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8 changes: 4 additions & 4 deletions DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -30,9 +30,9 @@ Description: Reporting tables often have structure that goes beyond simple
declaring table layouts and the corresponding computations, and then
applying them to data.
License: Apache License 2.0 | file LICENSE
URL: https://github.com/insightsengineering/rtables,
https://insightsengineering.github.io/rtables/
BugReports: https://github.com/insightsengineering/rtables/issues
URL: https://github.com/pharmaverse/rtables,
https://pharmaverse.github.io/rtables/
BugReports: https://github.com/pharmaverse/rtables/issues
Depends:
formatters (>= 0.5.12),
methods,
Expand Down Expand Up @@ -60,7 +60,7 @@ Suggests:
VignetteBuilder:
knitr,
rmarkdown
Config/Needs/verdepcheck: insightsengineering/formatters, mllg/checkmate,
Config/Needs/verdepcheck: pharmaverse/formatters, mllg/checkmate,
rstudio/htmltools, gagolews/stringi, tidymodels/broom, cran/car,
tidyverse/dplyr, davidgohel/flextable, yihui/knitr, r-lib/lifecycle,
davidgohel/officer, Merck/r2rtf, rstudio/rmarkdown, therneau/survival,
Expand Down
34 changes: 17 additions & 17 deletions NEWS.md
Original file line number Diff line number Diff line change
Expand Up @@ -248,12 +248,12 @@

### Bug Fixes
* Page-by splits which generate zero facets (and thus tables which would have zero pages when rendered) now throw an informative error at table build time.
* Removed superfluous warning which arose for custom split functions when reference group is is set (https://github.com/insightsengineering/rtables/issues/707#issuecomment-1678810598).
* Fixed `qtable` labeling via `row_labels` ([#698](https://github.com/insightsengineering/rtables/issues/698)).
* Removed superfluous warning which arose for custom split functions when reference group is is set (https://github.com/pharmaverse/rtables/issues/707#issuecomment-1678810598).
* Fixed `qtable` labeling via `row_labels` ([#698](https://github.com/pharmaverse/rtables/issues/698)).
* Error catching and test coverage for cases where `alt_counts_df` presents different splits from `df`.

### Miscellaneous
* Cleaned up spelling in documentation ([#685](https://github.com/insightsengineering/rtables/issues/685))
* Cleaned up spelling in documentation ([#685](https://github.com/pharmaverse/rtables/issues/685))
* Custom appearance vignette updated with decimal alignment support.
* Alignment checks have been moved into `formatters`: `formatters::check_aligns` superseded internal function `chk_rtables_align` and `formatters::list_valid_aligns` superseded `rtables_aligns`.

Expand Down Expand Up @@ -354,39 +354,39 @@
## 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](https://github.com/insightsengineering/rtables/issues/304)) 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/pharmaverse/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](https://github.com/insightsengineering/rtables/issues/329))
* Throw informative error messages when custom analysis, content or split functions fail ([#329](https://github.com/pharmaverse/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 `cbind`ing tables from working correctly ([#324]](https://github.com/insightsengineering/rtables/issues/324))
* fixed bug in handling of column extra arguments that was preventing `cbind`ing tables from working correctly ([#324]](https://github.com/pharmaverse/rtables/issues/324))

## rtables 0.5.1
* empty factor levels are now *not* dropped for column splits when ref_group is set ([#323](https://github.com/insightsengineering/rtables/issues/323))
* empty factor levels are now *not* dropped for column splits when ref_group is set ([#323](https://github.com/pharmaverse/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](https://github.com/insightsengineering/rtables/issues/314))
* `split_rows_by(var, child_labels="hidden")` no longer removes the structural subtable corresponding to levels of `var` ([#314](https://github.com/pharmaverse/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](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))
* Fix bug when function format combined with NULL `cfun` caused error ([#307](https://github.com/pharmaverse/rtables/issues/307))
* Fix bug in `path_enriched_df` (which powers `tsv` export), related to ([#308](https://github.com/pharmaverse/rtables/issues/308))

## rtables 0.4.1.0002
* added `table_shell` to display shell of table with formats
Expand All @@ -407,7 +407,7 @@
* `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 `[@wwojciech](https://github.com/wwojciech)`'s work in [#203](https://github.com/insightsengineering/rtables/issues/203)
* new `trim_levels_to_map` split function based on `[@wwojciech](https://github.com/wwojciech)`'s work in [#203](https://github.com/pharmaverse/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
Expand All @@ -422,17 +422,17 @@
* 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](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))
* Fix bug where tables output using `as_html` (or viewed in `Viewer`) were missing the table class attribute ([#194](https://github.com/pharmaverse/rtables/issues/194))
* inserting a `DataRow` with incorrect number of columns is now an error ([#199](https://github.com/pharmaverse/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))
* Fix extraneous footnote attribute bug ([#198](https://github.com/pharmaverse/rtables/issues/198))
* Fix max -Inf warning when content rows appear at positions whose children have 0 visible rows ([#200](https://github.com/pharmaverse/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](https://github.com/insightsengineering/rtables/issues/173))
* Fix column label ordering bug when value label variable is a factor ([#173](https://github.com/pharmaverse/rtables/issues/173))

## rtables 0.3.7

Expand Down Expand Up @@ -515,7 +515,7 @@ tables in the context of clinical trials.
## rtables 0.3.2.17.9034

* 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)
* `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/pharmaverse/rtables/issues/112)

## rtables 0.3.2.17.9033

Expand Down
2 changes: 1 addition & 1 deletion R/custom_split_funs.R
Original file line number Diff line number Diff line change
Expand Up @@ -165,7 +165,7 @@ NULL
if (are(vals, "SplitValue") && !are(vals, "LevelComboSplitValue")) {
if (!is.null(extr)) {
## in_ref_cols is in here for some reason even though its already in the SplitValue object.
## https://github.com/insightsengineering/rtables/issues/707#issuecomment-1678810598
## https://github.com/pharmaverse/rtables/issues/707#issuecomment-1678810598
## the if is a bandaid.
## XXX FIXME RIGHT
sq <- seq_along(vals)
Expand Down
2 changes: 1 addition & 1 deletion R/tt_dotabulation.R
Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,7 @@ gen_onerv <- function(csub, col, count, cextr, cpath,
alt_dfpart_fil <- alt_dfpart
}

## workaround for https://github.com/insightsengineering/rtables/issues/159
## workaround for https://github.com/pharmaverse/rtables/issues/159
if (NROW(dfpart) > 0) {
inds <- eval(csub, envir = dfpart)
dat <- dfpart[inds, , drop = FALSE]
Expand Down
4 changes: 2 additions & 2 deletions R/tt_sort.R
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ cont_n_allcols <- function(tt) {
#' @param j (`numeric(1)`)\cr index of column used for scoring.
#'
#' @seealso For examples and details, please read the documentation for [sort_at_path()] and the
#' [Sorting and Pruning](https://insightsengineering.github.io/rtables/latest-tag/articles/sorting_pruning.html)
#' [Sorting and Pruning](https://pharmaverse.github.io/rtables/latest-tag/articles/sorting_pruning.html)
#' vignette.
#'
#' @export
Expand Down Expand Up @@ -101,7 +101,7 @@ match_fun_args <- function(fun, ...) {
#'
#' Note that sorting needs a deeper understanding of table structure in `rtables`. Please consider reading the related
#' vignette
#' ([Sorting and Pruning](https://insightsengineering.github.io/rtables/latest-tag/articles/sorting_pruning.html))
#' ([Sorting and Pruning](https://pharmaverse.github.io/rtables/latest-tag/articles/sorting_pruning.html))
#' and explore table structure with useful functions like [table_structure()] and [row_paths_summary()]. It is also
#' very important to understand the difference between "content" rows and "data" rows. The first one analyzes and
#' describes the split variable generally and is generated with [summarize_row_groups()], while the second one is
Expand Down
46 changes: 23 additions & 23 deletions README.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -16,27 +16,27 @@ suppressPackageStartupMessages(library(rtables))
suppressPackageStartupMessages(library(dplyr))
```

# rtables <a href='https://github.com/insightsengineering/rtables'><img src="man/figures/logo.svg" align="right" height="200" width="200"/></a>
# rtables <a href='https://github.com/pharmaverse/rtables'><img src="man/figures/logo.svg" align="right" height="200" width="200"/></a>

<!-- start badges -->
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<!-- end badges -->

## Reporting Tables with R
Expand Down Expand Up @@ -74,17 +74,17 @@ or you can install the latest development version directly from GitHub with:

```r
# install.packages("pak")
pak::pak("insightsengineering/rtables")
pak::pak("pharmaverse/rtables")
```

Packaged releases (both those on CRAN and those between official CRAN releases) can be
found in the [releases list](https://github.com/insightsengineering/rtables/releases).
found in the [releases list](https://github.com/pharmaverse/rtables/releases).

To understand how to use this package, please refer to the [Introduction to `rtables`](https://insightsengineering.github.io/rtables/main/articles/rtables.html) article, which provides multiple examples of code implementation.
To understand how to use this package, please refer to the [Introduction to `rtables`](https://pharmaverse.github.io/rtables/main/articles/rtables.html) article, which provides multiple examples of code implementation.

## Cheatsheet

<a href="https://github.com/insightsengineering/rtables/blob/main/inst/cheatsheet/rtables_cheatsheet_01-24.pdf"><img src="https://raw.githubusercontent.com/insightsengineering/rtables/main/inst/cheatsheet/rtables_cheatsheet_01-24_thumbs.png" width="630" height="247"/></a>
<a href="https://github.com/pharmaverse/rtables/blob/main/inst/cheatsheet/rtables_cheatsheet_01-24.pdf"><img src="https://raw.githubusercontent.com/pharmaverse/rtables/main/inst/cheatsheet/rtables_cheatsheet_01-24_thumbs.png" width="630" height="247"/></a>

## Usage

Expand Down Expand Up @@ -149,9 +149,9 @@ Maximo Carreras, Francois Collins, Saibah Chohan, Tadeusz Lewandowski, Nick Pasz
- Generating Tables, Listings, and Graphs using NEST / [cardinal](https://pharmaverse.github.io/cardinal/) [[Video](https://www.youtube.com/watch?v=YPmbLPSYFYM)]
- BBS Session on Regulatory Submissions of Clinical Trials [[Video](https://www.youtube.com/watch?v=yZS4OBuJe_Q)]
- R Medicine Virtual Conference 2023 [[Video](https://www.youtube.com/watch?v=sxFsavKI7s4)]
- Advanced rtables Training 2023 [[Part 1 Slides](https://github.com/insightsengineering/rtables/blob/main/inst/extdata/Advanced_rtables_part1.pdf)] [[Part 2 Slides](https://github.com/insightsengineering/rtables/blob/main/inst/extdata/Advances_rtables_part2.pdf)]
- R in Pharma 2022 - Creating Submission-Quality Clinical Trial Reporting Tables in R with rtables [[Slides](https://github.com/insightsengineering/rtables/blob/main/inst/extdata/Clinical_Trial_Reporting_Tables_in_R.pdf)] [[Video](https://www.youtube.com/watch?v=zBm_NZ0VtKs)]
- Advanced rtables Training 2023 [[Part 1 Slides](https://github.com/pharmaverse/rtables/blob/main/inst/extdata/Advanced_rtables_part1.pdf)] [[Part 2 Slides](https://github.com/pharmaverse/rtables/blob/main/inst/extdata/Advances_rtables_part2.pdf)]
- R in Pharma 2022 - Creating Submission-Quality Clinical Trial Reporting Tables in R with rtables [[Slides](https://github.com/pharmaverse/rtables/blob/main/inst/extdata/Clinical_Trial_Reporting_Tables_in_R.pdf)] [[Video](https://www.youtube.com/watch?v=zBm_NZ0VtKs)]
- R Consortium 2022
- R Adoption Series - Reporting Table Creation in R [[Video](https://www.youtube.com/watch?v=1i6vOId2h4A)] [[Slides](https://github.com/insightsengineering/rtables/blob/main/inst/extdata/r_adoption_slides.pdf)]
- R Adoption Series - Reporting Table Creation in R [[Video](https://www.youtube.com/watch?v=1i6vOId2h4A)] [[Slides](https://github.com/pharmaverse/rtables/blob/main/inst/extdata/r_adoption_slides.pdf)]
- Tables in Clinical Trials with R [[Book](https://rconsortium.github.io/rtrs-wg/)]
- useR! 2020 - rtables Layouting and Tabulation Framework [[Video](https://www.youtube.com/watch?v=CBQzZ8ZhXLA)]
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