hidyverse / awesome-r-clinical-reporting

A curated list of R talks, tools, examples & articles useful for clinical reporting! All contributions welcome!

Awesome R Clinical Reporting

A curated list of R for end-to-end clinical study reporting docs, talks, tools, examples & articles. Inspired by Yilong Zhang's Post and R for Clinical Study Reporting by Yilong Zhang, Nan Xiao, Keaven Anderson, and Yalin Zhu.

Improving the quality, accuracy, and reproducibility of clinical study reporting with R.

Contents

• Featured (new releases)
• Support SDTM
• Generate TLG
• Reporting in R Logistics
• Community
• Follow

Legend: 📝 Publications · 💡 examples · 📖 docs · 🔌 libraries · 📦 packages · 📹 talks/video

Featured (new releases)

• 📝 Tplyr 1.2.1 release
• 📦 {cards} construct CDISC analysis results dataset (ARD) objects

Support SDTM

• 📦 {admiral} develop ADaM datasets in R

Generate TLG

Tables

• 📦 {falcon} standardized table creation functions
• 📦 {gtsummary} create publication-ready analytical and summary tables
• 📦 {gtreg} gtsummary for regulatory submissions
• 📦 {tfrmt} tabular structure from ARD
• 📦 {Tplyr} simplify the creation and traceability of common clinical summaries
• 📦 {vtree} display nested data

Listings

• 📦 {tidytlg} generate TLGs with tidyverse tools

Graphs

• 📦 {ggplot2} standardized plotting with grammar of graphics
• 📦 {ggsurvfit} ggplot2 x survival analysis

Reporting in R Logistics

Learning

• 📹 Posit Pharma Meetup: R for Clinical Study Reports & Submission with Yilong Zhang
• 📖 R for Clinical Study Reports and Submission
• 📝 A&R with R in regulated trial environment

Data aquisition

• 📦 {redcapR} pull data from REDCap

Project Management

• 📝 Late stage clinical trial project management

Software development

• 📝 SDLC in regulated environments
• 📝 Specification development of R functions for standardization
• 📝 Internal R package validation
• 📝 External package qualification

Format, Render, and Export

• 📦 {xportr} create CDISC compliant xpt files
• 📦 {r2rtf} production-ready tables and figures in RTF format

Community

• 📖 pharmaverse
• 📹 R/Pharma conference
• 📹 R/Medicine conference

Follow

• 📝 atorus blog
• 📖 ClinicalTrials CRAN Task View

Who else should we be following!?

Contributing

Contributions of any kind welcome, check out the guidelines!

Contributors

Thanks goes to these contributors!

awesome-r-clinical-reporting's Issues

Add CAMIS

Here is a new resource from a cross-industry group working on comparing analysis method implementations in software: https://psiaims.github.io/CAMIS/

I think this a useful resource to add because it helps increase awareness of the potential source of common differences between software, and ultimately, saves individual investigation time.

See this R Consortium blog post for more context about the project.

Update directory structure

It might make more sense to organize by trial stage (planning, reporting, etc.) and job function (statistics, data management, programming)

add packages for tabular output

Hi @hidyverse,
very useful packages for tabular output are also:
reactable - self explanatory
gt - very very great functionality as well as flexibility on a cell level basis. Can do plots in cells, cell highlighting etc.
tfrmt - very handy tool to set up tabular structures based on ARDs
rtables - pharmaverse and used inside TEAL etc.
falcon - pharmaverse FDA safety tables and figures
TLG catalog by Roche

Include GFM YAML metadata

I want to add metadata so I can use the RStudio visual editor as my default editor without breaking the lintr or adding that weird table to the top of the README

add randomizeR