Welcome!
Welcome to the R Consortium’s fourth newsletter. This quarterly newsletter puts together the latest updates about our organization’s activities, the progress each working group has made, upcoming R related events, and recordings of past events. In short, all you need to know about the R Consortium! We hope you enjoy it.
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A. Reflecting back on 2022
As we look back over 2022, we can see a number of accomplishments to be proud of. At the top of the list, are the grants that we made. We don’t have the final numbers yet, however, it looks like the Infrastructure Steering Committee awarded approximately $150,000 in technical grants and the RUGS program awarded approximately $86,000 in social infrastructure grants. Our Blog published over fifty-eight posts highlighting the everyday extraordinary work being done by user groups throughout the world. R Consortium volunteers together with the support of the Linux Foundation produced a fifth annual R/Medicine Conference. The R IDEA (R Inclusion, Diversity, Equity and Accessibility) working group took the lead on reviving the satRdays concept of bringinging small conferences to underserved areas of the world by hosting a virtual Francophone conference focusing on epidemiology in French-speaking Africa. With eight webinars on the adoption of R in the Pharmaceutical industry, one focused on the insurance industry and another on the use of R in production databases, the R Adoption Webinar series drew a sophisticated audience of attendees using R in big league industrial applications. ISC working groups continue to excel at leading industry-wide collaborative efforts that yield practical results. In collaboration with the FDA, the R Submissions Working group successfully sent two “all R” pilot submissions through the FDA electronic gateway. The RTRS (R Tables for Regulatory Submissions ) working group has begun publishing an electronic document that describes the workings of packages that are capable of making all of the tables required in a regulatory submission. The R Validation Hub working group began an effort to stand up a repository that would embody its risk metrics approach to validating R packages, and the R Repositories working group has made progress in understanding the details of CRAN’s package checking environments. We have also made good progress on internal projects such as improving our grant management system and on enlarging the curated videos on the R Consortium YouTube Channel. And last but not least, we brought you a series of quarterly newsletters.
B. Random R updates from our member companies
Posit
In November, RStudio rebranded to Posit. https://posit.co/
Oracle
Announcing custom third-party Python and R packages for use on Autonomous Database. https://blogs.oracle.com/machinelearning/post/third-party-python-and-r-packages-for-use-on-adb
Roche
Open source projects from Roche accelerating data science. https://codecollaboration.org/opensource/ + podcast “R and its rising role”
Software Engineering working group
Welcome to the homepage of the American Statistical Association (ASA) Biopharmaceutical Section (BIOP) Software Engineering Working Group (SWE WG)
C. Working groups updates
R/Business
| Topic | Content | Contact for details |
| Big plans for 2023 | With 2022 coming to an end and 2023 on our doorsteps, cannot think about a better moment to spill out some of our plans for the coming year! Major projects: Development of educational resources for budding accountants and actuaries in the form of blog posts and short tutorials (every fortnight – stay tuned!)A stream of webinars to showcase the use of R in accounting and actuarial science (once a month – Call for speakers will be done shortly!)CRAN task view for accounting and actuarial resources in R: yes, we have a lot to use! And if we are too optimistic – there are some package developments happening under covers! Call for action: coming soon! We are looking for enthusiastic data scientists who want to learn more about accounting and equally enthusiastic accountants eagerly seeking entry to the data science field! The potential areas to contribute: We have a number of topics for workshops lined up. Some examples: importing accounting data from different sources for further processing integration of financial data from structured and unstructured formats visualization of financial information (e.g. cost-variance analysis)Package development and development of repositories. Some examples: actuarial/accounting datasets for public access Repos with information about API access to available venues of financial dataPackage development specific to particular areas and applications. | Maria Prokofieva Maria.Prokofieva@vu.edu.au Further information: https://github.com/RConsortium/RBusiness |
R Certification
| Topic | Content | Contact for details |
| Exam Hosting | Evaluated exam hosting platforms and decided to move forward with the Linux Foundation as the vendor of choice. The next step is beta exam launch/evaluation in Q1 2023. | Joseph Korszun joseph@procogia.com Further information: https://github.com/RConsortium/R-Certification-WG |
R/Medicine
| Topic | Content | Contact for details |
| R/Medicine 2023 Conference | The R Consortium volunteers together with the support of the Linux Foundation to produce a fifth annual R/Medicine Conference on June 8 and 9th 2023. | r-medicine-conf@r-consortium.org |
R Tables for Regulatory Submission (RTRS)
| Topic | Content | Contact for details |
| Electronic document | Our working group has begun publishing an electronic document that describes the workings of packages that are capable of making all of the tables required in a regulatory submission. | Gabe Becker gabembecker@gmail.com Adrian Waddell adrian.waddell@gene.com Joseph Rickert joseph.rickert@rstudio.com Working Group GitHub repository: https://github.com/RConsortium/rtrs-wg |
R Validation Hub
| Topic | Content | Contact for details |
| Regulatory R Repository Working Group | The R Validation Hub completed the year by kicking off the new Regulatory R Repository Working Group. The new group will be tasked with designing and prototyping the tools to support a cross-pharma, collaborative repository of regulated use case suitable R packages. | Andy Nicholls andyofsmeg@hotmail.com |
| New paper published | We are pleased to share that a new paper, Risk Assessment of R Packages: Learnings and Reflections, has been published in the Fall edition of ASA Biopharmaceutical Report. |
Submissions
| Topic | Content | Contact for details |
| The R Consortium is happy to announce that on Nov 18th, 2022, the R Submissions Working Group successfully submitted a test submission package with a Shiny component through the FDA eCTD gateway! The submission package has been received by the FDA CDER staff. All submission materials can be found at: https://github.com/RConsortium/submissions-pilot2-to-fda The objective of the R Consortium R submission Pilot 2 Project is to test the concept that a Shiny application created with the R-language can be bundled into a submission package and transferred successfully to FDA reviewers. The application was built using the source data sets and analyses contained in the R submission Pilot 1 Project.To our knowledge, this is the first publicly available submission package that includes a Shiny component. We hope this submission package and our learnings can serve as a good reference for future regulatory submission efforts, when considering Shiny as a tool for a more user-friendly interface to navigate through analysis results. Additional agency feedback will be shared in future communications. To learn more about the R consortium R submission Working Group and the Pilot 1 submission, see: https://www.r-consortium.org/blog/2021/12/08/successful-r-based-test-package-submitted-to-fda https://www.r-consortium.org/blog/2022/03/16/update-successful-r-based-test-package-submitted-to-fda | Ning Leng leng.ning@gene.com Further information: https://github.com/RConsortium/submissions-wg |
Repositories
| Topic | Content | Contact for details |
| Replicating CRAN tests | The repositories working group is making progress with understanding and evaluating the test scripts used by the CRAN team to test packages submitted to CRAN. The goal is to be able to reproduce the multiple CRAN test environments with sufficient fidelity to significantly decrease the number of packages that fail CRAN checks. This is an ambitious undertaking because of the multiple operating systems involved, the complexity of the tests, and the dynamic nature of the scripts themselves. Test scripts may change several times a year for various reasons including the addition of new checks and performance experiments. Current efforts are focused on making it feasible for package developers to run either on a public server or with scripts package developers can run on their own. You can follow the progress of the working group by reading the minutes of the monthly meetings and tracking issues on the GitHub repository. | Joseph Rickert joseph.rickert@rstudio.com Further information: see the minutes of the WG meeting which contains a link to a video of the meeting and the recent rOpenSci newsletter. |
OOP
| Topic | Content | Contact for details |
| R Core presentation | In September, we presented the output of the working group, including proposed changes to R to enable the CRAN release, to R Core and received positive feedback. While we have yet to determine the feasibility of the proposed changes, we will collaborate with R Core to determine that feasibility and potentially implement them. | Michael Lawrence Hadley Wickham Further information: https://github.com/RConsortium/OOP-WG |
| Other activities | We continue to get useful feedback and suggestions via GitHub, and we have discussed some important topics in our meetings, including the ultimate name of the package and how to enable packages to implicitly share generics. |
D. Upcoming events
- Posit “Roche: shifting to an open-source backbone in clinical trials”:
- Jan 11th, Virtual
- The event will be live streamed through YouTube Live and the recording will be available immediately following the event YouTube link.
- Sign up: https://pos.it/roche-event
- R Adoption Series: “MMRM”
- Jan 26th, Virtual
- The ASA Software Engineering Working Group ASA BIOP SWE to share their experience of how the group formed and the types of problems they are trying to solve in the Open Source for the Pharmaceutical industry.
- R Adoption Series: “Teal”
- Feb 23rd, Virtual
- Teal is an open-source framework for building interactive data exploration applications in R. Developed at Roche, Teal allows users to quickly and easily create dynamic visualizations and tabulations of their data. It provides a range of pre-built, customizable modules and enables users to interact with their data in real-time. This allows users to quickly and easily explore their data, thus enabling fast insights generation.
- SatRdays event with Jumping Rivers
- April 2023, London
- https://satrdays.org
E. You’ve missed a recent event?
- R Adoption Series: Using Metadata for Speedy Delivery
- Oct 13th, Virtual
- In this R Adoption Series Webinar, the R Consortium invited two Pharmaceutical organizations to share their experience in leveraging metadata for automation pieces of the clinical delivery workflow.
- Recording
- R/Insurance: Upskilling on Data Handling and Communication at SwissRe
- Oct 27th, Virtual
- In the first-ever R/Insurance webinar, the R Consortium invites three team members of Swiss Re to share their use of R and Upskilling on data handling and communications. Four years ago Swiss Re set out for its actuarial community two ‘capability building’ objectives, to improve actuarial data handling and communication skills. Swiss Re launched a community-based initiative, the Atelier program, helping each other upskill whilst solving real-world business-as-usual problems. In this session, Swiss Re team members shared their approach to upskilling for data analytics before diving into an example of how to create automated (and stunning) actuarial reports.
- Recording
- R/Pharma 2022
- Nov 8-10th, Virtual
- R/Pharma 2020 and 2021 were huge successes as virtual events with over 2000 registrations for the 2021 event. We decided to keep the 2022 conference virtual in order to include as many participants as possible. For 2023 we are considering a hybrid event.
- Recording
- R Validation Hub “Regulatory R Repositories” Working Group Kick Off
- Nov 16th
- GitHub, Announcement
- R/Database: Using R at Scale on Database Data
- Dec 8th, Virtual
- If you missed the latest R/Database webinar, it is now available on youtube! Mark Hornick, Senior Director, Oracle Machine Learning, and Sherry LaMonica, Consulting MTS, Oracle Machine Learning present on how to increase overall solution performance with R tightly integrated with Oracle databases (OML4R). Check it out:
- Recording
We need you!
In this section, we highlight a few opportunities for getting more involved with the R Consortium.
Help promote the R Consortium message around the globe
- Follow @RConsortium on Twitter (https://twitter.com/RConsortium) and R Consortium on LinkedIn (https://www.linkedin.com/company/r-consortium)
- We’re working on updating and improving the R Consortium YouTube account (https://www.youtube.com/c/RConsortium). There’s great content there, from events, with talks and presentations covering many R topics.
- Like, comment, and share/retweet R Consortium content on an ongoing basis – new content appears frequently!
Participate in an R Consortium working group
R in Business
- (https://github.com/RConsortium/RBusiness), where the working group’s goal is to promote and support the R programming environment and the R ecosystem in business practices and business research
- Development of a community-based collaboration platform
- Organization and sponsorship of events
- Research on relevant topics in the intersection of business/accounting and technology
- Development of openly available courses/tutorials
- Development and maintenance of R packages
