diff --git a/DESCRIPTION b/DESCRIPTION
index 9ff6b59bc..3cf4cf660 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -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,
@@ -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,
diff --git a/NEWS.md b/NEWS.md
index 7a90cc0b4..20d268a16 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -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* Alignment checks have been moved into `formatters`: `formatters::check_aligns` superseded internal function `chk_rtables_align` and `formatters::list_valid_aligns` superseded `rtables_aligns`.
@@ -354,14 +354,14 @@
## 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.
@@ -369,24 +369,24 @@
## 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
@@ -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
@@ -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
@@ -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
diff --git a/R/custom_split_funs.R b/R/custom_split_funs.R
index 984fadd60..39851f3b7 100644
--- a/R/custom_split_funs.R
+++ b/R/custom_split_funs.R
@@ -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)
diff --git a/R/tt_dotabulation.R b/R/tt_dotabulation.R
index 5f66fde77..36d8eb7b1 100644
--- a/R/tt_dotabulation.R
+++ b/R/tt_dotabulation.R
@@ -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]
diff --git a/R/tt_sort.R b/R/tt_sort.R
index 84081eed5..7d0b24687 100644
--- a/R/tt_sort.R
+++ b/R/tt_sort.R
@@ -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
@@ -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
diff --git a/README.Rmd b/README.Rmd
index 49b23765c..51e64f526 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -16,27 +16,27 @@ suppressPackageStartupMessages(library(rtables))
suppressPackageStartupMessages(library(dplyr))
```
-# rtables 
+# rtables
-[](https://github.com/insightsengineering/rtables/actions/workflows/check.yaml)
-[](https://insightsengineering.github.io/rtables/)
-[](https://raw.githubusercontent.com/insightsengineering/rtables/_xml_coverage_reports/data/main/coverage.xml)
-
-
-
-
-
-
-
-
-
-
+[](https://github.com/pharmaverse/rtables/actions/workflows/check.yaml)
+[](https://pharmaverse.github.io/rtables/)
+[](https://raw.githubusercontent.com/pharmaverse/rtables/_xml_coverage_reports/data/main/coverage.xml)
+
+
+
+
+
+
+
+
+
+
[](https://www.repostatus.org/#active)
-[](https://github.com/insightsengineering/rtables/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)
+[](https://github.com/pharmaverse/rtables/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)
[](https://CRAN.R-project.org/package=rtables)
-[](https://github.com/insightsengineering/rtables/tree/main)
+[](https://github.com/pharmaverse/rtables/tree/main)
## Reporting Tables with R
@@ -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
-
+
## Usage
@@ -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)]
diff --git a/README.md b/README.md
index ba637b57d..e4bad0649 100644
--- a/README.md
+++ b/README.md
@@ -1,44 +1,44 @@
-# rtables
+# rtables
[](https://github.com/insightsengineering/rtables/actions/workflows/check.yaml)
+๐ ](https://github.com/pharmaverse/rtables/actions/workflows/check.yaml/badge.svg)](https://github.com/pharmaverse/rtables/actions/workflows/check.yaml)
[](https://insightsengineering.github.io/rtables/)
+๐](https://github.com/pharmaverse/rtables/actions/workflows/docs.yaml/badge.svg)](https://pharmaverse.github.io/rtables/)
[](https://raw.githubusercontent.com/insightsengineering/rtables/_xml_coverage_reports/data/main/coverage.xml)
+๐](https://raw.githubusercontent.com/pharmaverse/rtables/_xml_coverage_reports/data/main/badge.svg)](https://raw.githubusercontent.com/pharmaverse/rtables/_xml_coverage_reports/data/main/coverage.xml)
+forks](https://img.shields.io/github/forks/pharmaverse/rtables?style=social)
+stars](https://img.shields.io/github/stars/pharmaverse/rtables?style=social)
+activity](https://img.shields.io/github/commit-activity/m/pharmaverse/rtables)
+contributors](https://img.shields.io/github/contributors/pharmaverse/rtables)
+commit](https://img.shields.io/github/last-commit/pharmaverse/rtables)
+requests](https://img.shields.io/github/issues-pr/pharmaverse/rtables)
+size](https://img.shields.io/github/repo-size/pharmaverse/rtables)
+count](https://img.shields.io/github/languages/count/pharmaverse/rtables)
[](https://www.repostatus.org/#active)
[](https://github.com/insightsengineering/rtables/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)
+Issues](https://img.shields.io/github/issues-raw/pharmaverse/rtables?color=red&label=open%20issues)](https://github.com/pharmaverse/rtables/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)
[](https://CRAN.R-project.org/package=rtables)
[](https://github.com/insightsengineering/rtables/tree/main)
+Version](https://img.shields.io/github/r-package/v/pharmaverse/rtables/main?color=purple&label=Development%20Version)](https://github.com/pharmaverse/rtables/tree/main)
## Reporting Tables with R
@@ -87,21 +87,21 @@ 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).
+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)
+`rtables`](https://pharmaverse.github.io/rtables/main/articles/rtables.html)
article, which provides multiple examples of code implementation.
## Cheatsheet
-
+
## Usage
@@ -216,17 +216,17 @@ Nick Paszty, Nina Qi, Jana Stoilova, Heng Wang, Godwin Yung
- R Medicine Virtual Conference 2023
\[[Video](https://www.youtube.com/watch?v=sxFsavKI7s4)\]
- Advanced rtables Training 2023 \[[Part 1
- Slides](https://github.com/insightsengineering/rtables/blob/main/inst/extdata/Advanced_rtables_part1.pdf)\]
+ Slides](https://github.com/pharmaverse/rtables/blob/main/inst/extdata/Advanced_rtables_part1.pdf)\]
\[[Part 2
- Slides](https://github.com/insightsengineering/rtables/blob/main/inst/extdata/Advances_rtables_part2.pdf)\]
+ 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
- \[[Slides](https://github.com/insightsengineering/rtables/blob/main/inst/extdata/Clinical_Trial_Reporting_Tables_in_R.pdf)\]
+ \[[Slides](https://github.com/pharmaverse/rtables/blob/main/inst/extdata/Clinical_Trial_Reporting_Tables_in_R.pdf)\]
\[[Video](https://www.youtube.com/watch?v=zBm_NZ0VtKs)\]
- R Consortium 2022
- R Adoption Series - Reporting Table Creation in R
\[[Video](https://www.youtube.com/watch?v=1i6vOId2h4A)\]
- \[[Slides](https://github.com/insightsengineering/rtables/blob/main/inst/extdata/r_adoption_slides.pdf)\]
+ \[[Slides](https://github.com/pharmaverse/rtables/blob/main/inst/extdata/r_adoption_slides.pdf)\]
- Tables in Clinical Trials with R
\[[Book](https://rconsortium.github.io/rtrs-wg/)\]
- useR! 2020 - rtables Layouting and Tabulation Framework
diff --git a/inst/WORDLIST b/inst/WORDLIST
index ebe6642b1..ab9d7694c 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -1,56 +1,26 @@
+Abinaya
AE
AEs
-ARD
-ARDs
-BMEASIFL
-Bovรฉ
-CRAN's
-Carreras
-Cheatsheet
-Chohan
-FFFL
-Godwin
-Heng
-Hoffmann
-Kelkhoff
-Layouting
-Lewandowski
-Maximo
-Modelling
-NSE
-ORCID
-Paszty
-Pathing
-Pharma
-Phuse
-Postprocessing
-Pre
-Qi
-RStudio
-Resync
-Rua
-SKELETOMUSCULAR
-STUDYID
-Sabanรฉs
-Saibah
-Stoilova
-Subtable
-Subtables
-Tadeusz
-Tord
-Unstratified
-ValueWrapper
-Yung
afun
afuns
amongst
+ARD
ard
+ARDs
args
biomarker
+BMEASIFL
+Bov
+Bovรฉ
+Carreras
charset
+Cheatsheet
+Chohan
colcount
combinatorial
+CRAN's
customizations
+Davide
de
decrementing
df
@@ -61,46 +31,80 @@ elemtable
emph
facetted
facetting
+FFFL
formatter
forseeable
funder
+Garolini
getter
getters
+Godwin
+Heng
+Hoffmann
ie
indicies
ing
initializer
+Kelkhoff
labelled
+Layouting
layouting
+Lewandowski
mandatorily
+Maximo
modelled
+Modelling
monospace
+Mordig
multivariable
+NSE
+ORCID
orderable
orthogonally
oversimplifaction
+Paszty
pathability
pathable
pathed
+Pathing
pathing
+Pharma
+Phuse
postfix
+Postprocessing
postprocessing
+Pre
pre
+Qi
reindexed
repped
responder
+Resync
reusability
roadmap
+RStudio
+rtables
+Rua
+Saban
+Sabanรฉs
+Saibah
+SKELETOMUSCULAR
sortable
spl
+Stoilova
+STUDYID
subseting
subsplits
+Subtable
subtable
subtable's
+Subtables
subtables
summarization
tableone
+Tadeusz
todo
+Tord
traversable
truetype
unaggregated
@@ -110,8 +114,14 @@ uniquification
univariable
unnested
unpruned
+Unstratified
unstratified
useR
+ValueWrapper
visibilities
visibilty
+Waddell
xtable
+Yogasekaram
+Yung
+Zhu
diff --git a/man/rtables-package.Rd b/man/rtables-package.Rd
index fa8a83660..a7d0268cb 100644
--- a/man/rtables-package.Rd
+++ b/man/rtables-package.Rd
@@ -13,9 +13,9 @@ Reporting tables often have structure that goes beyond simple rectangular data.
\seealso{
Useful links:
\itemize{
- \item \url{https://github.com/insightsengineering/rtables}
- \item \url{https://insightsengineering.github.io/rtables/}
- \item Report bugs at \url{https://github.com/insightsengineering/rtables/issues}
+ \item \url{https://github.com/pharmaverse/rtables}
+ \item \url{https://pharmaverse.github.io/rtables/}
+ \item Report bugs at \url{https://github.com/pharmaverse/rtables/issues}
}
}
diff --git a/man/score_funs.Rd b/man/score_funs.Rd
index 9ce673c09..ac9f4e591 100644
--- a/man/score_funs.Rd
+++ b/man/score_funs.Rd
@@ -22,6 +22,6 @@ Score functions for sorting \code{TableTrees}
}
\seealso{
For examples and details, please read the documentation for \code{\link[=sort_at_path]{sort_at_path()}} and the
-\href{https://insightsengineering.github.io/rtables/latest-tag/articles/sorting_pruning.html}{Sorting and Pruning}
+\href{https://pharmaverse.github.io/rtables/latest-tag/articles/sorting_pruning.html}{Sorting and Pruning}
vignette.
}
diff --git a/man/sort_at_path.Rd b/man/sort_at_path.Rd
index 5a3aecbfa..1ab0ca176 100644
--- a/man/sort_at_path.Rd
+++ b/man/sort_at_path.Rd
@@ -70,7 +70,7 @@ summary given by \code{\link[=table_structure]{table_structure()}}.
Note that sorting needs a deeper understanding of table structure in \code{rtables}. Please consider reading the related
vignette
-(\href{https://insightsengineering.github.io/rtables/latest-tag/articles/sorting_pruning.html}{Sorting and Pruning})
+(\href{https://pharmaverse.github.io/rtables/latest-tag/articles/sorting_pruning.html}{Sorting and Pruning})
and explore table structure with useful functions like \code{\link[=table_structure]{table_structure()}} and \code{\link[=row_paths_summary]{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 \code{\link[=summarize_row_groups]{summarize_row_groups()}}, while the second one is
diff --git a/vignettes/ard_how_to.Rmd b/vignettes/ard_how_to.Rmd
index e64b92fea..11a3852f9 100644
--- a/vignettes/ard_how_to.Rmd
+++ b/vignettes/ard_how_to.Rmd
@@ -41,7 +41,7 @@ This vignette is a work in progress and subject to change.
## Creating an Example Table
-In order to generate an ARD (Analysis Results Dataset), we first need to create a table from which all the necessary information will be retrieved. We will borrow a simple table from [this vignette](https://insightsengineering.github.io/rtables/latest-tag/articles/clinical_trials.html) about clinical trials.
+In order to generate an ARD (Analysis Results Dataset), we first need to create a table from which all the necessary information will be retrieved. We will borrow a simple table from [this vignette](https://pharmaverse.github.io/rtables/latest-tag/articles/clinical_trials.html) about clinical trials.
```{r}
library(rtables)
diff --git a/vignettes/clinical_trials.Rmd b/vignettes/clinical_trials.Rmd
index 90aee9556..96e39fc17 100644
--- a/vignettes/clinical_trials.Rmd
+++ b/vignettes/clinical_trials.Rmd
@@ -53,7 +53,7 @@ relations that are commonly found when analyzing clinical trials data.
Note that all the data is created using random number generators. All
`ex_*` data which is currently attached to the `rtables` package is
provided by the
-[`formatters`](https://insightsengineering.github.io/formatters/)
+[`formatters`](https://pharmaverse.github.io/formatters/)
package and was created using the publicly available
[`random.cdisc.data`](https://insightsengineering.github.io/random.cdisc.data/)
R package.
@@ -666,7 +666,7 @@ trim_rows(adae_soc_tbl4)
```
Pruning is a larger topic with a [separate `rtables` package
-vignette](https://insightsengineering.github.io/rtables/latest-tag/articles/sorting_pruning.html).
+vignette](https://pharmaverse.github.io/rtables/latest-tag/articles/sorting_pruning.html).
### Adverse Events By ID and By Grade
diff --git a/vignettes/dev-guide/dg_split_machinery.Rmd b/vignettes/dev-guide/dg_split_machinery.Rmd
index 0fb3142e9..f1730b6c9 100644
--- a/vignettes/dev-guide/dg_split_machinery.Rmd
+++ b/vignettes/dev-guide/dg_split_machinery.Rmd
@@ -13,7 +13,7 @@ knitr::opts_chunk$set(echo = TRUE)
## Disclaimer
-This article is intended for use by developers only and will contain low-level explanations of the topics covered. For user-friendly vignettes, please see the [Articles](https://insightsengineering.github.io/rtables/latest-tag/articles/index.html) page on the `rtables` website.
+This article is intended for use by developers only and will contain low-level explanations of the topics covered. For user-friendly vignettes, please see the [Articles](https://pharmaverse.github.io/rtables/latest-tag/articles/index.html) page on the `rtables` website.
Any code or prose which appears in the version of this article on the `main` branch of the repository may reflect a specific state of things that can be more or less recent. This guide describes very important pieces of the split machinery that are unlikely to change. Regardless, we invite the reader to keep in mind that the current repository code may have drifted from the following material in this document, and it is always the best practice to read the code directly on `main`.
@@ -23,13 +23,13 @@ Being that this a working document that may be subjected to both deprecation and
## Introduction
-The scope of this article is understanding how `rtables` creates facets by splitting the incoming data into hierarchical groups that go from the root node to singular `rcell`s. The latter level, also called the leaf-level, contains the final partition that is subjected to analysis functions. More details from the user perspective can be found in the [Split Functions vignette](https://insightsengineering.github.io/rtables/latest-tag/articles/split_functions.html) and in function documentation like `?split_rows_by` and `?split_funcs`.
+The scope of this article is understanding how `rtables` creates facets by splitting the incoming data into hierarchical groups that go from the root node to singular `rcell`s. The latter level, also called the leaf-level, contains the final partition that is subjected to analysis functions. More details from the user perspective can be found in the [Split Functions vignette](https://pharmaverse.github.io/rtables/latest-tag/articles/split_functions.html) and in function documentation like `?split_rows_by` and `?split_funcs`.
The following article will describe how the split machinery works in the row domain. Further information on how the split machinery works in the column domain will be covered in a separate article.
## Process and Methods
-Beforehand, we encourage the reader to familiarize themselves with the [Debugging in {rtables} article](https://insightsengineering.github.io/rtables/latest-tag/articles/dev-guide/dg_debug_rtables.html) from the `rtables` Developers Guide. This document is generally valid for R programming, but has been tailored to study and understand complex packages that rely heavily on S3 and S4 object programming like `rtables`.
+Beforehand, we encourage the reader to familiarize themselves with the [Debugging in {rtables} article](https://pharmaverse.github.io/rtables/latest-tag/articles/dev-guide/dg_debug_rtables.html) from the `rtables` Developers Guide. This document is generally valid for R programming, but has been tailored to study and understand complex packages that rely heavily on S3 and S4 object programming like `rtables`.
Here, we explore and study the split machinery with a growing amount of complexity, following relevant functions and methods throughout their execution. By going from basic to complex and by discussing important and special cases, we hope to be able to give you a good understanding of how the split machinery works.
@@ -128,7 +128,7 @@ We will see where and how input parameters are used. The most important paramete
We will start by looking at the first function called from `do_split`. This will give us a good overview of how the split itself is defined. This function is, of course, the check function (`check_validsplit`) that is used to verify if the split is valid for the data. In the following we will describe the split-class hierarchy step-by-step, but we invite the reader to explore this further on their own as well.
-Let's first search the package for `check_validsplit`. You will find that it is defined as a generic in `R/split_funs.R`, where it is applied to the following "split" classes: `VarLevelSplit`, `MultiVarSplit`, `VAnalyzeSplit`, `CompoundSplit`, and `Split`. Another way to find this information, which is more useful for more spread out and complicated objects, is by using `showMethods(check_validsplit)`. The virtual class `VAnalyzeSplit` (by convention virtual classes start with "V") defines the main parent of the analysis split which we discuss in detail in the related vignette `vignette()` (xxx). From this, we can see that the `analyze()` calls actually mimic split objects as they create different results under a specific final split (or node). Now, notice that `check_validsplit` is also called in another location, the main `R/tt_dotabulation.R` source file. This is again something related to making "analyze" rows as it mainly checks for `VAnalyzeSplit`. See the [Tabulation article](https://insightsengineering.github.io/rtables/latest-tag/articles/dev-guide/dg_tabulation.html) for more details. We will discuss the other classes as they appear in our examples. See more about class hierarchy in the [Table Hierarchy article](https://insightsengineering.github.io/rtables/latest-tag/articles/dev-guide/dg_table_hierarchy.html).
+Let's first search the package for `check_validsplit`. You will find that it is defined as a generic in `R/split_funs.R`, where it is applied to the following "split" classes: `VarLevelSplit`, `MultiVarSplit`, `VAnalyzeSplit`, `CompoundSplit`, and `Split`. Another way to find this information, which is more useful for more spread out and complicated objects, is by using `showMethods(check_validsplit)`. The virtual class `VAnalyzeSplit` (by convention virtual classes start with "V") defines the main parent of the analysis split which we discuss in detail in the related vignette `vignette()` (xxx). From this, we can see that the `analyze()` calls actually mimic split objects as they create different results under a specific final split (or node). Now, notice that `check_validsplit` is also called in another location, the main `R/tt_dotabulation.R` source file. This is again something related to making "analyze" rows as it mainly checks for `VAnalyzeSplit`. See the [Tabulation article](https://pharmaverse.github.io/rtables/latest-tag/articles/dev-guide/dg_tabulation.html) for more details. We will discuss the other classes as they appear in our examples. See more about class hierarchy in the [Table Hierarchy article](https://pharmaverse.github.io/rtables/latest-tag/articles/dev-guide/dg_table_hierarchy.html).
For the moment, we see with `class(spl)` (from the main `do_split` function) that we are dealing with an `AllSplit` object. By calling `showMethods(check_validsplit)` we produce the following:
@@ -192,7 +192,7 @@ AllSplit <- function(split_label = "",
}
```
-We can also print this information by calling `getClass("AllSplit")` for the general slot definition, or by calling `getClass(spl)`. Note that the first call will give also a lot of information about the class hierarchy. For more information regarding class hierarchy, please refer to the relevant article [here](https://insightsengineering.github.io/rtables/latest-tag/articles/dev-guide/dg_talbe_hierarchy.html). We will discuss the majority of the slots by the end of this document. Now, let's see if we can find some of the values described in the constructor within our object. To do so, we will show the more compact representation given by `str`. When there are multiple and hierarchical slots that contain objects themselves, calling `str` will be much less or not at all informative if the maximum level of nesting is not set (e.g. `max.level = 2`).
+We can also print this information by calling `getClass("AllSplit")` for the general slot definition, or by calling `getClass(spl)`. Note that the first call will give also a lot of information about the class hierarchy. For more information regarding class hierarchy, please refer to the relevant article [here](https://pharmaverse.github.io/rtables/latest-tag/articles/dev-guide/dg_talbe_hierarchy.html). We will discuss the majority of the slots by the end of this document. Now, let's see if we can find some of the values described in the constructor within our object. To do so, we will show the more compact representation given by `str`. When there are multiple and hierarchical slots that contain objects themselves, calling `str` will be much less or not at all informative if the maximum level of nesting is not set (e.g. `max.level = 2`).
```c
# rtables 0.6.2
@@ -601,11 +601,11 @@ function(df,
}
```
-There are many pre-made split functions included in `rtables`. A list of these functions can be found in the [Split Functions vignette](https://insightsengineering.github.io/rtables/latest-tag/articles/split_functions.html), or via `?split_funcs`. We leave it to the developer to look into how some of these split functions work, in particular `trim_levels_to_map` may be of interest.
+There are many pre-made split functions included in `rtables`. A list of these functions can be found in the [Split Functions vignette](https://pharmaverse.github.io/rtables/latest-tag/articles/split_functions.html), or via `?split_funcs`. We leave it to the developer to look into how some of these split functions work, in particular `trim_levels_to_map` may be of interest.
### Creating Custom Split Functions
-Now we will create a custom split function. Firstly, we will see how the system manages error messages. For a general understanding of how custom split functions are created, please read the [Custom Split Functions section](https://insightsengineering.github.io/rtables/latest-tag/articles/advanced_usage.html#custom-split-functions) of the Advanced Usage vignette or see `?custom_split_funs`. In the following code we use `browser()` to enter our custom split functions. We invite the reader to activate `options(error = recover)` to investigate cases where we encounter an error. Note that you can revert to default behavior by restarting your `R` session, by caching the default option value, or by using `callr` to retrieve the default as follows: `default_opts <- callr::r(function(){options()}); options(error = default_opts$error)`.
+Now we will create a custom split function. Firstly, we will see how the system manages error messages. For a general understanding of how custom split functions are created, please read the [Custom Split Functions section](https://pharmaverse.github.io/rtables/latest-tag/articles/advanced_usage.html#custom-split-functions) of the Advanced Usage vignette or see `?custom_split_funs`. In the following code we use `browser()` to enter our custom split functions. We invite the reader to activate `options(error = recover)` to investigate cases where we encounter an error. Note that you can revert to default behavior by restarting your `R` session, by caching the default option value, or by using `callr` to retrieve the default as follows: `default_opts <- callr::r(function(){options()}); options(error = default_opts$error)`.
```{r}
# rtables 0.6.2
@@ -693,7 +693,7 @@ It is also possible to provide a list of functions, as it can be seen in the exa
#### `.spl_context` - Adding Context to Our Splits
-The best way to understand what split context does, and how to use it, is to read the [Leveraging `.spl_context` section](https://insightsengineering.github.io/rtables/latest-tag/articles/advanced_usage.html#leveraging--spl_context) of the Advanced Usage vignette, and to use `browser()` within a split function to see how it is structured. As `.spl_context` is needed for rewriting core functions, we propose a wrapper of `do_base_split` here, which is a handy redirection to the standard `do_split` without the split function part (i.e. it is a wrapper of `.apply_split_inner`, the real core splitting machinery). Out of curiosity, we set `trim = TRUE` here. This trimming only works when there is a mixed table (some values are 0s and some have content), for which it will trim 0s. This is rarely the case, and we encourage using the replacement functions `trim_levels_to_group` and `trim_levels_to_map` for trimming. Nowadays, it should even be impossible to set it differently from `trim = FALSE`.
+The best way to understand what split context does, and how to use it, is to read the [Leveraging `.spl_context` section](https://pharmaverse.github.io/rtables/latest-tag/articles/advanced_usage.html#leveraging--spl_context) of the Advanced Usage vignette, and to use `browser()` within a split function to see how it is structured. As `.spl_context` is needed for rewriting core functions, we propose a wrapper of `do_base_split` here, which is a handy redirection to the standard `do_split` without the split function part (i.e. it is a wrapper of `.apply_split_inner`, the real core splitting machinery). Out of curiosity, we set `trim = TRUE` here. This trimming only works when there is a mixed table (some values are 0s and some have content), for which it will trim 0s. This is rarely the case, and we encourage using the replacement functions `trim_levels_to_group` and `trim_levels_to_map` for trimming. Nowadays, it should even be impossible to set it differently from `trim = FALSE`.
(write an issue informative error for not list xxx).
```{r, eval=FALSE}
@@ -750,7 +750,7 @@ Here we can see what the split column variable is (`split`, first column) at thi
### Extra Arguments: `extra_args`
-This functionality is well-known and used in the setting of analysis functions (a somewhat complicated example of this can be found in the [Example Complex Analysis Function vignette](https://insightsengineering.github.io/rtables/latest-tag/articles/example_analysis_coxreg.html#constructing-the-table)), but we will show here how this can also apply to splits.
+This functionality is well-known and used in the setting of analysis functions (a somewhat complicated example of this can be found in the [Example Complex Analysis Function vignette](https://pharmaverse.github.io/rtables/latest-tag/articles/example_analysis_coxreg.html#constructing-the-table)), but we will show here how this can also apply to splits.
```{r, eval=FALSE}
# rtables 0.6.2
@@ -905,7 +905,7 @@ tbl
For both row split cases (`*_cuts` and `*_cutfun`), we have empty levels that are not dropped. This is to be expected and can be avoided by using a dedicated split function. Intentionally looking at the future split is possible in order to determine if an element is present in it. At the moment it is not possible to add `spl_fun` to dedicated split functions like `split_rows_by_cuts`.
-Note that in the previous table we only used `summarize_row_groups`, with no `analyze` calls. This rendered the table nicely, but it is not the standard method to use as `summarize_row_groups` is intended *only* to decorate row groups, i.e. rows with labels. Internally, these rows are called content rows and that is why analysis functions in `summarize_row_groups` are called `cfun` instead of `afun`. Indeed, the tabulation machinery also presents these two differently as is described in the [Tabulation with Row Structure section](https://insightsengineering.github.io/rtables/latest-tag/articles/tabulation_concepts.html#tabulation-with-row-structure) of the Tabulation vignette.
+Note that in the previous table we only used `summarize_row_groups`, with no `analyze` calls. This rendered the table nicely, but it is not the standard method to use as `summarize_row_groups` is intended *only* to decorate row groups, i.e. rows with labels. Internally, these rows are called content rows and that is why analysis functions in `summarize_row_groups` are called `cfun` instead of `afun`. Indeed, the tabulation machinery also presents these two differently as is described in the [Tabulation with Row Structure section](https://pharmaverse.github.io/rtables/latest-tag/articles/tabulation_concepts.html#tabulation-with-row-structure) of the Tabulation vignette.
We can try to construct the split function for cuts manually with `make_split_fun`:
diff --git a/vignettes/dev-guide/dg_table_hierarchy.Rmd b/vignettes/dev-guide/dg_table_hierarchy.Rmd
index 89b7ebd6e..0c7826ad5 100644
--- a/vignettes/dev-guide/dg_table_hierarchy.Rmd
+++ b/vignettes/dev-guide/dg_table_hierarchy.Rmd
@@ -13,7 +13,7 @@ knitr::opts_chunk$set(echo = TRUE)
## Disclaimer
-This article is intended for use by developers only and will contain low-level explanations of the topics covered. For user-friendly vignettes, please see the [Articles](https://insightsengineering.github.io/rtables/latest-tag/articles/index.html) page on the `rtables` website.
+This article is intended for use by developers only and will contain low-level explanations of the topics covered. For user-friendly vignettes, please see the [Articles](https://pharmaverse.github.io/rtables/latest-tag/articles/index.html) page on the `rtables` website.
Any code or prose which appears in the version of this article on the `main` branch of the repository may reflect a specific state of things that can be more or less recent. This guide describes very important aspects of table hierarchy that are unlikely to change. Regardless, we invite the reader to keep in mind that the current repository code may have drifted from the following material in this document, and it is always the best practice to read the code directly on `main`.
diff --git a/vignettes/dev-guide/dg_tabulation.Rmd b/vignettes/dev-guide/dg_tabulation.Rmd
index 3a4832c55..f06799880 100644
--- a/vignettes/dev-guide/dg_tabulation.Rmd
+++ b/vignettes/dev-guide/dg_tabulation.Rmd
@@ -13,7 +13,7 @@ knitr::opts_chunk$set(echo = TRUE)
## Disclaimer
-This article is intended for use by developers only and will contain low-level explanations of the topics covered. For user-friendly vignettes, please see the [Articles](https://insightsengineering.github.io/rtables/latest-tag/articles/index.html) page on the `rtables` website.
+This article is intended for use by developers only and will contain low-level explanations of the topics covered. For user-friendly vignettes, please see the [Articles](https://pharmaverse.github.io/rtables/latest-tag/articles/index.html) page on the `rtables` website.
Any code or prose which appears in the version of this article on the `main` branch of the repository may reflect a specific state of things that can be more or less recent. This guide describes very important aspects of the tabulation process that are unlikely to change. Regardless, we invite the reader to keep in mind that the current repository code may have drifted from the following material in this document, and it is always the best practice to read the code directly on `main`.
@@ -23,7 +23,7 @@ Being that this a working document that may be subjected to both deprecation and
## Introduction
-Tabulation in `rtables` is a process that takes a pre-defined layout and applies it to data. The layout object, with all of its splits and `analyze`s, can be applied to different data to produce valid tables. This process happens principally within the `tt_dotabulation.R` file and the user-facing function `build_table` that resides in it. We will occasionally use functions and methods that are present in other files, like `colby_construction.R` or `make_subset_expr.R`. We assume the reader is already familiar with the documentation for `build_table`. We suggest reading the [Split Machinery article](https://insightsengineering.github.io/rtables/latest-tag/articles/dev-guide/dg_split_machinery.html) prior to this one, as it is instrumental in understanding how the layout object, which is essentially built out of splits, is tabulated when data is supplied.
+Tabulation in `rtables` is a process that takes a pre-defined layout and applies it to data. The layout object, with all of its splits and `analyze`s, can be applied to different data to produce valid tables. This process happens principally within the `tt_dotabulation.R` file and the user-facing function `build_table` that resides in it. We will occasionally use functions and methods that are present in other files, like `colby_construction.R` or `make_subset_expr.R`. We assume the reader is already familiar with the documentation for `build_table`. We suggest reading the [Split Machinery article](https://pharmaverse.github.io/rtables/latest-tag/articles/dev-guide/dg_split_machinery.html) prior to this one, as it is instrumental in understanding how the layout object, which is essentially built out of splits, is tabulated when data is supplied.
## Tabulation
@@ -65,7 +65,7 @@ lyt@.Data # might not preserve the names # it works only when it is another clas
# We suggest doing extensive testing about these behaviors in order to do choose the appropriate one
```
-Along with the various checks and defensive programming, we find `PreDataAxisLayout` which is a virtual class that both row and column layouts inherit from. Virtual classes are handy for group classes that need to share things like labels or functions that need to be applicable to their relative classes. See more information about the `rtables` class hierarchy in the dedicated article [here](https://insightsengineering.github.io/rtables/latest-tag/articles/dev-guide/dg_table_hierarchy.html).
+Along with the various checks and defensive programming, we find `PreDataAxisLayout` which is a virtual class that both row and column layouts inherit from. Virtual classes are handy for group classes that need to share things like labels or functions that need to be applicable to their relative classes. See more information about the `rtables` class hierarchy in the dedicated article [here](https://pharmaverse.github.io/rtables/latest-tag/articles/dev-guide/dg_table_hierarchy.html).
Now, we continue with `build_table`. After the checks, we notice `TreePos()` which is a constructor for an object that retains a representation of the tree position along with split values and labels. This is mainly used by `create_colinfo`, which we enter now with `debugonce(create_colinfo)`. This function creates the object that represents the column splits and everything else that may be related to the columns. In particular, the column counts are calculated in this function. The parameter inputs are as follows:
diff --git a/vignettes/example_analysis_coxreg.Rmd b/vignettes/example_analysis_coxreg.Rmd
index f4ead8acc..746543a14 100644
--- a/vignettes/example_analysis_coxreg.Rmd
+++ b/vignettes/example_analysis_coxreg.Rmd
@@ -27,7 +27,7 @@ knitr::opts_chunk$set(
## Introduction
-In this vignette we will demonstrate how a complex analysis function can be constructed in order to build highly-customized tables with `rtables`. This example will detail the steps in creating an analysis function to calculate a basic univariable Cox regression summary table to analyze the treatment effect of the `ARM` variable and any covariate/interaction effects for a survival analysis. For a Cox regression analysis function with more customization options and the capability of fitting multivariable Cox regression models, see the [`summarize_coxreg()`](https://insightsengineering.github.io/tern/main/reference/cox_regression.html) function from the [`tern`](https://insightsengineering.github.io/tern/main/index.html) package, which builds upon the concepts used in the construction of this example.
+In this vignette we will demonstrate how a complex analysis function can be constructed in order to build highly-customized tables with `rtables`. This example will detail the steps in creating an analysis function to calculate a basic univariable Cox regression summary table to analyze the treatment effect of the `ARM` variable and any covariate/interaction effects for a survival analysis. For a Cox regression analysis function with more customization options and the capability of fitting multivariable Cox regression models, see the [`summarize_coxreg()`](https://pharmaverse.github.io/tern/main/reference/cox_regression.html) function from the [`tern`](https://pharmaverse.github.io/tern/main/index.html) package, which builds upon the concepts used in the construction of this example.
The packages used in this vignette are:
diff --git a/vignettes/exploratory_analysis.Rmd b/vignettes/exploratory_analysis.Rmd
index 056289f65..39d29bee2 100644
--- a/vignettes/exploratory_analysis.Rmd
+++ b/vignettes/exploratory_analysis.Rmd
@@ -284,5 +284,5 @@ Here is what we have learned in this vignette:
As the intended use of `qtable()` is for exploratory data analysis,
there is limited functionality for building very complex tables. For
details on how to get started with the core `rtables` layout
-functionality see the [`introduction`](https://insightsengineering.github.io/rtables/latest-release/articles/rtables.html)
+functionality see the [`introduction`](https://pharmaverse.github.io/rtables/latest-release/articles/rtables.html)
vignette.
diff --git a/vignettes/format_precedence.Rmd b/vignettes/format_precedence.Rmd
index 315217e14..2e744c236 100644
--- a/vignettes/format_precedence.Rmd
+++ b/vignettes/format_precedence.Rmd
@@ -26,7 +26,7 @@ knitr::opts_chunk$set(comment = "#")
Users of the `rtables` package can specify the format in which the
numbers in the reporting tables are printed. Formatting functionality
is provided by the
-[`formatters`](https://insightsengineering.github.io/formatters/) R
+[`formatters`](https://pharmaverse.github.io/formatters/) R
package. See `formatters::list_valid_format_labels()` for a list of
all available formats. The format can be
specified by the user in a few different places. It may happen that,
@@ -46,7 +46,7 @@ ADSL <- ex_adsl
Note that all `ex_*` data which is currently attached to the `rtables`
package is provided by the
-[`formatters`](https://insightsengineering.github.io/formatters/)
+[`formatters`](https://pharmaverse.github.io/formatters/)
package and was created using the publicly available
[`random.cdisc.data`](https://insightsengineering.github.io/random.cdisc.data/)
R package.
diff --git a/vignettes/introspecting_tables.Rmd b/vignettes/introspecting_tables.Rmd
index b66a6d37e..f233ca24a 100644
--- a/vignettes/introspecting_tables.Rmd
+++ b/vignettes/introspecting_tables.Rmd
@@ -89,7 +89,7 @@ coltree_structure(tbl)
```
Further information about the column structure can be found in the vignette on
-[`col_counts`](https://insightsengineering.github.io/rtables/latest-tag/articles/col_counts.html).
+[`col_counts`](https://pharmaverse.github.io/rtables/latest-tag/articles/col_counts.html).
The `make_row_df()` and `make_col_df()` functions each create a `data.frame` with a variety of information about
the table's structure. Most useful for introspection purposes are the `label`, `name`, `abs_rownumber`, `path` and
@@ -160,11 +160,11 @@ value_formats(tbl)
## Applications
Knowing the structure of an `rtable` object is helpful for retrieving specific values from the table.
-For examples, see the [Path Based Cell Value Accessing](https://insightsengineering.github.io/rtables/latest-tag/articles/subsetting_tables.html#path-based-cell-value-accessing)
+For examples, see the [Path Based Cell Value Accessing](https://pharmaverse.github.io/rtables/latest-tag/articles/subsetting_tables.html#path-based-cell-value-accessing)
section of the Subsetting and Manipulating Table Contents vignette.
Understanding table structure is also important for post-processing processes such as sorting and pruning. More details
-on this are covered in the [Pruning and Sorting Tables vignette](https://insightsengineering.github.io/rtables/latest-tag/articles/sorting_pruning.html)
+on this are covered in the [Pruning and Sorting Tables vignette](https://pharmaverse.github.io/rtables/latest-tag/articles/sorting_pruning.html)
vignette.
## Summary
diff --git a/vignettes/rtables.Rmd b/vignettes/rtables.Rmd
index 577c222ff..fc5bdc391 100644
--- a/vignettes/rtables.Rmd
+++ b/vignettes/rtables.Rmd
@@ -122,7 +122,7 @@ to tabulation with the `rtables` layout framework, you can use this
convenience wrapper to create many types of two-way frequency tables.
The purpose of `qtable` is to enable quick exploratory data analysis. See the
-[`exploratory_analysis`](https://insightsengineering.github.io/rtables/latest-tag/articles/exploratory_analysis.html) vignette for more details.
+[`exploratory_analysis`](https://pharmaverse.github.io/rtables/latest-tag/articles/exploratory_analysis.html) vignette for more details.
Here is the code to recreate the table above:
```{r}
@@ -235,7 +235,7 @@ The first column represents the data in `df` where `df$arm == "A" &
df$gender == "Female"` and the second column the data in `df` where
`df$arm == "A" & df$gender == "Male"`, and so on.
-More information on column structure can be found in the [`col_counts`](https://insightsengineering.github.io/rtables/latest-tag/articles/col_counts.html) vignette.
+More information on column structure can be found in the [`col_counts`](https://pharmaverse.github.io/rtables/latest-tag/articles/col_counts.html) vignette.
## Adding Row Structure
@@ -399,6 +399,6 @@ In this vignette you have learned:
The other vignettes in the `rtables` package will provide more
detailed information about the `rtables` package. We recommend that
you continue with the
-[`tabulation_dplyr`](https://insightsengineering.github.io/rtables/latest-tag/articles/tabulation_dplyr.html)
+[`tabulation_dplyr`](https://pharmaverse.github.io/rtables/latest-tag/articles/tabulation_dplyr.html)
vignette which compares the information derived by the table in this
vignette using `dplyr`.
diff --git a/vignettes/subsetting_tables.Rmd b/vignettes/subsetting_tables.Rmd
index f9ff90f1f..1c9cfd684 100644
--- a/vignettes/subsetting_tables.Rmd
+++ b/vignettes/subsetting_tables.Rmd
@@ -85,7 +85,7 @@ The `[` and `[<-` accessor functions operate largely the same as their
rows. Note in general the result of such an ordering is unlikely to
be structurally valid. To change the order of values, please read
[sorting and
- pruning](https://insightsengineering.github.io/rtables/latest-tag/articles/sorting_pruning.html)
+ pruning](https://pharmaverse.github.io/rtables/latest-tag/articles/sorting_pruning.html)
vignette or relevant function (`sort_at_path()`).
- `character` indices are treated as paths, not vectors of names in
both `[` and `[<-`
@@ -170,7 +170,7 @@ tbl[1:3, 3, keep_topleft = TRUE]
If the referenced entry is present in the subsetting, also the
referential footnote will appear. Please consider reading relevant
vignette about [referential
-footnotes](https://insightsengineering.github.io/rtables/latest-tag/articles/title_footer.html#referential-footnotes). In
+footnotes](https://pharmaverse.github.io/rtables/latest-tag/articles/title_footer.html#referential-footnotes). In
case of subsetting, the referential footnotes are by default indexed
again, as if the produced table is a new one.
diff --git a/vignettes/tabulation_dplyr.Rmd b/vignettes/tabulation_dplyr.Rmd
index 76abbebdb..a0acf5702 100644
--- a/vignettes/tabulation_dplyr.Rmd
+++ b/vignettes/tabulation_dplyr.Rmd
@@ -41,7 +41,7 @@ In this vignette, we would like to discuss the similarities and differences betw
Much of the `rtables` framework focuses on tabulation/summarizing of data and then the visualization of the table. In this vignette, we focus on summarizing data using `dplyr` and contrast it to `rtables`. We won't pay attention to the table visualization/markup and just derive the cell content.
-Using `dplyr` to summarize data and `gt` to visualize the table is a good way if the tabulation is of a certain nature or complexity. However, there are tables such as the table created in the [`introduction`](https://insightsengineering.github.io/rtables/latest-release/articles/rtables.html) vignette that take some effort to create with `dplyr`. Part of the effort is due to fact that when using `dplyr` the table data is stored in `data.frame`s or `tibble`s which is not the most natural way to represent a table as we will show in this vignette.
+Using `dplyr` to summarize data and `gt` to visualize the table is a good way if the tabulation is of a certain nature or complexity. However, there are tables such as the table created in the [`introduction`](https://pharmaverse.github.io/rtables/latest-release/articles/rtables.html) vignette that take some effort to create with `dplyr`. Part of the effort is due to fact that when using `dplyr` the table data is stored in `data.frame`s or `tibble`s which is not the most natural way to represent a table as we will show in this vignette.
If you know a more elegant way of deriving the table content with `dplyr` please let us know and we will update the vignette.
@@ -51,7 +51,7 @@ library(rtables)
library(dplyr)
```
-Here is the table and data used in the [`introduction`](https://insightsengineering.github.io/rtables/latest-release/articles/rtables.html) vignette:
+Here is the table and data used in the [`introduction`](https://pharmaverse.github.io/rtables/latest-release/articles/rtables.html) vignette:
```{r}
n <- 400
@@ -84,7 +84,7 @@ tbl
## Getting Started
-We will start by deriving the first data cell on row 3 (note, row 1 and 2 have content cells, see the [`introduction`](https://insightsengineering.github.io/rtables/latest-release/articles/rtables.html) vignette). Cell 3,1 contains the mean age for left handed & female Canadians in "Arm A":
+We will start by deriving the first data cell on row 3 (note, row 1 and 2 have content cells, see the [`introduction`](https://pharmaverse.github.io/rtables/latest-release/articles/rtables.html) vignette). Cell 3,1 contains the mean age for left handed & female Canadians in "Arm A":
```{r}
@@ -244,4 +244,4 @@ In this vignette learned that:
* if tables have group summaries then repeating of information is required
* `rtables` streamlines the construction of complex tables
-We recommend that you continue reading the [`clinical_trials`](https://insightsengineering.github.io/rtables/latest-tag/articles/clinical_trials.html) vignette where we create a number of more advanced tables using layouts.
+We recommend that you continue reading the [`clinical_trials`](https://pharmaverse.github.io/rtables/latest-tag/articles/clinical_trials.html) vignette where we create a number of more advanced tables using layouts.