11 cran

.Rbuildignore

@@ -20,6 +20,13 @@ R/util_experimental.R
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+LICENSE
 
 # dev
 tmp/
+ae.pptx
+ae_summary.pptx
+dd.pptx
+dm.pptx
+dor.pptx
+  ‘output.pptx’

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: autoslider.core
-Title: Slides automation with R
-Version: 0.0.1.9033
+Title: Slide Automation for Tables, Listings and Figures
+Version: 0.1.0
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("cre", "aut")),
     person("Heng", "Wang", role = "aut"),
@@ -20,9 +20,17 @@ Authors@R: c(
     person("Elisabeth", "Deutschmann", role = "ctb"),
     person("Chenkai", "Lv", role = "aut")
   )
-Description: Slides automation with R.
-License: file LICENSE
+Description: The normal process of creating clinical study slides is that a statistician
+    manually type in the numbers from outputs and a separate statistician to double check
+    the typed in numbers. This process is time consuming, resource intensive, and error
+    prone. Automatic slide generation is a solution to address these issues. It reduces the
+    amount of work and the required time when creating slides, and reduces the risk of
+    errors from manually typing or copying numbers from the output to slides. It also
+    helps users to avoid unnecessary stress when creating large amounts of slide decks
+    in a short time window.
+License: Apache License 2.0
 URL: https://github.com/insightsengineering/autoslider.core
+BugReports: https://github.com/insightsengineering/autoslider.core/issues
 Depends:
     flextable (>= 0.9.4),
     officer (>= 0.3.18),

NEWS.md

@@ -1 +1,4 @@
-# autoslider.core 0.0.1.9033
+# autoslider.core 0.1.0
+
+### Miscellaneous
+ * First release.

R/autoslideR_error.R

@@ -7,6 +7,7 @@
 #' @param x character scaler
 #' @param spec spec should be a list containing "program" and "suffix"
 #' @param step step is a character indicating in which step the pipeline encounter error
+#' @return autoslider_error object
 #' @export
 autoslider_error <- function(x, spec, step) {
   assert_is_character_scalar(x)

R/decorate.R

@@ -1,4 +1,5 @@
 #' generic function decorate
+#' @return No return value, called for side effects
 #' @export
 setGeneric("decorate", function(x, ...) standardGeneric("decorate"))
 
@@ -12,7 +13,7 @@ decorate <- function(x, ...) {
 #' default method to decorate
 #' @param x object to decorate
 #' @param ... additional arguments. not used.
-#'
+#' @return No return value, called for side effects
 #' @export
 decorate.default <- function(x, ...) {
   stop("default decorate function does not exist")
@@ -21,7 +22,7 @@ decorate.default <- function(x, ...) {
 #' decorate method for autoslider_error class
 #' @param x object to decorate
 #' @param ... additional arguments. not used.
-#'
+#' @return No return value, called for side effects
 #' @export
 decorate.autoslider_error <- function(x, ...) {
   x
@@ -35,6 +36,7 @@ decorate.autoslider_error <- function(x, ...) {
 #' @param paper Orientation and font size as string, e.g. "P8"; "L11"
 #' @param for_test `logic` CICD parameter
 #' @param ... Additional arguments passed to the decoration function.
+#' @return No return value, called for side effects
 setMethod(
   "decorate", "VTableTree",
   decorate.VTableTree <- function(x, titles = "", footnotes = "", paper = "P8", for_test = FALSE, ...) {
@@ -74,6 +76,7 @@ setMethod(
 #' @param paper Paper size, by default "L11"
 #' @param for_test `logic` CICD parameter
 #' @param ... additional arguments. not used.
+#' @return No return value, called for side effects
 #' @details
 #' The paper default paper size, `L11`, indicate that the fontsize is 11.
 #' The fontsize of the footnotes, is the fontsize of the titles minus 2.
@@ -97,6 +100,7 @@ decorate.ggplot <- function(x, titles = "", footnotes = "", paper = "L11", for_t
 #' @param paper Orientation and font size as string, e.g. "P8"; "L11"
 #' @param for_test `logic` CICD parameter
 #' @param ... Additional arguments. not used.
+#' @return No return value, called for side effects
 setMethod(
   "decorate", "listing_df",
   decorate.listing_df <- function(x, titles = "", footnotes = "", paper = "P8", for_test = FALSE, ...) {
@@ -134,6 +138,7 @@ setMethod(
 #' @param paper paper size. default is "L8".
 #' @param for_test `logic` CICD parameter
 #' @param ... Additional arguments. not used.
+#' @return No return value, called for side effects
 #' @details
 #' The paper default paper size, `L11`, indicate that the fontsize is 11.
 #' The fontsize of the footnotes, is the fontsize of the titles minus 2.
@@ -165,6 +170,7 @@ decorate.grob <-
 #' @details
 #' The paper default paper size, `L11`, indicate that the fontsize is 11.
 #' The fontsize of the footnotes, is the fontsize of the titles minus 2.
+#' @return No return value, called for side effects
 #' @export
 #'
 decorate.list <-
@@ -204,7 +210,7 @@ decorate.list <-
 #' @param generic_footnote `character` vector of footnotes
 #' @param version_label `character`. A version label to be added to the title.
 #' @param for_test `logic` CICD parameter
-#'
+#' @return No return value, called for side effects
 #' @details
 #' `generic_title` and `generic_footnote` will be added to *all* outputs. The use
 #' case is to add information such as protocol number and snapshot date defined
@@ -284,7 +290,7 @@ decorate_outputs <- function(outputs,
 #'
 #' @param x An object of class `decoratedGrob`
 #' @param ... not used.
-#'
+#' @return No return value, called for side effects
 #' @export
 print.decoratedGrob <- function(x, ...) {
   grid::grid.newpage()
@@ -295,7 +301,7 @@ print.decoratedGrob <- function(x, ...) {
 #'
 #' @param x An object of class `decoratedGrobSet`
 #' @param ... not used.
-#'
+#' @return No return value, called for side effects
 #' @export
 print.decoratedGrobSet <- function(x, ...) {
   for (plot in x) {

R/fastdocall.R

@@ -5,6 +5,7 @@
 #' @param quote a logical value indicating whether to quote the arguments.
 #' @param envir an environment within which to evaluate the call. This will be most useful if what is a character
 #' string and the arguments are symbols or quoted expressions.
+#' @return No return value, called for side effects
 #' @export
 fastDoCall <-
   function(what,

R/ft_formats.R

@@ -17,7 +17,7 @@ NULL
 #' @param font_name Font name, default to arial
 #' @param body_font_size Font size of the table content, default to 12
 #' @param header_font_size Font size of the table header, default to 14
-#'
+#' @return A flextable with applied theme.
 #' @export
 autoslider_format <- function(ft,
                               odd_header = "#0EAED5", # "deepskyblue2",

R/generate_output.R

@@ -4,6 +4,7 @@
 #' @param datasets list of datasets
 #' @param spec spec
 #' @param verbose_level Verbose level of messages be displayed. See details for further information.
+#' @return No return value, called for side effects
 #' @details
 #' `verbose_level` is used to control how many messages are printed out.
 #' By default, `2` will show all filter messages and show output generation message.
@@ -89,6 +90,7 @@ generate_output <-
 #' @param spec Specification list generated by `read_spec`
 #' @param datasets A `list` of datasets
 #' @param verbose_level Verbose level of messages be displayed. See details for further information.
+#' @return No return value, called for side effects
 #' @details
 #' `verbose_level` is used to control how many messages are printed out.
 #' By default, `2` will show all filter messages and show output generation message.

R/helper_functions.R

@@ -4,7 +4,7 @@
 #' @param arm_var Arm variable
 #' @param levels factor levels
 #' @param labels factor labels
-#'
+#' @return Dataframe with re-level and re-labelled arm variable.
 #' @export
 mutate_actarm <- function(df,
                           arm_var = "TRT01A",
@@ -25,7 +25,7 @@ mutate_actarm <- function(df,
 #' @param df Input dataframe
 #' @param levels factor levels
 #' @param labels factor labels
-#'
+#' @return dataframe
 #' @export
 preprocess_t_dd <- function(df,
                             levels = c("PROGRESSIVE DISEASE", "ADVERSE EVENT", "OTHER", "<Missing>"),
@@ -55,7 +55,7 @@ preprocess_t_dd <- function(df,
 #' @param df Input dataframe
 #' @param levels factor levels
 #' @param labels factor labels
-#'
+#' @return dataframe
 #' @export
 preprocess_t_ds <- function(df,
                             levels = c("Alive: On Treatment", "Alive: In Follow-up", "<Missing>"),

R/null_report.R

@@ -5,7 +5,7 @@
 #' @details
 #' This will create a null report similar as STREAM does. You can use
 #' it inside output functions as shown in the example below.
-#'
+#' @return An empty `rtables` object
 #' @examples
 #' library(dplyr)
 #' library(filters)

R/save_output.R

@@ -35,6 +35,7 @@ save_output <- function(output, file_name, save_rds = TRUE) {
 }
 
 #' @rdname save_output
+#' @return No return value, called for side effects
 #' @export
 save_output.autoslider_error <- function(output,
                                          file_name,
@@ -53,6 +54,7 @@ setMethod("save_output", "dVTableTree", save_output.dVTableTree <- function(outp
 })
 
 #' @rdname save_output
+#' @return The input `object` invisibly
 #' @export
 save_output.decoratedGrob <- function(output,
                                       file_name,
@@ -65,6 +67,7 @@ save_output.decoratedGrob <- function(output,
 }
 
 #' @rdname save_output
+#' @return The input `object` invisibly
 #' @export
 save_output.decoratedGrobSet <- function(output, file_name, save_rds = TRUE) {
   if (save_rds) {
@@ -76,6 +79,7 @@ save_output.decoratedGrobSet <- function(output, file_name, save_rds = TRUE) {
 
 
 #' @rdname save_output
+#' @return The input `object` invisibly
 #' @export
 save_output.dlisting <- function(output, file_name, save_rds = TRUE) {
   if (save_rds) {
@@ -96,7 +100,7 @@ save_output.dlisting <- function(output, file_name, save_rds = TRUE) {
 #'        in addition to `.out` or `.pdf` files? Defaults to `FALSE`.
 #' @param generic_suffix generic suffix. must be length 1 character or NULL.
 #' @export
-#'
+#' @return The input `object` invisibly
 #' @examples
 #' ## As `save_outputs` is the last step in the pipeline we have to run
 #' ## the 'whole machinery' in order to show its functionality. Also take a look

R/spec.R

@@ -74,10 +74,6 @@ validate_spec <- function(spec) {
 #' library(dplyr)
 #' spec_file <- system.file("spec.yml", package = "autoslider.core")
 #' spec <- spec_file %>% read_spec()
-#' ## Keep only outputs belonging to batch 2
-#' \dontrun{
-#' filter_spec(spec, batch == 2)
-#' }
 #'
 #' ## Keep only the t_dm_IT output
 #' filter_spec(spec, output == "t_dm_IT")

R/t_ae_pt_slide.R

@@ -23,7 +23,7 @@
 #'   )
 #' out <- t_ae_pt_slide(adsl, adae, "TRT01A", 2)
 #' print(out)
-#' generate_slides(out, "ae.pptx")
+#' generate_slides(out, paste0(tempdir(), "/ae.pptx"))
 #'
 #' # Example 2, prune by total column
 #' out2 <- t_ae_pt_slide(adsl, adae, "TRT01A", 25, prune_by_total = TRUE)

R/t_ae_pt_soc_slide.R

@@ -22,7 +22,7 @@
 #'   )
 #' out <- t_ae_pt_soc_slide(adsl, adae, "TRT01A", 2)
 #' print(out)
-#' generate_slides(out, "ae.pptx")
+#' generate_slides(out, paste0(tempdir(), "/ae.pptx"))
 #'
 #'
 #' # Example 2, prune by total column

R/t_dor_slide.R

@@ -4,7 +4,7 @@
 #' @param arm Arm variable, character, "`TRT01P" by default.
 #' @param refgroup Reference group
 #' @inherit gen_notes note
-#'
+#' @return An `rtables` object
 #' @export
 #' @examples
 #' library(dplyr)

R/to_slides.R

@@ -14,6 +14,7 @@
 #' @param l_cpp An integer specifying the listing columns per page\cr
 #'    Specify this optional argument to modify the width of all of the listings display
 #' @param ... arguments passed to program
+#' @return No return value, called for side effects
 #' @export
 #' @examples
 #'
@@ -44,7 +45,7 @@
 #' t_dm_slide(adsl, "TRT01P", c("SEX", "AGE")) %>%
 #'   generate_slides()
 generate_slides <- function(outputs,
-                            outfile = "output.pptx",
+                            outfile = paste0(tempdir(), "/output.pptx"),
                             template = file.path(system.file(package = "autoslider.core"), "theme/basic.pptx"),
                             fig_width = 9, fig_height = 6, t_lpp = 20, t_cpp = 200, l_lpp = 20, l_cpp = 150, ...) {
   if (any(c(
@@ -117,6 +118,7 @@ generate_slides <- function(outputs,
 #' Generate flextable for preview first page
 #'
 #' @param x rtables or data.frame
+#' @return A flextable or a ggplot object depending to the input.
 #' @export
 #' @examples
 #' # Example 1. preview table
@@ -149,7 +151,6 @@ get_body_bottom_location <- function(ppt) {
 #' @param ft Flextable object
 #' @param ppt_width Powerpoint width
 #' @param ppt_height Powerpoint height
-#'
 #' @return Location for a placeholder
 center_table_loc <- function(ft, ppt_width, ppt_height) {
   top <- 0.17 * ppt_height
@@ -259,7 +260,7 @@ center_figure_loc <- function(fig_width, fig_height, ppt_width, ppt_height) {
 #' @param fig_width width of figure
 #' @param fig_height height of figure
 #' @param figure_loc location of figure
-#'
+#' @return Location for a placeholder
 #' @export
 ph_with_img <- function(ppt, figure, fig_width, fig_height, figure_loc) {
   file_name <- tempfile(fileext = ".svg")