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reduce the amount of spelling issues / WORDLIST (#685)
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* first attempt on WORDLIST reduction

* finalize wordlist reduction

* Update vignettes/introduction.Rmd

Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>

* Update tests/testthat/test-lyt-tabulation.R

Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>

* Update tests/testthat/test-lyt-tabulation.R

Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>

* update NEWS

---------

Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>
Signed-off-by: Joe Zhu <joe.zhu@roche.com>
Co-authored-by: Joe Zhu <joe.zhu@roche.com>
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m7pr and shajoezhu committed Jul 28, 2023
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73 changes: 37 additions & 36 deletions NEWS.md
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## rtables 0.6.2.9000
* 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.
Expand Down Expand Up @@ -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`
Expand All @@ -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).
Expand All @@ -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`
Expand All @@ -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
Expand All @@ -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


Expand All @@ -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

Expand All @@ -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
Expand All @@ -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
Expand All @@ -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

Expand All @@ -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

Expand Down Expand Up @@ -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()`.

Expand Down
10 changes: 5 additions & 5 deletions R/00tabletrees.R
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Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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
Expand All @@ -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.
Expand Down Expand Up @@ -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.
Expand Down
4 changes: 2 additions & 2 deletions R/Viewer.R
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#' @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}
#'
#'
Expand Down
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