Merge branch 'main' into 568_dev_guide_split@main

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9013
+    rev: v0.3.2.9019
     hooks: 
     -   id: roxygenize
         # roxygen requires loading pkg -> add dependencies from DESCRIPTION

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rtables
 Title: Reporting Tables
-Version: 0.6.2.9000
-Date: 2023-07-20
+Version: 0.6.2.9002
+Date: 2023-08-11
 Authors@R: c(
     person("Gabriel", "Becker", , "gabembecker@gmail.com", role = c("aut", "cre")),
     person("Adrian", "Waddell", , "adrian.waddell@gene.com", role = "aut"),

NAMESPACE

@@ -118,6 +118,7 @@ export(prune_empty_level)
 export(prune_table)
 export(prune_zeros_only)
 export(qtable)
+export(qtable_layout)
 export(rawvalues)
 export(rbindl_rtables)
 export(rcell)

NEWS.md

@@ -1,4 +1,5 @@
-## rtables 0.6.2.9000
+## rtables 0.6.2.9002
+ * Cleaned up spelling in documentation ([#685](https://github.com/insightsengineering/rtables/issues/685))
 
 ## rtables 0.6.2
  * Fixed major regressions for `page_by` machinery caused by migration to `formatters` 0.5.1 pagination framework.
@@ -42,7 +43,7 @@
  * extended and clarified documentation
  * `export_as_pdf` now correctly takes `margins` into account when calculating `lpp` and `cpp` from page size.
  * exporters now pass down non-default `colwidths` values correctly
- * `nlines` `TableRow` method (used for both rows and column label extent in paginaton) now correctly handles column spanning
+ * `nlines` `TableRow` method (used for both rows and column label extent in pagination) now correctly handles column spanning
  * pagination with `verbose = TRUE` now includes original and adjusted lines-per page information
  * `cont_n_allcols` and `cont_n_onecol` score functions now throw errors when they are applied to subtables that
    have no content table, instead of the previously returned `NA`
@@ -58,13 +59,13 @@
 
 ## rtables 0.5.3
  * `[<-` now treats character `i` and `j` values as paths, the same as `[` always has.
- * `[<-` `CellValue` method now preserves CellValue attributes (e.g., format)
+ * `[<-` `CellValue` method now preserves `CellValue` attributes (e.g., format)
  * More detailed subsetting and modification vignette
  * `nlines` methods now accept both `colwidths` and `max_width`
  * `max_width` is now used during pagination to determine lines taken up by referential footnotes
  * `make_col_df` now accepts `colwidths` argument, and can be called directly on `InstantiatedColumnInfo` objects
  * versioned dependency on `formatters` increase to `>0.3.3.12`
- * wordwrapping title/footer materials no longer fails in the presence of `""` values.
+ * word wrapping title/footer materials no longer fails in the presence of `""` values.
  * versioned dependency on `formatters` increase to `>0.3.3.11`
  * `paginate_table` now accepts `tf_wrap` and `max_width` and respects title/footer word wrapping when present
  * export functions now accepts `tf_wrap` and `max_width` and use them in both pagination (when turned on) *and* `toString` when used (pdf, txt exporters).
@@ -81,10 +82,10 @@
  * Increase versioned dependency on `formatters` to `>0.3.3.5` for `table_inset` support
  * Use `exact=TRUE` in all calls to `attr` within access functions
  * Increase versioned dependency on `formatters` to `>0.3.3.4`
- * layouting instructions now accept na_str argument, which specifies na string with the same
+ * layouting instructions now accept `na_str` argument, which specifies `na` string with the same
    inheritance rules as formats
- * (pre-data) Split and (post tabulation) Table/row S4 classes now carry around na_str information
- * Increase versioned dependency on `formatters` to `>= 0.3.3.3` for support of na_strs with `NA_character_` values
+ * (pre-data) Split and (post tabulation) Table/row S4 classes now carry around `na_str` information
+ * Increase versioned dependency on `formatters` to `>= 0.3.3.3` for support of `na_str`s with `NA_character_` values
  * `paginate_table` now takes page dimension and font information and uses `formatters::page_lcpp` to
    calculate `lpp` and `cpp` automatically when those are provided.
  * Increase versioned dependency on `formatters` to `>= 0.3.3.2` for `page_lcpp`
@@ -97,39 +98,39 @@
 ## rtables 0.5.1.5
  * Support for section dividers (`section_div` argument in `split_rows_by*` function)
  * Updated versioned dependency on `formatters` to `>=0.3.2.3`
- * Equivalent split functions with different enclosing environments (e.g., 2 identical calls to `add_combo_levels` #340) no longer block `rbind`ing
+ * Equivalent split functions with different enclosing environments (e.g., 2 identical calls to `add_combo_levels` [#340](https://github.com/insightsengineering/rtables/issues/304)) no longer block `rbind`ing
  * Fixed various documentation bugs where description section was being added to header.
 
 ## rtables 0.5.1.4
  * empty level check for splitting variables reinstated.
 
 ## rtables 0.5.1.3
- * Throw informative error messages when custom analysis, content or split functions fail (#329)
+ * Throw informative error messages when custom analysis, content or split functions fail ([#329](https://github.com/insightsengineering/rtables/issues/329))
 
 ## rtables 0.5.1.2
  * empty level check for splitting variables temporarily removed. It is very likely to be reinstated in a future release.
 
 ## rtables 0.5.1.1
  * `col_counts` getter and setter now accept `path` argument.
  * empty levels of a splitting variable now result in an informative error message (character and factor cases).
- * fixed bug in handling of column extra arguments that was preventing cbinding tables from working correctly (#324)
+ * fixed bug in handling of column extra arguments that was preventing `cbind`ing tables from working correctly ([#324]](https://github.com/insightsengineering/rtables/issues/324))
 
 ## rtables 0.5.1
- * empty factor levels are now *not* dropped for column splits when ref_group is set (#323)
+ * empty factor levels are now *not* dropped for column splits when ref_group is set ([#323](https://github.com/insightsengineering/rtables/issues/323))
  * `linesep` argument to `toString` and related functions renamed to `hsep`
  * Increase versioned dependency on `formatters` to `>=0.3.0`
  * Default "line separator" between header and body now falls back to "-" non-UTF charset locales.
  * New `hsep` argument to `build_table` which sets the horizontal separator for the constructed table (and subtables thereof)
  * New `horizontal_sep` and `horizontal_sep<-` accessors for constructed tables, the latter of which is mandatorily recursive.
- * `split_rows_by(var, child_labels="hidden")` no longer removes the structural subtable corresponding to levels of `var` (#314)
+ * `split_rows_by(var, child_labels="hidden")` no longer removes the structural subtable corresponding to levels of `var` ([#314](https://github.com/insightsengineering/rtables/issues/314))
 
 ## rtables 0.5.0
  * `formatable` dependency renamed to `formatters` for suitability of release to CRAN
  * Update versioned dependency of `formatters` (previously `formatable`) to `>=0.2.0` 
 
 ## rtables 0.4.1.0004
- * Fix bug when function format combined with NULL cfun caused error (#307)
- * Fix bug in `path_enriched_df` (which powers tsv export), related to (#308)
+ * Fix bug when function format combined with NULL `cfun` caused error ([#307](https://github.com/insightsengineering/rtables/issues/307))
+ * Fix bug in `path_enriched_df` (which powers `tsv` export), related to ([#308](https://github.com/insightsengineering/rtables/issues/308))
 
 ## rtables 0.4.1.0002
  * added `table_shell` to display shell of table with formats
@@ -150,12 +151,12 @@
  * `value_at` and `cell_values` functions now have methods for `TableRow` objects making them usable in sorting/pruning functions
 
 ## rtables 0.3.8.9001
- * new `trim_levels_to_map` split function based on wwojtek's work in #203
+ * new `trim_levels_to_map` split function based on `[@wwojciech](https://github.com/wwojciech)`'s work in [#203](https://github.com/insightsengineering/rtables/issues/203)
  * support for column referential footnotes
  * support for adding footnotes to existing table via `fnotes_at_path<-` function
  * `trim_levels_in_group` now trims empty levels of outer (split) variable by default
- * `value_at` and `cell_values` now work for tablerow objects
- * Fixed `as_html` bug in multivar split columns case 
+ * `value_at` and `cell_values` now work for `tablerow` objects
+ * Fixed `as_html` bug in `multivar` split columns case 
  * Fixed pagination off-by-one error
 
 
@@ -164,34 +165,34 @@
 ## rtables 0.3.8
  * Add experimental support for newlines in column names, row labels, and cell values (not supported in top-left annotations)
  * `as_html` refactored to support newlines while respecting table structure
- * self_extent column of df returned by `make_row_df` now reflects extent *in lines*, thus will return larger values if the row-label or any cell values contain newlines.
- * Fix bug where tables output using `as_html` (or viewed in `Viewer`) were missing the table class attribute (#194)
- * inserting a DataRow with incorrect number of columns is now an error (#199)
- * Referential footer machinery now works in colspan case.
- * Fix extraneous footnote attribute bug (#198)
- * Fix max -Inf warning when content rows appear at positions whose children have 0 visible rows (#200)
- * Resync NEWS.md file
+ * self_extent column of `df` returned by `make_row_df` now reflects extent *in lines*, thus will return larger values if the row-label or any cell values contain newlines.
+ * Fix bug where tables output using `as_html` (or viewed in `Viewer`) were missing the table class attribute ([#194](https://github.com/insightsengineering/rtables/issues/194))
+ * inserting a `DataRow` with incorrect number of columns is now an error ([#199](https://github.com/insightsengineering/rtables/issues/199))
+ * Referential footer machinery now works in `colspan` case.
+ * Fix extraneous footnote attribute bug ([#198](https://github.com/insightsengineering/rtables/issues/198))
+ * Fix max -Inf warning when content rows appear at positions whose children have 0 visible rows ([#200](https://github.com/insightsengineering/rtables/issues/200))
+ * Resync `NEWS.md` file
  * Introduce titles and footnotes
  * Support automatic population of top-left
  * Introduce referential footnote support for cells and row labels
  * Added `vars_in_layout` to list (explicitly named only) variables used in a layout
- * Fix column label ordering bug when value label variable is a factor (#173)
+ * Fix column label ordering bug when value label variable is a factor ([#173](https://github.com/insightsengineering/rtables/issues/173))
 
 ## rtables 0.3.7
 
-Synchronize release with GitHub commit sha.
+Synchronize release with GitHub commit `sha`.
 
 ## rtables 0.3.6
 
 Documentation revisions as requested by CRAN. No change to package code.
 
 ## rtables 0.3.5
 
-Documentation-text only changes to introduction vignette to pass CRAN's URL checks. All package, example, test, and vignette code fully identical to that in tagged github release 0.3.4
+Documentation-text only changes to introduction vignette to pass CRAN's URL checks. All package, example, test, and vignette code fully identical to that in tagged GitHub release 0.3.4
 
 ## rtables 0.3.4
 
-Minor changes to the 0.3.3 version in order to submit rtables to CRAN.
+Minor changes to the 0.3.3 version in order to submit `rtables` to CRAN.
 
 ## rtables 0.3.3
 
@@ -206,11 +207,11 @@ tables in the context of clinical trials.
 
 ## rtables 0.3.2.17.9046
 
-* `make_afun` now `force()`s all customization arguments immediately, which prevents problems when called within loop/lapply constructs.
+* `make_afun` now `force()`s all customization arguments immediately, which prevents problems when called within loop/`lapply` constructs.
 
 ## rtables 0.3.2.17.9045
 
-* Tabulation machinery no longer removes NAs mandatorily in some cases, including multivar column splits
+* Tabulation machinery no longer removes NAs mandatorily in some cases, including `multivar` column splits
 * `analyze_colvars`'s `inclNAs` argument now respected.
 
 ## rtables 0.3.2.17.9044
@@ -225,8 +226,8 @@ tables in the context of clinical trials.
 
 ## rtables 0.3.2.17.9042
 
-* Fix naming/pathing for columns in multivar case (split itself now has default name "multivars")
-* Fix labeling bug when same variable appears multiple times in MultiVarSplit with different associated levels
+* Fix naming/pathing for columns in `multivar` case (split itself now has default name `"multivars"`)
+* Fix labeling bug when same variable appears multiple times in `MultiVarSplit` with different associated levels
 
 
 ## rtables 0.3.2.17.9041
@@ -240,7 +241,7 @@ tables in the context of clinical trials.
 
 ## rtables 0.3.2.17.9039
 
-* Fix bug in display of column information when column structure is not symmetric, as with recursive cbinds.
+* Fix bug in display of column information when column structure is not symmetric, as with recursive `cbind`s.
 
 ## rtables 0.3.2.17.9036
 
@@ -257,16 +258,16 @@ tables in the context of clinical trials.
 
 ## rtables 0.3.2.17.9034
 
-* Fix internal `value_formats` accessor so it operates on CellValues rather than the raw contained values (thus always returning NULL)
-* `rrow` constructor no longer interprets cell formats a row format when they are the same across all cells. Fixes bug in  "correct way" code discussed in #112
+* Fix internal `value_formats` accessor so it operates on `CellValue`s rather than the raw contained values (thus always returning NULL)
+* `rrow` constructor no longer interprets cell formats a row format when they are the same across all cells. Fixes bug in  "correct way" code discussed in [#112](https://github.com/insightsengineering/rtables/issues/112)
 
 ## rtables 0.3.2.17.9033
 
 * Interpret .formats in `in_rows` as *cell* formats rather than row formats.
 
 ## rtables 0.3.2.17.9031
 
-* cbind_rtables can now take more than 2 tables.
+* `cbind_rtables` can now take more than 2 tables.
 
 ## rtables 0.3.2.17.9029
 
@@ -332,7 +333,7 @@ tables in the context of clinical trials.
 
 ## rtables 0.1.0.5
 
-* Added `sprintf_format` for formatting rcells (thanks to Doug Kelkhoff for the suggestion).
+* Added `sprintf_format` for formatting `rcell`s (thanks to Doug Kelkhoff for the suggestion).
 * Added `"(N=xx)"` and `">999.9"` format labels.
 * `rtabulate` has now an argument `col_N` and the function `col_N()`.
 

R/00tabletrees.R

@@ -8,7 +8,7 @@
 ## quantilecut: cut on quantiles of observed values for a variable
 ## missing: split obs based on missingness of a variable/observation. This could be used for compare to ref_group??
 ## multicolumn: each child analyzes a different column
-## arbitrary: children are not related to eachother in any systematic fashion.
+## arbitrary: children are not related to each other in any systematic fashion.
 
 
 ## null is ok here.
@@ -271,7 +271,7 @@ setClass("ManualSplit", contains = "AllSplit",
 #' @inheritParams lyt_args
 #' @inheritParams constr_args
 #' @inheritParams gen_args
-#' @param levels character. Levels of the split (ie the children of the manual
+#' @param levels character. Levels of the split (i.e. the children of the manual
 #'   split)
 #' @author Gabriel Becker
 #' @return A \code{ManualSplit} object.
@@ -1025,7 +1025,7 @@ LayoutColLeaf <- function(lev = 0L,
 ## various aspects of the column layout
 ## once its applied to the data.
 
-#' InstantiatedColumnInfo
+#' `InstantiatedColumnInfo`
 #' @inheritParams gen_args
 #' @exportClass InstantiatedColumnInfo
 #' @rdname cinfo
@@ -1043,7 +1043,7 @@ setClass("InstantiatedColumnInfo",
 
 #' @rdname cinfo
 #' @export
-#' @param treelyt LayoutColTree.
+#' @param treelyt `LayoutColTree`.
 #' @param csubs list. List of subsetting expressions
 #' @param extras list. Extra arguments associated with the columns
 #' @param cnts integer. Counts.
@@ -1272,7 +1272,7 @@ etable_validity  <- function(object) {
 }
 ## nocov end
 
-#' TableTree classes
+#' `TableTree` classes
 #' @exportClass ElementaryTable
 #' @author Gabriel Becker
 #' @return A formal object representing a populated table.

R/Viewer.R

@@ -1,14 +1,14 @@
 #' @importFrom utils  browseURL
 NULL
 
-#' Display an \code{\link{rtable}} object in the Viewer pane in RStudio or in a
+#' Display an \code{\link{rtable}} object in the Viewer pane in `RStudio` or in a
 #' browser
 #'
 #' The table will be displayed using the bootstrap styling for tables.
 #'
 #' @param x object of class \code{rtable} or \code{shiny.tag} (defined in \code{htmltools})
 #' @param y optional second argument of same type as \code{x}
-#' @param row.names.bold row.names.bold boolean, make rownames bold
+#' @param row.names.bold row.names.bold boolean, make `row.names` bold
 #' @param ... arguments passed to \code{as_html}
 #'
 #'