Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/insightsengineering/rtables

Reporting tables with R
https://github.com/insightsengineering/rtables

pharmaceuticals r tables

Last synced: 7 days ago
JSON representation

Reporting tables with R

Awesome Lists containing this project

README

        

---
output: github_document
editor_options:
chunk_output_type: console
---

```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-"
)
suppressPackageStartupMessages(library(rtables))
suppressPackageStartupMessages(library(dplyr))
```

# rtables

[![Check 🛠](https://github.com/insightsengineering/rtables/actions/workflows/check.yaml/badge.svg)](https://github.com/insightsengineering/rtables/actions/workflows/check.yaml)
[![Docs 📚](https://github.com/insightsengineering/rtables/actions/workflows/docs.yaml/badge.svg)](https://insightsengineering.github.io/rtables/)
[![Code Coverage 📔](https://raw.githubusercontent.com/insightsengineering/rtables/_xml_coverage_reports/data/main/badge.svg)](https://raw.githubusercontent.com/insightsengineering/rtables/_xml_coverage_reports/data/main/coverage.xml)

![GitHub forks](https://img.shields.io/github/forks/insightsengineering/rtables?style=social)
![GitHub repo stars](https://img.shields.io/github/stars/insightsengineering/rtables?style=social)

![GitHub commit activity](https://img.shields.io/github/commit-activity/m/insightsengineering/rtables)
![GitHub contributors](https://img.shields.io/github/contributors/insightsengineering/rtables)
![GitHub last commit](https://img.shields.io/github/last-commit/insightsengineering/rtables)
![GitHub pull requests](https://img.shields.io/github/issues-pr/insightsengineering/rtables)
![GitHub repo size](https://img.shields.io/github/repo-size/insightsengineering/rtables)
![GitHub language count](https://img.shields.io/github/languages/count/insightsengineering/rtables)
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![Open Issues](https://img.shields.io/github/issues-raw/insightsengineering/rtables?color=red\&label=open%20issues)](https://github.com/insightsengineering/rtables/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)

[![CRAN Version](https://www.r-pkg.org/badges/version/rtables)](https://CRAN.R-project.org/package=rtables)
[![Current Version](https://img.shields.io/github/r-package/v/insightsengineering/rtables/main?color=purple\&label=Development%20Version)](https://github.com/insightsengineering/rtables/tree/main)

## 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` 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:

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

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

## 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)]