From 2c84daeca7a7098b9ad3594426be3eac4707a675 Mon Sep 17 00:00:00 2001
From: James Lamb <jaylamb20@gmail.com>
Date: Mon, 14 Aug 2023 09:18:02 -0500
Subject: [PATCH] [R] [doc] remove documentation index entries for internal
 functions (#9477)

---
 R-package/R/xgb.ggplot.R                  |  2 ++
 R-package/man/normalize.Rd                | 18 ---------------
 R-package/man/prepare.ggplot.shap.data.Rd | 27 -----------------------
 3 files changed, 2 insertions(+), 45 deletions(-)
 delete mode 100644 R-package/man/normalize.Rd
 delete mode 100644 R-package/man/prepare.ggplot.shap.data.Rd

diff --git a/R-package/R/xgb.ggplot.R b/R-package/R/xgb.ggplot.R
index f96a8a37f..69d26e2c4 100644
--- a/R-package/R/xgb.ggplot.R
+++ b/R-package/R/xgb.ggplot.R
@@ -142,6 +142,7 @@ xgb.ggplot.shap.summary <- function(data, shap_contrib = NULL, features = NULL,
 #'
 #' @return A data.table containing the observation ID, the feature name, the
 #'   feature value (normalized if specified), and the SHAP contribution value.
+#' @noRd
 prepare.ggplot.shap.data <- function(data_list, normalize = FALSE) {
   data <- data_list[["data"]]
   shap_contrib <- data_list[["shap_contrib"]]
@@ -170,6 +171,7 @@ prepare.ggplot.shap.data <- function(data_list, normalize = FALSE) {
 #' @param x Numeric vector
 #'
 #' @return Numeric vector with mean 0 and sd 1.
+#' @noRd
 normalize <- function(x) {
   loc <- mean(x, na.rm = TRUE)
   scale <- stats::sd(x, na.rm = TRUE)
diff --git a/R-package/man/normalize.Rd b/R-package/man/normalize.Rd
deleted file mode 100644
index 6a05e8342..000000000
--- a/R-package/man/normalize.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/xgb.ggplot.R
-\name{normalize}
-\alias{normalize}
-\title{Scale feature value to have mean 0, standard deviation 1}
-\usage{
-normalize(x)
-}
-\arguments{
-\item{x}{Numeric vector}
-}
-\value{
-Numeric vector with mean 0 and sd 1.
-}
-\description{
-This is used to compare multiple features on the same plot.
-Internal utility function
-}
diff --git a/R-package/man/prepare.ggplot.shap.data.Rd b/R-package/man/prepare.ggplot.shap.data.Rd
deleted file mode 100644
index 57f71a3ff..000000000
--- a/R-package/man/prepare.ggplot.shap.data.Rd
+++ /dev/null
@@ -1,27 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/xgb.ggplot.R
-\name{prepare.ggplot.shap.data}
-\alias{prepare.ggplot.shap.data}
-\title{Combine and melt feature values and SHAP contributions for sample
-observations.}
-\usage{
-prepare.ggplot.shap.data(data_list, normalize = FALSE)
-}
-\arguments{
-\item{data_list}{List containing 'data' and 'shap_contrib' returned by
-\code{xgb.shap.data()}.}
-
-\item{normalize}{Whether to standardize feature values to have mean 0 and
-standard deviation 1 (useful for comparing multiple features on the same
-plot). Default \code{FALSE}.}
-}
-\value{
-A data.table containing the observation ID, the feature name, the
-  feature value (normalized if specified), and the SHAP contribution value.
-}
-\description{
-Conforms to data format required for ggplot functions.
-}
-\details{
-Internal utility function.
-}