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Novartis · Nov 15, 2024 · 2e8e815 · 2e8e815
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Showing 34 changed files with 67 additions and 85 deletions.
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
diff --git a/R/ActivityTable.R b/R/ActivityTable.R
@@ -24,7 +24,7 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-#' @title Activity Table class definition
+#' @title Class that defines the Activity Table in the Generic Report
 #'
 #' @description This R6 class relates to the activity table in the generic report 
 #' that documents the person who perfomed the activity and the person who validated 

diff --git a/R/ChangelogTable.R b/R/ChangelogTable.R
@@ -24,7 +24,7 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-#' @title Changelog Table Row class definition
+#' @title Class that defines the Changelog Table Row Table in the Generic Report
 #'
 #' @description This R6 class controls one row of the Changelog table that documents
 #' the date, version, reason and what changed in the update on the document.
@@ -121,7 +121,7 @@ ChangelogTableRow <- R6::R6Class(
   )
 )
 
-#' @title Changelog Table class definition
+#' @title Class that defines the Changelog Table in the Generic Report
 #'
 #' @description This R6 class controls one row of the Changelog table that documents
 #' the date, version, reason and what changed in the update on the document.

diff --git a/R/ReplaceOutputs.R b/R/ReplaceOutputs.R
@@ -24,7 +24,7 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-#' @title Replace Outputs in a word document
+#' @title Class that defines the Replace Outputs
 #'
 #' @description This R6 class allows to, given a template word document and a list
 #' of outputs, to add them at the given location in the text. It automates the

diff --git a/R/SignaturesTable.R b/R/SignaturesTable.R
@@ -24,7 +24,7 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-#' @title Signatures Table Row class definition
+#' @title Class that defines the Signatures Table Row in the Generic Report
 #'
 #' @description This R6 class controls one row of the Signatures table that documents
 #' the date, version, reason and what changed in the update on the document.
@@ -95,7 +95,7 @@ SignaturesTableRow <- R6::R6Class(
   )
 )
 
-#' @title Signatures Table class definition
+#' @title Class that defines the Signatures Table in the Generic Report
 #'
 #' @description This R6 class controls one row of the Signatures table that documents
 #' the date, version, reason and what changed in the update on the document.

diff --git a/R/TitlePage.R b/R/TitlePage.R
@@ -24,7 +24,7 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-#' @title Title page class definition
+#' @title Class that defines the Title Page in the Generic Report
 #'
 #' @description This R6 class relates to the Title Page in a report that adds all
 #' the required fields of the Generic Report Title Page

diff --git a/R/utils.R b/R/utils.R
@@ -36,6 +36,8 @@
 #'
 #' @import officer
 #' @importFrom magrittr `%>%`
+#' 
+#' @keywords internal
 #'
 #' @examples
 #' \dontrun{
@@ -68,6 +70,8 @@ replace_text <- function(doc, old_value, new_value) {
 #' @import checkmate
 #' @import officer
 #' @importFrom magrittr `%>%`
+#' 
+#' @keywords internal
 #'
 #' @examples
 #' \dontrun{
@@ -130,6 +134,8 @@ find_and_delete_output = function(template_docx,
 #'
 #' @import flextable
 #' @importFrom magrittr `%>%`
+#' 
+#' @keywords internal
 #'
 #' @examples
 #' \dontrun{
@@ -189,6 +195,8 @@ table_styling <- function(flex_table,
 #' character to ensure proper escaping.
 #'
 #' @return escaped caption
+#' 
+#' @keywords internal
 #'
 #' @examples
 #' \dontrun{
@@ -213,6 +221,8 @@ escape_caption <- function(caption) {
 #' @import utils
 #' @import stats
 #' @importFrom magrittr `%>%`
+#' 
+#' @keywords internal
 #'
 #' @examples
 #' \dontrun{
@@ -254,6 +264,8 @@ change_table <- function(template_doc,
 #' @import tools
 #' @import magick
 #' @importFrom magrittr `%>%`
+#' 
+#' @keywords internal
 #'
 #' @examples
 #' \dontrun{
@@ -298,6 +310,8 @@ change_figure <- function(template_doc,
 #' @param doc_final_path Location to save
 #'
 #' @import officer
+#' 
+#' @keywords internal
 #'
 #' @examples
 #' \dontrun{
@@ -316,6 +330,8 @@ save_updated_document <- function(document,
 #' @return formatted version "_v00", "_v02", _v13"
 #'
 #' @import checkmate
+#' 
+#' @keywords internal
 #'
 #' @examples
 #' \dontrun{
@@ -345,6 +361,8 @@ version_number <- function(version) {
 #' path could be and its associated source path text
 #'
 #' @import xml2
+#' 
+#' @keywords internal
 #'
 #' @examples
 #' \dontrun{
@@ -404,6 +422,8 @@ cursor_reach_list <- function(x, keyword) {
 #'
 #' @param yaml_file List. Already read yaml file to be checked for duplicates
 #' @import dplyr
+#' 
+#' @keywords internal
 #'
 search_for_duplicates = function(yaml_file) {
 
@@ -456,6 +476,8 @@ search_for_duplicates = function(yaml_file) {
 #'
 #' @return List figure_table_captions_sources contaning the figure_table_captions
 #' and its corresponding sources paths
+#' 
+#' @keywords internal
 #'
 #' @examples
 #' \dontrun{
@@ -513,6 +535,7 @@ extract_figure_table_captions = function(doc_path) {
 #'
 #' @return updated caption without Figure or Table number
 #'
+#' @keywords internal
 #' @examples
 #' \dontrun{
 #' example_caption <- 
@@ -579,6 +602,8 @@ remove_fig_table_part = function(caption) {
 #'
 #' @import yaml
 #' @import stringr
+#' 
+#' @keywords internal
 #'
 #' @examples
 #' \dontrun{

diff --git a/R/utils_checks.R b/R/utils_checks.R
@@ -31,6 +31,8 @@
 #' @param date_format String. Expected date format. Default is dd-Mmm-yyyy.
 #'
 #' @return the original date str if matches conditions, FALSE if not
+#' 
+#' @keywords internal
 #'
 #' @examples
 #' \dontrun{
@@ -54,6 +56,8 @@ check_string_is_date <- function(date_str, date_format = "%d-%b-%Y") {
 #'
 #' @return the original date str if matches conditions, FALSE if not
 #' @import checkmate
+#' 
+#' @keywords internal
 #'
 #' @examples
 #' \dontrun{
@@ -72,6 +76,8 @@ check_name <- function(name_str){
 #' @param variable object to check
 #'
 #' @return the variable if matches conditions, error if not
+#' 
+#' @keywords internal
 #'
 #' @examples
 #' \dontrun{

diff --git a/README.Rmd b/README.Rmd
@@ -15,6 +15,8 @@ knitr::opts_chunk$set(
 
 # rdocx
 
+# rdocx <img src="man/figures/hex-rdocx.png" align="right" width="80" alt="rdocx website" /></a>
+
 <!-- badges: start -->
 [![R-CMD-check.yaml](https://github.com/Novartis/rdocx/actions/workflows/check_package.yml/badge.svg)](https://github.com/Novartis/rdocx/actions/workflows/check_package.yml)
 [![pkgdown](https://github.com/Novartis/rdocx/actions/workflows/pkgdown.yml/badge.svg)](https://github.com/Novartis/rdocx/actions/workflows/pkgdown.yml)

diff --git a/README.md b/README.md
@@ -3,6 +3,8 @@
 
 # rdocx
 
+# rdocx <img src="man/figures/hex-rdocx.png" align="right" width="80" alt="rdocx website" /></a>
+
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/Novartis/rdocx/actions/workflows/check_package.yml/badge.svg)](https://github.com/Novartis/rdocx/actions/workflows/check_package.yml)
 [![pkgdown](https://github.com/Novartis/rdocx/actions/workflows/pkgdown.yml/badge.svg)](https://github.com/Novartis/rdocx/actions/workflows/pkgdown.yml)

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,9 +1,8 @@
 url: https://opensource.nibr.com/rdocx/
 template:
+  bootstrap: 5
   bootswatch: minty
   light-switch: true
-  theme: gruvbox-light
-  theme-dark: gruvbox-dark
 
 development:
   mode: auto
@@ -22,6 +21,7 @@ reference:
       - SignaturesTableRow
       - TitlePage
       - rmd_render
+      - generic_report_template
 
   - title: Automated Reporting
 

diff --git a/man/ActivityTable.Rd b/man/ActivityTable.Rd
diff --git a/man/ChangelogTable.Rd b/man/ChangelogTable.Rd
diff --git a/man/ChangelogTableRow.Rd b/man/ChangelogTableRow.Rd
diff --git a/man/ReplaceOutputs.Rd b/man/ReplaceOutputs.Rd
diff --git a/man/SignaturesTable.Rd b/man/SignaturesTable.Rd
diff --git a/man/SignaturesTableRow.Rd b/man/SignaturesTableRow.Rd
diff --git a/man/TitlePage.Rd b/man/TitlePage.Rd
diff --git a/man/change_figure.Rd b/man/change_figure.Rd
diff --git a/man/change_table.Rd b/man/change_table.Rd
diff --git a/man/check_name.Rd b/man/check_name.Rd
diff --git a/man/check_null_or_flextable.Rd b/man/check_null_or_flextable.Rd