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update #29

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Jan 10, 2025
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shajoezhu Jan 10, 2025
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shajoezhu Jan 10, 2025
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2 changes: 0 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -46,8 +46,6 @@ Suggests:
VignetteBuilder:
knitr,
rmarkdown
Remotes:
insightsengineering/rtables@981_cran_v0.6.11
Config/Needs/verdepcheck: insightsengineering/formatters,
insightsengineering/rtables, tidyverse/magrittr, mllg/checkmate,
rstudio/htmltools, gagolews/stringi, tidymodels/broom, cran/car,
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138 changes: 21 additions & 117 deletions README.Rmd
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Expand Up @@ -12,146 +12,50 @@ knitr::opts_chunk$set(
comment = "#>",
fig.path = "man/figures/README-"
)
suppressPackageStartupMessages(library(rtables.officer))
suppressPackageStartupMessages(library(rtables))
suppressPackageStartupMessages(library(dplyr))
```

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

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

## Reporting Tables with R

The `rtables` R package was designed to create and display complex tables with R. The cells in an `rtable` may contain
any high-dimensional data structure which can then be displayed with cell-specific formatting instructions. Currently,
`rtables` can be outputted in `ascii` `html`, and `pdf`, as well Power Point (via conversion to `flextable` objects). `rtf` support is in development and will be in a future release.
`rtables` can be outputted in `ascii` `html`, and `pdf`, as well Power Point (via conversion to `flextable` objects). This package `rtables.officer` is designed to support the exporting outputs relate Microsoft office software such as `word` and `powerpoint`.

`rtables` is developed and copy written by `F. Hoffmann-La Roche` and it is released open source under Apache
`rtables` and `rtables.officer` is developed and copy written by `F. Hoffmann-La Roche` and it is released open source under Apache
License Version 2.

`rtables` development is driven by the need to create regulatory ready tables for health authority review. Some of the key requirements for this undertaking are listed below:

* cell values and their visualization separate (i.e. no string based tables)
- values need to be programmatically accessible in their non-rounded state for cross-checking
* multiple values displayed within a cell
* flexible tabulation framework
* flexible formatting (cell spans, rounding, alignment, etc.)
* multiple output formats (html, ascii, latex, pdf, xml)
* flexible pagination in both horizontal and vertical directions
* distinguish between name and label in the data structure to work with `CDISC` standards
* title, footnotes, cell cell/row/column references

`rtables` currently covers virtually all of these requirements, and further advances remain under active development.

## Installation

`rtables` is available on CRAN and you can install the latest released version with:

```r
install.packages("rtables")
```

or you can install the latest development version directly from GitHub with:
`rtables.officer` can be installed with the latest development version directly from GitHub with:

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

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).

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.

## 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>

## Usage

We first demonstrate with a demographic table-like example and then show the creation of a more complex table.

```{r, message=FALSE}
library(rtables)

lyt <- basic_table() %>%
split_cols_by("ARM") %>%
analyze(c("AGE", "BMRKR1", "BMRKR2"), function(x, ...) {
if (is.numeric(x)) {
in_rows(
"Mean (sd)" = c(mean(x), sd(x)),
"Median" = median(x),
"Min - Max" = range(x),
.formats = c("xx.xx (xx.xx)", "xx.xx", "xx.xx - xx.xx")
)
} else if (is.factor(x) || is.character(x)) {
in_rows(.list = list_wrap_x(table)(x))
} else {
stop("type not supported")
}
})

build_table(lyt, ex_adsl)
```

```{r, message=FALSE}
library(rtables)
library(dplyr)

## for simplicity grab non-sparse subset
ADSL <- ex_adsl %>% filter(RACE %in% levels(RACE)[1:3])

biomarker_ave <- function(x, ...) {
val <- if (length(x) > 0) round(mean(x), 2) else "no data"
in_rows(
"Biomarker 1 (mean)" = rcell(val)
)
}

basic_table(show_colcounts = TRUE) %>%
split_cols_by("ARM") %>%
split_cols_by("BMRKR2") %>%
split_rows_by("RACE", split_fun = trim_levels_in_group("SEX")) %>%
split_rows_by("SEX") %>%
summarize_row_groups() %>%
analyze("BMRKR1", biomarker_ave) %>%
build_table(ADSL)
```

# Acknowledgments

We would like to thank everyone who has made `rtables` a better project by providing feedback and improving examples & vignettes. The following list of contributors is alphabetical:

Maximo Carreras, Francois Collins, Saibah Chohan, Tadeusz Lewandowski, Nick Paszty, Nina Qi, Jana Stoilova, Heng Wang, Godwin Yung

## Presentations

- R in Pharma 2023
- 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)]
- 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)]
- 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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