TLGs (tables, listings, and graphs - also known as TLFs/TFLs with F for figures) refer to the packages that take data, and convert then into a human intepretable insight.

There are two relevant stages of TLGs - static TLGs, which as of today are the only type of evidence submitted to regulatory bodies, and interactive TLGs, which are predominantly, but not limited to, shiny apps.

For tables, we recommend the effort from R Consortium - Tables in Clinical Trials with R - as a useful read to compare examples from several of the below packages.

Tables

rtables

A framework for declaring complex multi-level tabulations and then applying them to data

pharmaRTF

Enhanced RTF wrapper written in R for use with existing R tables packages such as huxtable or GT

Tplyr

To simplify the data manipulation necessary to create clinical reports

tfrmt

A language for defining display-related metadata to automate the transformation from an Analysis Results Dataset (ARD) to a table

tidytlg

Generate table, listings, and graphs (TLG) using the Tidyverse

Plots

visR

The goal of visR is to enable fit-for-purpose, reusable clinical and medical research focused visualizations and tables with sensible defaults and based on sound graphical principles.

ggsurvfit

Eases the creation of time-to-event (aka survival) summary figures

While ggplot2 is a lower level, non-pharma specific plotting package. It is universally accepted as the package for graphics, so included here and as a non-pharma package.

ggplot2

An implementation of the Grammar of Graphics in R, and the most popular plotting package for static plots in R.

Interactive

tidyCDISC

A shiny app to easily create custom tables and figures from ADaM-ish data sets

rhino

Supports creating and extending enterprise Shiny applications using best practices

Frameworks

The following frameworks allow for the engine used to generate the output to be modified. For example, they could be used with ggplot2, rtables, plotly, visR or Tplyr.

tern

Layers analytics from descriptive summaries to more complex statistics on top of the foundational table layouts, analytic and content controls

teal

Framework developed that leverages the R Shiny package to scale development of our shiny apps

Tables, Listings, and Graphs Catalogs with many examples are available here:

• TLG Catalog
• Biomarker Catalog

There are publicly available example Shiny applications created using these:

• The efficacy APP Efficacy
• The safety APP Safety
• The exploratory APP Exploratory

Upcoming packages for consideration

The following are being worked up towards open sourcing to be considered for later inclusion into the pharmaverse - we felt important to share here in case others are working in a similar space and would be interested to collaborate with the respective developers.

chevron

Holds TLG template standards to feed into other tabulation packages OPEN SOURCE RELEASE EXPECTED ~END-2023 Contact Lena Wang (wangx216@gene.com)

falcon

Implementation of FDA Safety Tables and Figures OPEN SOURCE COLLABORATION IN PROGRESS Contact Pawel Rucki (pawel.rucki@roche.com) to get involved