R Resources and Links

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Resource map

Pharma ecosystem pharmaverse, admiral Visualisation ggplot2, plotly, visR R Shiny apps, dashboards Training courses, books Tech stack Posit, Quarto, renv Community PSI, R/Pharma, GitHub R in Pharma & Data Science Click any cluster
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Overview

R in Pharma & Data Science

R has grown from an academic statistics tool to a central pillar of pharma data science, covering everything from ADaM dataset derivation to regulatory submission outputs and interactive clinical dashboards.

The ecosystem is coordinated across initiatives including pharmaverse, openpharma, the R Consortium, and industry groups like PSI and PHUSE. Select any cluster to explore curated resources in that area.

Pharma ecosystem

Pharma-specific packages & initiatives

pharmaverse and the Roche NEST project provide a coordinated ecosystem of R packages for clinical reporting, ADaM construction, and regulatory submissions. Below are key entry points.

Pharmaverse
pharmaverse Curated collection of clinical R packages working together end-to-end from data to submission. pharmaverse.org pharmaverse on R-universe Browse and install pharmaverse packages via R-universe. pharmaverse.r-universe.dev/packages R-universe (full) Personal package repositories for R — search across all open-source R packages. r-universe.dev
Admiral — ADaM construction
admiral ADaM in R Asset Library — the go-to package for deriving ADaM datasets from SDTM. pharmaverse.github.io/admiral admiralonco Oncology extension for admiral. pharmaverse.github.io/admiralonco admiralophtha Ophthalmology extension for admiral. pharmaverse.github.io/admiralophtha admiralvaccine Vaccine extension for admiral. pharmaverse.github.io/admiralvaccine
Outputs & clinical reporting
cardinal Standard clinical reporting tables and analysis results. pharmaverse.github.io/cardinal Roche TLG Catalogue Comprehensive catalogue of tables, listings, and graphs with R code. insightsengineering.github.io/tlg-catalog R for Clinical Study Reports and Submission End-to-end guide for producing CSR outputs in R. r4csr.org RTRS — R Tables for Regulatory Submissions R Consortium working group for submission-grade tables. rconsortium.github.io/rtrs-wg
Working groups & initiatives
CAMIS Comparing Analysis Method Implementations in Software — a PHUSE DVOST working group. psiaims.github.io/CAMIS R Submissions Working Group R Consortium group driving R adoption in regulatory submissions. rconsortium.github.io/submissions-wg R Validation Hub Resources and frameworks for validating R packages in a regulated environment. pharmar.org openstatsware Working group for high-quality open-source statistical software in regulated pharma. openstatsware.org
Data
CDISC pilot ADaM data PHUSE pilot ADaM datasets — standard test data for clinical reporting development. github.com/phuse-org/phuse-scripts (ADaM) CDISC pilot SDTM data PHUSE pilot SDTM datasets. github.com/phuse-org/phuse-scripts (SDTM) random.cdisc.data (Roche) Generate random SDTM and ADaM datasets for development and testing. insightsengineering.github.io/random.cdisc.data cards (Roche) Analysis Results Data — structured output format for clinical analysis results. insightsengineering.github.io/cards
Visualisation

Visualisation packages & resources

ggplot2 is the foundation for static regulatory graphics in pharma — audit-friendly, code-driven, and publication-ready. A growing set of extensions handles clinical plot types. Below are curated resources from your collection.

Core ggplot2
ggplot2: Elegant Graphics for Data Analysis (3e) Hadley Wickham's definitive book on ggplot2. Free online. ggplot2-book.org ggplot2 extensions gallery Official gallery of packages extending ggplot2 — geoms, themes, stats and more. exts.ggplot2.tidyverse.org/gallery ggplot2 aesthetic specifications Reference for shapes, lines, colours, and other aesthetic parameters. ggplot2.tidyverse.org
Courses — Cédric Scherer
Graphic Design with ggplot2 rstudio::conf 2022 workshop by Dr Cédric Scherer. Design-focused ggplot2 techniques. rstudio-conf-2022.github.io/ggplot2-graphic-design Engaging and Beautiful Data Visualizations with ggplot2 posit::conf 2023 course by Dr Cédric Scherer. posit-conf-2023.github.io/dataviz-ggplot2
Clinical visualisation
visR openpharma initiative for clinical graphs adhering to graphical principles. Strong KM plot support. openpharma.github.io/visR Novartis graphics principles Principles for effective graphics in clinical and regulatory settings. graphicsprinciples.github.io CDISC Pilot efficacy tables (pilot1wrappers) Live example of regulatory-submission TLF outputs built in R. rconsortium.github.io/submissions-pilot1 Clinical Tables in R with gt (Phil Bowsher) Workshop materials for building clinical tables using the gt package. github.com/philbowsher
Chart choice & best practices
R Graph Gallery Hundreds of R chart examples with reproducible code. Essential reference. r-graph-gallery.com Top 50 ggplot2 visualizations Master list of ggplot2 chart types with full R code. r-statistics.co From data to Viz Decision tree tool for choosing the right chart type for your data. data-to-viz.com RSS best practices — choosing a visualisation Royal Statistical Society guide to selecting appropriate visualisation types. royal-statistical-society.github.io/datavisguide Financial Times visual vocabulary Classic chart-type reference poster from the FT data team. github.com/Financial-Times/chart-doctor
Colour tools
R colours — full list with hex Complete reference for R named colours with hex codes and previews. r-charts.com/colors Colour-blind friendly palettes for ggplot2 Practical guide to accessible colour choices in ggplot2. datanovia.com Coblis — colour blindness simulator Upload any image to check how it appears to users with colour vision deficiencies. color-blindness.com/coblis Darken colour hex tool mdigi.tools/darken-color Image color picker Pick hex values from any image. imagecolorpicker.com
Inspiration
Dataviz Inspiration Hundreds of chart examples for creative data visualisation ideas. dataviz-inspiration.com VIS-SIG Blog Visualisation special interest group blog — pharma-relevant dataviz examples. vis-sig.github.io/blog Dr Cédric Scherer Portfolio and blog from one of the leading ggplot2 visualisation practitioners. cedricscherer.com Dr Liam D. Bailey Data visualisation work and tutorials. liamdbailey.com/dataviz
R Shiny

R Shiny — apps & dashboards

Shiny powers interactive clinical data exploration, trial monitoring dashboards, and safety review tools. The Roche NEST/teal framework builds pharma-specific Shiny applications on top of ADaM data.

Core resources
Mastering Shiny Hadley Wickham's free online book — the definitive guide to Shiny development. mastering-shiny.org R Shiny Gallery (Posit) Official gallery of Shiny app examples with source code. shiny.posit.co/r/gallery Shinylive Run Shiny apps entirely in the browser — no server required. shinylive.io/r/examples Appsilon Shiny demo gallery High-quality Shiny app demos from a leading Shiny consultancy. explore.appsilon.com htmlwidgets for R Interactive JavaScript visualisations in R — works in Shiny, R Markdown, and Quarto. htmlwidgets.org
Clinical Shiny examples
Roche Teal Gallery Pharma-grade Shiny apps built on the teal framework for clinical data exploration.
Efficacy app Safety app Exploratory app FDA app
CDISC Pilot — Realtime Clinical Summaries Shiny implementation of the CDISC pilot data for regulatory-submission summaries. realtimeclinical.shinyapps.io/rsum safetyGraphics Interactive safety graphics for clinical trial data. Open-source, extensible. safetygraphics.github.io
Dashboards & UI frameworks
flexdashboard R Markdown format for flexible, easy-to-build dashboards. pkgs.rstudio.com/flexdashboard Leaflet + flexdashboard + DT + Crosstalk (schools example) Example combining interactive mapping, tables, and cross-filtering in a dashboard. matt-dray.github.io esquisse Drag-and-drop ggplot2 builder. Great for rapid visualisation prototyping. dreamrs.shinyapps.io/esquisse
Training

Training & learning resources

A strong mix of free and paid resources exists for R learners at all levels, including pharma-specific pathways. Many of the best resources are free online books or recorded conference workshops.

Books (free online)
R for Data Science (2e) Hadley Wickham. The definitive tidyverse introduction — data import, wrangling, visualisation, and communication. r4ds.hadley.nz Advanced R Hadley Wickham. Deep dive into R internals — environments, functional programming, and performance. adv-r.hadley.nz R Packages (2e) Hadley Wickham & Jenny Bryan. How to build, test, and share your own R packages. r-pkgs.org Mastering Shiny Hadley Wickham. The definitive Shiny book. mastering-shiny.org R Markdown: The Definitive Guide Yihui Xie. Complete reference for R Markdown (predecessor to Quarto). bookdown.org/yihui/rmarkdown Big Book of R Oscar Baruffa's curated directory of R books — hundreds of free titles organised by topic. bigbookofr.com Data Visualization — A practical introduction Kieran Healy. Sociology-oriented but highly practical guide to data visualisation in R. socviz.co What They Forgot to Teach You About R Jenny Bryan & Jim Hester. Essential R workflow topics — projects, file paths, R startup, and environment management. rstats.wtf
Pharma-specific courses
Introduction to R for SAS programmers pharmaverse workshop bridging SAS concepts to R equivalents. Free. pharmaverse.github.io/intro-to-r-for-sas-programmers-workshop Hands On Clinical Reporting Using R — Coursera Practical course covering clinical reporting workflows in R. coursera.org GSK — Introduction to R and the tidyverse GSK's open-source introduction to R training materials. gsk-biostatistics.github.io GSK — R Graphics with ggplot2 GSK's open-source ggplot2 training materials. gsk-biostatistics.github.io
Platforms & general courses
Posit Recipes Bite-sized R code snippets for common tasks — great for quick reference. posit.cloud/learn/recipes Data Science in a Box Mine Çetinkaya-Rundel's complete open-source data science course teaching R. datasciencebox.org Remaster the Tidyverse Garret Grolemund's tidyverse workshop planning repository. github.com/rstudio-education/remaster-the-tidyverse Data Science Learning Community — YouTube Live book-reading sessions and R tutorials. Great for working through books with others. youtube.com/@dslcvids
Blogs & newsletters
R-bloggers Aggregator of R blog posts from across the community. New content daily. r-bloggers.com R Weekly Weekly curated digest of the best R blog posts, packages, and news. rweekly.org R for the Rest of Us — blog Accessible R tutorials and insights aimed at non-programmers. rfortherestofus.com/blog Nicola Rennie — blog Data visualisation and R tutorials from a PSI dataviz contributor. nrennie.rbind.io/blog Building Stories With Data — Cara Thompson Data storytelling and ggplot2 tutorials. cararthompson.com/posts
Community

Community, conferences & GitHub

A strong open-source community has formed around R in pharma, spanning annual conferences, cross-industry working groups, and active GitHub organisations. PSI AIMS SIG is the natural home for UK statisticians in this space.

Industry groups
PSI AIMS SIG PSI's Advance Innovation and Modernisation of Statistics Special Interest Group — open-source and R focus. psiaims.github.io/website R/Pharma conference Annual conference dedicated to R in pharma and biotech. Free virtual access, archived talks. rinpharma.com R in Pharma — YouTube Full archive of R/Pharma conference talks and workshops on YouTube. youtube.com/@RinPharma PHUSE Data Visualisation & Open Source Technology PHUSE working group focused on data visualisation and open-source tools in pharma. advance.phuse.global R Consortium — R Adoption Series Webinar series on R adoption in pharma and regulated industries. r-consortium.org/webinars
Conference materials
PharmaSUG Pharmaceutical SAS Users Group — cross-language conference with strong R content. pharmasug.org lexjansen.com Archive of SAS and pharma conference proceedings including PHUSE and PharmaSUG papers. lexjansen.com Katja Glass conference videos Curated collection of pharma conference video recordings. glacon.eu/portal/confVideos
GitHub organisations
pharmaverse Coordinated open-source R packages for clinical reporting, ADaM, and submissions. pharmaverse.org openpharma Cross-industry open-source pharma projects including visR and ecosystem tooling. github.com/openpharma insightsengineering (Roche NEST) Roche NEST project: teal, rtables, tern, nestcolor, random.cdisc.data and more. github.com/insightsengineering R Consortium — RTRS Working Group R Tables for Regulatory Submissions working group repository. github.com/RConsortium/rtrs-wg