, but some methods like `readRDS` might get executed before such
+#' accept an `nthreads` parameter, but some methods like [readRDS()] might get executed before such
 #' parameter can be supplied.
 #'
 #' The number of OMP threads can in turn be configured for example through an environment variable
 #' `OMP_NUM_THREADS` (needs to be set before R is started), or through `RhpcBLASctl::omp_set_num_threads`.
 #' @rdname xgbConfig
-#' @title Set and get global configuration
 #' @name xgb.set.config, xgb.get.config
 #' @export xgb.set.config xgb.get.config
 #' @param ... List of parameters to be set, as keyword arguments
 #' @return
-#' \code{xgb.set.config} returns \code{TRUE} to signal success. \code{xgb.get.config} returns
+#' `xgb.set.config()` returns `TRUE` to signal success. `xgb.get.config()` returns
 #' a list containing all global-scope parameters and their values.
 #'
 #' @examples