# Chapter 2 Overview of table R packages

There are many R packages available that can help with the creation of production-ready tables for clinical research. We provide here a listing of the most notable packages available for this purpose. The descriptions are meant to provide a basic overview of what each package is capable of, and, the general focus area for each. Word of warning: the list is by no means complete. There are possibly dozens of such packages, but we were selective in choosing which of those to present here (mostly in the interest of not presenting too much material, so as to not burden the reader with too many alternatives).

## 2.1 gt

The *gt* package (Iannone et al. 2023, website) provides
a high-level and declarative interface for composing tables. The package
contains a large variety of formatting functions for transforming cell values
from an input data frame to the desired reporting values. There are options for
scientific notation, percentages, localized currencies, expressing uncertainties
and ranges, dates and times, etc.). The package has the ability to generate summary
rows, footnotes, source notes, and structure the table with a stub and column
spanners. Multiple output formats are supported with the same declarative interface
(e.g., HTML, LaTeX/PDF, RTF, and Word).

The *gt* source code is on GitHub and the
project website provides a wealth of documentation. The
package is also available on CRAN.

## 2.2 rtables

The *rtables* package (Becker and Waddell 2023, website) defines a pipe-able grammar for declaring complex table
structure layouts via nested splitting – in row- and column-space – and the
specification of analysis functions which will calculate cell values within that
structure. These pre-data table layouts are then applied to data to build the
table, during which all necessary data grouping implied by the row and column
splits, cell value calculation, and tabulation occurs automatically. Additional
table features such as titles, footers, and referential footnotes are supported.
ASCII, HTML, and PDF are supported as output formats for rendering tables.

The *rtables* package is available on
CRAN. Its source code
GitHub and
documentation are
also available on Github, where development of the package occurs.

*rtables* is also the table engine used (as wrapped by *tern*) in the open source
TLG Catalog.

## 2.3 tern (+ rtables)

The *tern* package (Zhu et al. 2023,
website) is an open
sourced, opinionated TLG generation package for clinical trials. With
respect to tables, *tern* acts as wrapper around the core *rtables*
tabulation engine which performs two functions with respect to
standard tables clinical trial tables: implementation of statistical
logic, and providing convenience wrappers for common table layout
patterns. In particular, *tern* implements and open-sources the
statistical choices used by Roche ™ when constructing clinical
trial tables.

The open source TLG
Catalog uses
*tern* and *rtables* to implement over 220 stanard clinical trial
table variants across 8 table categories. The catalog includes open
source-permissively licensed, runnable code for each entry.

The *tern* package is available on
CRAN. Its source code
GitHub and
documentation are also
available on Github, where development of the package occurs.

## 2.4 flextable

*flextable* (Gohel and Skintzos 2023, website)
provides a *grammar* for creating and customizing tables. The
following formats are supported: ‘Word’ (*.docx), ‘PowerPoint’ (*.pptx), ‘RTF’, ‘PDF’
,‘HTML’ and R ‘Grid Graphics’. The syntax is the same for the user regardless of
the type of output to be produced. A set of functions allows the creation,
definition of cell arrangement, addition of headers or footers, formatting and
definition of cell content (i.e. text and or images). The package also offers a
set of high-level functions that allow, for example, tabular reporting of
statistical models and the creation of complex cross tabulations.

Source code is on GitHub and a user manual is available. The package is also available on CRAN.

## 2.5 tfrmt

The *tfrmt* (Krouse et al. 2023, website) package
provides a language for defining display-related metadata and table formatting
before any data is available. This package offers an intuitive interface for
defining and layering standard or custom formats, to which ARD (analysis
results data) is supplied. It also presents the novel ability to easily
generate mock displays using metadata that will be used for the actual
displays. *tfrmt* is built on top of the *gt* package, which is intended to
support a variety of output formats in the future. Table features (titles,
header, footnotes, etc.) as well as specific formatting (e.g. rounding,
scientific notation, alignment, spacing) are supported.

The *tfrmt* source code is on GitHub and
documentation can be found in the project website.
The package is also available on CRAN.

## 2.6 tables

The *tables* package (Murdoch 2023, website) provides a formula-driven interface for
computing the contents of tables and formatting them. It was
inspired by `SAS PROC TABULATE`

, but is not compatible with it.

The user computes a table object by specifying a formula, with the left-hand side giving the rows, and the right-hand side giving the columns; the formula describes the summary functions to apply and how to organize them. The objects can be subsetted or combined using matrix-like operations. Tables can be rendered in plain text, LaTeX code to appear in a PDF document, or HTML code for a web document.

The package is on CRAN. Source is maintained on Github at
https://github.com/dmurdoch/tables/. Vignettes in the package serve as a user manual;
browse them at https://dmurdoch.github.io/tables/, or install the package, then run
`browseVignettes(package = "tables")`

.

## 2.7 tidytlg

The *tidytlg* package (Masel et al. 2023, website) provides a framework for creating tables, listings, and graphs (TLGs) using
Tidyverse (Wickham et al. 2019). It offers a suite of analysis functions to summarize descriptive statistics
(univariate statistics and counts or percentages) for table creation and a function
to convert analysis results to rtf/html outputs. For graphic output, tidytlg can
integrate plot objects created by ggplot2 or a png file with titles and footnotes
to produce rtf/html output.

*tidytlg* source code and documentation
are on Github.

### References

*Rtables: Reporting Tables*. R package version 0.6.3. https://github.com/insightsengineering/rtables.

*Flextable: Functions for Tabular Reporting*. R package version 0.9.4. https://ardata-fr.github.io/flextable-book/.

*Gt: Easily Create Presentation-Ready Display Tables*. R package version 0.10.0. https://gt.rstudio.com.

*Tfrmt: Applies Display Metadata to Analysis Results Datasets*. R package version 0.1.0. https://GSK-Biostatistics.github.io/tfrmt/.

*Tidytlg: Create TLGs Using the Tidyverse*. R package version 0.1.4. https://github.com/pharmaverse/tidytlg.

*Tables: Formula-Driven Table Generation*. R package version 0.9.17. https://dmurdoch.github.io/tables/.

*Journal of Open Source Software*4 (43): 1686. https://doi.org/10.21105/joss.01686.

*Tern: Create Common TLGs Used in Clinical Trials*. R package version 0.9.0. https://github.com/insightsengineering/tern.