Driving Consensus Through Repos

R/Pharma Summit @ Posit Conf 2024, August 11th

Slides: 🔗 bit.ly/PositConf24


On behalf of the R Validation Hub team:

Aaron Clark Arcus Biosciences

Doug Kelkhoff Roche

👋 Who We Are

The R Validation Hub is a collaboration to support the adoption of R within a biopharmaceutical regulatory setting (pharmaR.org)

  • Grew out of R/Pharma 2018
  • Led by participants from ~10 organizations
  • With frequent involvement from health authorities (primarily the FDA)
  • And subscribers from ~60 organizations spanning multiple industries

🤝 Affiliates:

Works with and provides support to the R Foundation and to the key organizations developing, maintaining, distributing and using R software


Key Pharma Activities

  • The R Validation Hub
  • R Submission Working Group
  • R/Medicine
  • R-Hub
  • R Repositories Working Group (ie CRAN enhancements, future development)

Impact

Community Grants & Sponsorships

Over USD $1.4 Million

Organizing Large Scale Collaborative Projects

R Validation Hub, R-Ladies

Co-Host Multidisciplinary Data Science Forums

Stanford Data Institute

Direct Support for Key R Events

R/Medicine, R/Pharma, useR!, LatinR, and more

Direct Worldwide Support for R User Groups

Join the R Consortium

r-consortium.org

  • Help guide the future direction of the R language
  • Collaborate on cross industry initiatives
  • Raise your leadership profile in the R Community
  • Protect your investment in R while supporting the common good

👷‍♂️ The R Validation Hub: What We Do

Products

White Paper

Guidance on compliant use of R and management of packages

Repositories

Building a public, validation-ready resource for R packages

Coline Zeballos

Communications

Connecting validation experts across the industry

Jaxon Abercrombie, Anuja Das, Antal Martinecz

{riskmetric}

Gather and report on risk heuristics to support validation decision-making

Eric Milliman

{riskassessment}

A web interface to {riskmetric}, supporting review, annotation and cataloging of decisions

Aaron Clark, Jeff Thompson

{riskscore}

An R data package capturing risk metrics across all of CRAN

Aaron Clark

📊 A Quick Survey

Keep your hand raised if…

  • It’s early morning and you need an excuse to stretch
  • This isn’t your first time hearing about the R Validation Hub
  • Your org leverages the R Validation Hub guidelines (risk-based approach)
  • Your org uses R Validation Hub tools ({riskmetric}, {riskassessment})
  • Your org contributes to the R Validation Hub

🗓️ Agenda

  • Communications Workstream 6min
  • {riskassessment} App Workstream 7min
  • {riskmetric} workstream 7min
    Watch for big changes coming
  • Repositories Workstream 25min
  • Room Discussion 10 - 15min
  • Closing

📜 Workstream Updates

📣 Communications Workstream

  • 📞 Community Meetings
  • 🚧 Website Revamp
  • 📜 Case Studies Refresh
  • 🆕 Gathering GxP Package Lists

📞 Community Meetings


Past meetups 📆

  • Jun 27, 2023 - Learnings & Reflections from Case Studies
  • Aug 09, 2023 - {riskmetric} & the {riskassessment} app – A 2-part Mini Series
  • Nov 28, 2023 - Wrapping Up 2023 and Welcoming 2024
  • Feb 03, 2024 - Unraveling the Term “Validation”
  • May 21, 2024 - Tackling Hurdles: Embracing Open-Source Packages in Projects

📞 Next Community Meeting


🗓️ Tues, Aug 20, 2024

👩‍🦰 Bríd Roberts

⌨️ Novartis

Analyzing change in assessed risk across package releases

The Software Open Source (SOS) team manages and executes the risk assessment process for R package validation at Novartis. The team uses an internally developed R package to classify the risk of each package as “low”, “medium”, or “high”.

We analysed the risk assessment data over two time points to determine the impact on the assigned risk categorisation for packages with AND without version changes.

In this talk, we showcase the risk assessments over time, the causes of any risk class changes, and their impact on various teams within our organizations as a result.

📞 Community Meetings


How do I sign up?

🚧 Website: pharmaR.org THEN

🚧 Website: pharmaR.org NOW

📜 Case Studies Refresh

🆕 Gathering GxP Package Lists


  • What?
    • Pkg name, version, assessment date, risk decision
  • Why?
    • R Val Hub will analyze & report observed trends & consensus in aggregate
    • Regulatory Repo WG to help identify which thresholds for certain quality benchmarks
  • How?
    • Will publish a form on pharmaR.org to Sign Up
    • Can be 100% anonymous, or consider open-source
    • 6 pharma Orgs verbally committed, 2 delivered already

🆕 Open-sourced Package List

🔗 insightsengineering.github.io/rvalidationhub-packages/

{riskassessment} App

  • ⏰ Latest features
  • 🛣️ Where we’re headed next
  • 🆕 New Collaborative Deployment

{riskassessment} App

Latest Features Recap

  • Decision automation by {riskmetric} assessment values
  • New Function Explorer for (1) source code, (2) help docs, and (3) tests
  • Tons more…
    • Non-{shinymanager} deployment options
    • Expanded Dependency Support
    • Added an 'About' tab

New Post!