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R/Medicine Coming June 10-14, 2024 – Call for Abstracts Open – Keynotes Announced

By Announcement, Blog, Events

The R/Medicine conference provides a forum for sharing R based tools and approaches used to analyze and gain insights from health data. Conference workshops provide a way to learn and develop your R skills. Midweek demos allow you to try out new R packages and tools, and our hackathon provides an opportunity to learn how to develop new R tools. The conference talks share new packages, and successes in analyzing health, laboratory, and clinical data with R and Shiny with a vigorous ongoing discussion with speakers (with pre-recorded talks) in the chat.

Keynote Addresses

Stephanie Hicks

Statistical Challenges in Single-Cell and Spatial Transcriptomics

Thursday, June 13

Biography

Stephanie Hicks, PhD, MA and Associate Professor of Biomedical Engineering and Biostatistics at Johns Hopkins University, is an applied statistician working at the intersection of genomics and biomedical data science.

Gundula Bosch

Reproducibility in Medical Research

Friday, June 14

Biography

Gundula Bosch, PhD, MEd ’16, MS, is a scientist and educator leading global education reform through training programs in critical, broad, and interdisciplinary scientific thinking. She is the director of the R3 Center for Innovation and Science Education at the Johns Hopkins School of Public Health.

Call for Abstracts

R/Medicine is seeking abstracts for:

  • Lightning talks (10 min, Thursday, June 13, or Friday, June 14) Can pre-record so that you can be live on chat to answer questions
  • Regular talks (20 min, Thursday, June 13, or Friday, June 14) Can pre-record so that you can be live on chat to answer questions
  • Demos (1 hour demo of an approach or a package, Wednesday, June 12) Done live, preferably interactive
  • Workshops (2-3 hours per topic, Monday, June 10, or Tuesday June 11, usually with a website and a repo, participants can choose to code along. Usual 5-10 min breaks each hour.
  • Posters for poster session on Wednesday, June 12. Can include live demos of an app or a package.

Confirmed Workshops (Monday, June 10, and Tues, June 11)

Note: Final dates and times TBD. More workshops being added. Check the R/Medicine website for updates.

  • Causal Inference with R – Lucy D’Agostino and Malcolm Barrett
  • Tidying your REDCap data with REDCap Tidier – Stephan Kadauke and Will Beasley
  • Next Generation Shiny apps with bslib – Garrick Aden-Buie

The R/Medicine website is being updated as we receive the latest information. Please check in again soon!

Join our R/Medicine Webinar: Quarto for Reproducible Medical Manuscripts

By Blog, Events

Join the R Consortium for an enlightening webinar on March 20th, 2024, at 4:00 PM ET, featuring Mine Cetinkaya-Rundel, Professor of the Practice of Statistical Science at Duke University. Discover the innovative Quarto tool to streamline the creation of reproducible, publication-ready manuscripts.

Register here!

Key Highlights:

  • Quarto Manuscripts Introduction: Learn how to easily integrate reproducibility into your research with Quarto’s user-friendly features, creating comprehensive bundled outputs ready for journal submission.
  • Interactive Demo: Witness a live demonstration of Quarto in action, showcasing how to enhance your current manuscript preparation process and address common challenges.
  • Expert Guidance: Gain insights from Mine Cetinkaya-Rundel’s extensive experience in statistical science and reproducible research, offering valuable tips for improving your workflow.

Event Details:

When: March 20th, 2024, at 4:00 PM ET

Don’t miss this opportunity to refine your manuscript preparation process with the latest advancements in reproducibility technology.

Register now!

From Vision to Action: Pfizer’s R Adoption Odyssey – Join the Webinar on February 8, 2024

By Blog, Events

In the rapidly evolving sphere of pharmaceutical data analysis, a significant transition is taking place – the shift from traditional SAS to the versatile R programming language. Pfizer, a trailblazer in the pharmaceutical industry, is leading this change. We are excited to invite you to an exclusive webinar that will cover details about how Pfizer has succeeded and what the benefits are: “From Vision to Action: The Pfizer R Center of Excellence-led Journey to R Adoption,” scheduled for February 8th, 2024, at 3:00 pm ET.

Register Now!

Pfizer’s Progressive Shift to R:

At the heart of Pfizer’s data analysis revolution is the adoption of R – a language known for its robust community-driven development and open-source nature. This move is not just about changing tools; it’s about embracing a culture of innovation and collaboration.

The journey began with an internal query at Pfizer: How many of our colleagues are proficient in R? The answer led to the unveiling of a latent community of R users, eager yet unconnected. In 2022, an internal survey highlighted the presence of over 1,500 R users, a clear sign of a burgeoning community within Pfizer.

In response, Pfizer established the R Center of Excellence (CoE) in 2022. This initiative marked a shift from scattered individual efforts to a cohesive, strategic approach to R adoption. The CoE, celebrating its first anniversary in 2023, has become a linchpin in nurturing Pfizer’s vibrant R community.

Webinar Highlights:

This upcoming webinar, hosted by the R consortium, is more than just a case study. It’s a treasure trove of insights for fostering an engaged R community. The session will cover:

  • Pfizer’s journey in building a robust R community.
  • Practical strategies applicable across various industries.
  • Understanding the critical role of an engaged R community in data analysis.

Join Us for the Webinar:

This is an unmissable opportunity for anyone interested in data science, R programming, or community building within large organizations. By attending this webinar, you will gain firsthand insights into how Pfizer successfully integrated R into its data analysis practices and how you can apply these learnings to your organization.

Don’t miss this opportunity to learn from Pfizer’s experience and expertise. Register now for the webinar on February 8, 2024, at 3:00 pm ET and be a part of the conversation shaping the future of pharmaceutical data analysis.

Register Now!

Harness the Power of R for Survival Analysis: Join Our {ggsurvfit} Webinar!

By Blog, Events

Hello, Data Enthusiasts!

Are you ready to take your data visualization skills to the next level in the fascinating world of survival analysis? We’re thrilled to invite you to our exclusive webinar: “Visualizing Survival Data with the {ggsurvfit} R Package.” Mark your calendars for January 25, 2024, at 7:00 PM Eastern Time (ET)!

Register here! 

Why This Webinar is a Must-Attend

The {ggsurvfit} package is designed for both beginners and seasoned data scientists. It streamlines the process of generating publication-quality, time-to-event, or survival analysis graphs. And the best part? It’s built on the backbone of the beloved {ggplot2} package, marrying simplicity with sophistication.

What You Will Learn

Our interactive session will dive deep into how the {ggsurvfit} functions, like add_confidence_interval() and add_risktable(), seamlessly integrate as {ggplot2} ‘geoms.’ This means you can spruce up your plots using the familiar {ggplot2} toolkit sans the headache of mastering new coding syntax.

It’s not just about learning a new tool – it’s about enriching your data storytelling capabilities.

The Perks of Joining

  • Interactive Learning: Engage with experts and peers in an interactive online setting.
  • Skill Enhancement: Elevate your data visualization prowess, specifically in survival analysis.
  • Network Building: Connect with fellow data enthusiasts and professionals from diverse fields.

Register Now! 

See you there, where data meets innovation!

New R/Insurance Webinar Series: The Journey from Excel to High-Performance Programming in R

By Blog, Events

Introduction:

The actuarial profession is on the cusp of a transformation spearheaded by integrating programming into the traditional spreadsheet-based workflow. Georgios Bakoloukas, Head Model and Analytics, Swiss Re and Benedikt Schamberger, Head Atelier Technology & AI Consulting, Swiss Re, are at the forefront of this paradigm shift. 

This blog encapsulates 4 upcoming webinars showcasing the journey from Excel to high-performance programming in R. The webinars are scheduled to be broadcast in January 2024, and you can participate directly. Beginners are welcome.

Webinars by Georgios Bakoloukas:

  1. From Excel to Programming in R

            Date: January 10th, 2023

            Duration: 30 minutes

Georgios will introduce a compelling case for why actuaries should embrace R programming while continuing to use Excel. The session promises to demystify the transition, using insurance industry examples, to demonstrate the benefits of adopting a programming mindset alongside familiar spreadsheet computing.

  1. Putting R into Production

            Date: January 17th, 2023

            Duration: 30 minutes

The follow-up webinar takes the discussion from solving problems in R to sharing these solutions. Georgios will cover documentation, testing, and dissemination using R’s packaging, Web API creation, and GUI generation through Shiny. This practical approach ensures that coding efforts are not siloed but add value across the organization.

Webinars by Benedikt Schamberger:

  1. R Performance Culture

            Date: January 24th, 2023

            Duration: 30 minutes

Benedikt will address the nuances of optimizing code performance in R. Acknowledging that premature optimization might be detrimental, he will provide insights into when and how to refine code. The session includes a look at R’s design philosophy regarding performance and the tools available for tuning.

  1. High-Performance Programming in R

            Date: January 31st, 2023

            Duration: 30 minutes

Continuing the performance theme, Benedikt will delve into the limitations of CSV files and introduce binary formats that bolster efficiency. He will explore the arrow R package and the Parquet file format, demonstrating their potential to reduce time and disk space requirements significantly.

Conclusion:

These webinars offer a roadmap for actuarial professionals keen on enhancing their toolkit with programming capabilities. As the industry evolves, the skills taught by Georgios and Benedikt will become increasingly indispensable, marking a step towards a more innovative and efficient actuarial future.

Please join us to learn more about actuarial science here.

Webinar: Use of R in Japan’s Pharma Industry

By Blog, Events

The use of the R programming language has seen exponential growth across industries, with its role being especially pronounced in the pharmaceutical sector. Japan stands out in this growth narrative, thanks in part to the initiatives of the Japan Pharmaceutical Manufacturers Association (JPMA). Before diving into the webinar insights, understanding JPMA’s profound influence and contributions is essential.

About JPMA

Established in 1968, JPMA is a voluntary consortium of 71 research-centric pharmaceutical firms. With its core mission of “realizing patient-oriented healthcare,” JPMA has tirelessly worked towards enhancing global healthcare through the formulation of pioneering ethical drugs.

Summary of the Webinar’s Concept

The Adoption of R in Japan’s Pharma Industry talk and panel discussion will be led by key industry experts from the JPMA R Task Force Team. The webinar explores the usage and adoption of the R in the pharmaceutical industry, specifically focusing on the findings of the JPMA Drug Evaluation Committee, R Task Force Team, and the JPMA Report. The report references various open source works and publications, including those from the R Consortium pilot submissions, Package Validation Hub, and webinar training.

Agenda of the Webinar:

  • General Background (10-15 minutes)
    • PMDA: Highlighting the intricacies of submissions with R.
    • JPMA R Task Force: Delving into past activities and shedding light on future initiatives.
  • JPMA Survey Report (15-20 minutes)
    • Background: Understanding the rationale and motivation behind the JPMA survey.
    • Results: Discuss key findings and their implications for the industry.
  • Q&A Session (15 minutes)

Date and Time: Tues, Jan 9, 2024 at 9:00 am JST / Jan 8, 2024 at 4:00 pm PT / 7:00 pm ET

Conclusion:

Under the auspices of JPMA’s guiding principles, the webinar will present a comprehensive glimpse into R’s evolving role in Japan’s pharmaceutical landscape. The dedication of JPMA, combined with the increasing relevance of R, signifies an exciting chapter in the pharmaceutical domain’s data-driven journey.

Join the JPMA webinar to learn more about R’s pharmaceutical achievements! 

Register here!

R Validation Hub: Wrapping up 2023 and Welcoming 2024!

By Blog, Events

Abstract:

Join us on November 28th for our last Community meeting of 2023. The R Validation Hub’s Executive Committee will summarize this year’s achievements, our presence at conferences and other key moments to celebrate.

Agenda:

  • Looking Back on 2023 (20 minutes): Review the year’s highlights, including conferences and working group summaries.
  • Focus of the Reg R Repo Working Group (20 minutes): Insights into the group’s initiatives and achievements.
  • Open Discussion (20 minutes): An interactive session for feedback and community engagement.

Conclusion:

Don’t miss this opportunity to reflect on 2023 and contribute to shaping our direction for 2024. Join us for a session filled with insights, networking, and community spirit.

Join the community call! (Microsoft Teams meeting)

Webinar: Discover the Future of R in Regulatory Submissions

By Blog, Events

Are you an analyst, statistician, or data science enthusiast keen on understanding how open source software like R shapes the future of regulatory submissions? This webinar is for you!

“R and Shiny in Regulatory Submission”

  • When: Dec 11, 2023
  • Time: 3:00 p.m. – 4:30 p.m. EDT
  • Duration: 1.5 hours
  • Where: Zoom – Virtual Event
  • Hosts: FDA Statistical Association and R Consortium

Agenda Highlights:

  • Opening Remarks by Ning Leng, People and Product Lead in Product Development Data Sciences at Roche.
  • Presentation on Open Source Software for Regulatory Submissions by Paul Scheutte, FDA. 
  • Dive into R Consortium R Submission Pilot 2 with Eric Nantz from Eli Lilly. Discover how an R-based submission with a shiny component unfolded.
  • Reviewing Experience of R-based Submissions with Hye Soo Cho, FDA. Understand the nuances and challenges faced during the review process.
  • Interactive Panel Discussion moderated by Ning Leng. Join Paul Schuette, Hye Soo Cho, and Eric Nantz as they delve deep into the R adoption journey and discuss practical challenges and solutions.

Why Should You Attend?


The data science world is rapidly evolving, and R is at the forefront of this transformation. With a robust open source community backing it, R brings many cutting-edge statistical tools—a standout feature. R shiny offers unparalleled flexibility and interactivity, revolutionizing how data scientists operate. Recently, the R consortium broke new ground by introducing a Shiny component in a submission package, a pivotal moment marking the fusion of open source capabilities with formal regulatory processes.

In the upcoming webinar, the FDA and industry speakers will share their unique experiences with R-based and shiny-based submissions. Whether you’re an industry professional or an aspiring data scientist, this is an opportunity to stay ahead of the curve.

Conclusion


Integrating open source software in regulatory processes represents a leap toward more transparent, efficient, and adaptable systems. Don’t miss this golden opportunity to learn, interact, and contribute to this transformative journey.

Register for the Webinar Now!

About the R consortium R Adoption Series


The R consortium R adoption series is a curated set of webinars focusing on the growing adoption of the R programming language in the data science community. Each webinar provides insights through a compelling case study and offers an interactive platform for attendees to pose questions and learn. This series is a collaborative effort by the R consortium, PhUSE, and PSI. Dive deep into the series here: R-Adoption Webinar Series.

PHUSE Connect EU 2023 –  Clinical Data Science Conference – Coming in Early November

By Blog, Events

Blog post for R Consortium partner PHUSE

Join PHUSE in Birmingham, UK, from November 5-8 for an event that promises to energise your learning through connection with the PHUSE Community and hearing from our experts on the topics that are most important to industry today.

The R Consortium is participating directly in one session on Tuesday, November 11, starting at 11am local time. Dive deep into the world of open source in pharma by joining a panel discussion that includes Mehar Pratap Singh, Chairman of the Board of Directors at the R Consortium, Director Sumesh Kalappurakal, and other open source representatives entitled “Let’s Discuss Open Source Openly: A New Path in Pharma.” This is an excellent opportunity to engage in a meaningful discussion and gain insights from leading voices in the industry. 

One of the highlights of this event will be “Let’s Discuss Open Source Openly, A New Path in Pharma,” a session led by Director Sumesh Kalappurakal, Mehar Pratap Singh, Chairman of the Board of Directors at the R Consortium, and other open source representatives. Dive deep into the world of open source in pharma, understanding its implications and the potential it holds for the future. This is a golden opportunity to engage in meaningful discussions and gain insights from a leading voice in the industry. 

It’s not too late to register your place or secure a sponsorship opportunity! View full information via the links below and explore the agenda to see what’s in store for attendees.

Agenda: https://phuse.s3.eu-central-1.amazonaws.com/Events/2023/EU+Connect+%E2%80%93+Birmingham/Agenda/EU+Connect+Agenda.pdf 

Event Information: https://www.phuse-events.org/attend/19/home 

Sponsorship: https://phuse.s3.eu-central-1.amazonaws.com/Events/2024/Connect+Prospectus.pdf 

R-Ladies Morelia, Mexico, hosts First Anniversary Event on July 31, 2023

By Blog, Events

R-Ladies Morelia is celebrating its first anniversary on the 31st of July 2023, and hosting a hybrid event to mark this occasion. In this event, they plan on providing the Center of Mathematical Science at UNAM with an analysis of their recruitment, graduation, and research data. 

Nelly Sélem, co-founder and organizer of the group also discussed the group’s rapid growth over the course of a year. She also shared how she uses R for her work as a bioinformatics researcher.

Please share about your background and involvement with the RUGS group.

I am a professor at the Center for Mathematical Sciences at UNAM in Morelia, Mexico. I earned a degree in Mathematics from the University of Guanajuato and a master’s degree from CIMAT. Then, I did a Ph.D. and a Post-doctorate in Integrative Biology at the Evolution of Metabolic Diversity lab at Langebio-Cinvestav. I care about teaching. I have taught at prestigious México Universities: UNAM, ITESM, IPN, and CINVESTAV. I contributed to the educational community by developing a metagenomics open-source lesson in “The Carpentries Incubator.” I’m a founder member of BetterLab, a biotechnology and software startup, and I’m also a member of the Mexican SARS-CoV-2 Genomic Surveillance Consortium.

As a scientist, I have proposed and developed bioinformatics solutions to biological problems of comparative genomics of microorganisms. I am interested in the genome evolution of Archaea, Bacteria, and Fungi. 

I founded the R Ladies Morelia chapter with Haydee and Claudia last year. We try to organize meetings every month more or less. And this year on our first anniversary we plan to hold a big annual meeting in which we will get to meet more people. 

Can you share what the R community is like in Mexico?

I can only talk about the R Ladies chapters in Mexico, as I am more familiar with them. We have several chapters in Mexico and each year there is an annual meeting for all cities. 

The Mexico City and Cuernavaca chapters are rather big. I would say, overall, there is a lot of interest on social media and members of R-Ladies chapters are inviting other girls to learn to code. 

Our chapter is also growing rapidly as we started with four members and now we have a stable community. On the best days, we have up to 90 people attending our events but on average we have between 12 to 20 attendees. 

Most of the R-Ladies chapters in Mexico are being run by people from academia and sponsored by universities. I do know that some of us work in the area of bioinformatics and Bioconductor. 

We are also close to the international R community because we are following the R Champions program. I think it’s for Latin America and we are trying to get connected with that program.

You have a Meetup on “Graphics for the Center of Mathematical Science,” can you share more on the topic covered? Why this topic? 

For this meetup, which is also our first anniversary, we plan on giving the Center of Mathematical Science, National University of Mexico an evaluation. It would include a comparison of the number of students being graduated each year and the quality standard of researchers against other universities from Mathematics in Mexico and Latin America. The center has sponsored us for the past year, and it is going through the process of becoming a bigger institute. 

With this event, we are trying to give back to the center with data analysis of its basic statistics. The audience will learn to use dataframes and ggplot to visualize data. We will be working in teams to teach basic ggplot visualizations. And on the second day, we will be giving small workshops and sharing our work with each other. All our events are Hybrid so this one is also going to be Hybrid and people will attend both physically and virtually. 

We hope to grow our community through this event and also contribute to the annual report of the Center of Mathematical Sciences. 

Any techniques you recommend using for planning for or during the event? (Github, zoom, other) Can these techniques be used to make your group more inclusive to people that are unable to attend physical events in the future?   

Meetup has been very helpful for keeping everything organized, and we use Zoom for our virtual meetings. We also share code through our GitHub repo and people can go back to it after meetings. For communication between organizers, we mostly use WhatsApp chat. 

At the start of the semester, we plan events for that semester with dates, speakers, and topics to be covered. We work in teams, so we can help each other. Sometimes we go through chapters of a book, or we just go for an R package. We consider ourselves a community of practice. Even if people don’t know a lot, we do some data analysis and share the code on the meeting day.

Please share about a project you are currently working on or have worked on in the past using the R language. Goal/reason, result, anything interesting, especially related to the industry you work in?

I would like to mention MetaEvoMining, a project one of my undergrad students is working on for his thesis. We are trying to treat metagenomic data in order to look for some gene families that are going through expansions. And maybe these expansions conduce to recruitment into antibiotic gene producers. So we are looking for something different in gene families that may be recruited to new antibiotic gene families. This has been researched in genomes but not in metagenomes and there is a lot more data available in metagenomes. We want to develop an R package for this purpose. For the project, we are using Posit (RStudio). We are also using packages like ggplot and RString. We are also using tidyverse in general.