Merge branch 'main' into 848_clean_up_docs@main

Signed-off-by: Emily de la Rua <[email protected]>

DESCRIPTION

@@ -29,7 +29,7 @@ URL: https://github.com/insightsengineering/rtables,
     https://insightsengineering.github.io/rtables/
 BugReports: https://github.com/insightsengineering/rtables/issues
 Depends:
-    formatters (>= 0.5.5),
+    formatters (>= 0.5.5.9005),
     magrittr (>= 1.5),
     methods,
     R (>= 2.10)
@@ -47,6 +47,7 @@ Suggests:
     lifecycle (>= 0.2.0),
     officer (>= 0.5.0),
     r2rtf (>= 0.3.2),
+    rmarkdown (>= 2.19),
     survival (>= 3.3-1),
     testthat (>= 3.0.4),
     tibble (>= 3.2.1),
@@ -57,10 +58,10 @@ VignetteBuilder:
     knitr
 Config/Needs/verdepcheck: insightsengineering/formatters,
     tidyverse/magrittr, mllg/checkmate, rstudio/htmltools,
-    gogolewski/stringi, tidymodels/broom, cran/car, tidyverse/dplyr,
-    davidgohel/flextable, yihui/knitr, r-lib/lifecycle, davidgohel/officer, 
-    Merck/r2rtf, r-lib/testthat, tidyverse/tibble, tidyverse/tidyr, 
-    r-lib/withr, r-lib/xml2
+    gagolewski/stringi, tidymodels/broom, cran/car, tidyverse/dplyr,
+    davidgohel/flextable, yihui/knitr,  r-lib/lifecycle, davidgohel/officer, 
+    Merck/r2rtf, rstudio/rmarkdown, r-lib/testthat, tidyverse/tibble, 
+    tidyverse/tidyr, r-lib/withr, r-lib/xml2
 Encoding: UTF-8
 Language: en-US
 LazyData: true

NEWS.md

@@ -9,6 +9,7 @@
  * Fixed issue with `rtables_root` not being removed when using `as_result_df`.
  * Fixed edge case bug in `as_result_df` where rows of the table have only `"root"` as path index.
  * Fixed `sort_at_path` pathing to ignore leading `"root"` element (regardless of actual root element name) to match current `tt_at_path` behavior.
+ * Fixed `section_div` for analysis of multiple variables (`AnalyzeMultiVars`).
 
 ### Miscellaneous
 * Removed deprecated functions `add_analyzed_var` and `trim_zero_rows`.

R/00tabletrees.R

@@ -802,6 +802,7 @@ AnalyzeMultiVars <- function(var,
     cformat <- .repoutlst(cformat, nv)
     ##        split_format = .repoutlst(split_format, nv)
     inclNAs <- .repoutlst(inclNAs, nv)
+    section_div_if_multivar <- if (length(var) > 1) NA_character_ else section_div
     pld <- mapply(AnalyzeVarSplit,
       var = var,
       split_name = child_names,
@@ -818,7 +819,7 @@ AnalyzeMultiVars <- function(var,
         label_pos = show_kidlabs,
         split_format = split_format,
         split_na_str = split_na_str,
-        section_div = section_div
+        section_div = section_div_if_multivar
       ), ## rvis),
       SIMPLIFY = FALSE
     )

R/tt_dotabulation.R

@@ -679,6 +679,8 @@ setMethod(
       ...
     ))
 
+    kids <- .set_kids_section_div(kids, spl_section_div(spl), "VTableTree")
+
     ## XXX this seems like it should be identical not !identical
     ## TODO FIXME
     if (!identical(make_lrow, FALSE) && !have_controws && length(kids) == 1) {

R/utils.R

@@ -108,7 +108,7 @@ paste_vec <- function(vec) {
 # Utility for checking if a package is installed
 check_required_packages <- function(pkgs) {
   for (pkgi in pkgs) {
-    if (!requireNamespace(pkgi)) {
+    if (!requireNamespace(pkgi, quietly = TRUE)) {
       stop(
         "This function requires the ", pkgi, " package. ",
         "Please install it if you wish to use it"

inst/WORDLIST

@@ -1,82 +1,83 @@
+amongst
 Arg
-CRAN's
 Carreras
+charset
 Cheatsheet
 Chohan
-FFFL
-Godwin
-Heng
-Kelkhoff
-Layouting
-Lewandowski
-Maximo
-Modelling
-NSE
-Paszty
-Pharma
-Phuse
-Postprocessing
-Pre
-Qi
-RStudio
-Resync
-STUDYID
-Saibah
-Stoilova
-Subtable
-Subtables
-TableTree
-Tadeusz
-Unstratified
-Yung
-amongst
-charset
 combinatorial
+CRAN's
 customizations
 decrementing
 dimensioned
 dplyr
 emph
 facetted
 facetting
+FFFL
 formatter
 getter
 getters
+Godwin
+Heng
 ing
 initializer
 integerish
 iteratively
+Kelkhoff
 labelled
+Layouting
 layouting
+Lewandowski
 mandatorily
+Maximo
+Modelling
 multivariable
+NSE
 orderable
+Paszty
 pathing
+Pharma
+Phuse
 postfix
+Postprocessing
 postprocessing
+Pre
 pre
 priori
 programmatically
+Qi
 quartiles
 reindexed
 repo
 repped
 responder
+Resync
 reusability
 roadmap
+RStudio
+rtables
+Saibah
 sortable
 spl
+Stoilova
+STUDYID
+Subtable
 subtable
 subtable's
+Subtables
 subtables
 summarization
 tableone
+TableTree
+Tadeusz
 todo
 unaggregated
 unicode
 univariable
 unnested
 unpruned
+Unstratified
 unstratified
 useR
 xtable
+Yung

tests/testthat/setup-fakedata.R

@@ -223,3 +223,10 @@ tt_for_nl <- tt_to_test_newline_chars()
     nchar(str) - nchar(gsub(chr, "", str, fixed = TRUE))
   }
 }
+
+# Utility function for section_div tests
+check_pattern <- function(element, letter, len) {
+  # Regular expression to match exactly len of the same letter
+  regex <- paste0(rep(letter, len), collapse = "")
+  return(grepl(regex, element, fixed = TRUE))
+}

tests/testthat/test-accessors.R

@@ -225,12 +225,6 @@ test_that("header sep setting works", {
 })
 
 # section_div tests ------------------------------------------------------------
-check_pattern <- function(element, letter, len) {
-  # Regular expression to match exactly len of the same letter
-  regex <- paste0(rep(letter, len), collapse = "")
-  return(grepl(regex, element, fixed = TRUE))
-}
-
 test_structure_with_a_getter <- function(tbl, getter, val_per_lev) {
   # Main table obj
   expect_identical(tbl %>% getter(), val_per_lev$global)

tests/testthat/test-exporters.R

@@ -390,7 +390,7 @@ test_that("Can create flextable object that works with different styles", {
 
   # internal package check
   not_a_pkg <- "bwrereloakdosirabttjtaeerr"
-  suppressMessages(expect_error(check_required_packages(c("flextable", not_a_pkg)), not_a_pkg))
+  expect_error(check_required_packages(c("flextable", not_a_pkg)), not_a_pkg)
 })
 
 test_that("export_as_doc works thanks to tt_to_flextable", {

tests/testthat/test-printing.R

@@ -397,6 +397,34 @@ test_that("section_div works throughout", {
   expect_identical(length(mylns), 31L) ## sect div not printed for last one
 })
 
+test_that("section_div works when analyzing multiple variables", {
+  # Regression test for #835
+  lyt <- basic_table() %>%
+    split_rows_by("Species", section_div = "|") %>%
+    analyze(c("Petal.Width", "Petal.Length"),
+      afun = function(x) list("m" = mean(x), "sd" = sd(x)), section_div = "-"
+    )
+
+  tbl <- build_table(lyt, iris)
+  out <- strsplit(toString(tbl), "\n")[[1]]
+
+  expect_true(check_pattern(out[11], "|", length(out[1])))
+  expect_true(check_pattern(out[16], "-", length(out[1])))
+
+  # One-var still works
+  lyt <- basic_table() %>%
+    split_rows_by("Species", section_div = "|") %>%
+    analyze("Petal.Width",
+      afun = function(x) list("m" = mean(x), "sd" = sd(x)), section_div = "-"
+    )
+
+  tbl <- build_table(lyt, iris)
+  out <- strsplit(toString(tbl), "\n")[[1]]
+
+  expect_true(check_pattern(out[7], "|", length(out[1])))
+  expect_true(check_pattern(out[10], "-", length(out[1])))
+})
+
 test_that("Inset works for table, ref_footnotes, and main footer", {
   general_inset <- 3
 

vignettes/introduction.Rmd

@@ -51,7 +51,7 @@ table object, a formatted table can be printed in ASCII format, or exported to a
 variety of other formats (`.txt`, `.pdf`, `.docx`, etc.).
 
 ```{r echo=FALSE, fig.align='center'}
-knitr::include_graphics("../man/figures/rtables-basics.png")
+knitr::include_graphics("./images/rtables-basics.png")
 ```
 
 ## Data