Merge pull request #63 from Oppkey/62-add-new-blogs

Added 4 new blog posts

posts/news-from-r-submissions-working-group-pilot-3/index.qmd

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+---
+title: "News from R Submissions Working Group – Pilot 3 Successfully Reviewed by FDA"
+description: "The R Consortium is pleased to announce the successful completion of the Pilot 3 Submission which extended the work done in Pilots 1 and 2 by generating the ADaM datasets. The complete FDA response letter is available."
+author: "R Consortium"
+date: "08/26/2024"
+---
+
+_Blog contributed by Ning Leng, People and Product Leader, Roche-Genentech and Joel Laxamana, Principal Data Scientist, Roche-Genentech_
+
+The R Consortium is pleased to announce the successful completion of the Pilot 3 Submission which extended the work done in Pilots 1 and 2 by generating the ADaM datasets. The complete [FDA response letter](https://github.com/RConsortium/submissions-wg/blob/main/_Documents/Summary_R_Pilot3_Submission.pdf) is available.  
+
+The objective of the R Consortium R Submission Pilot 3 Project is to test the concept that an R-language based submission package for ADaMs and TLFs can meet the needs and the expectations of the FDA reviewers, including assessing code review and analyzing reproducibility. All submission materials and communications from this pilot are publicly available, with the aim of providing a working example for future R-language based FDA submissions. This is an FDA-industry collaboration through the non-profit organization R Consortium.
+
+All submission materials can be found at: [submissions-pilot3-adam-to-fda](https://github.com/RConsortium/submissions-pilot3-adam-to-fda). This is the first publicly available R-based FDA submission package including R scripts to generate Analysis Data Models (ADaM) and Tables, Listings & Figures (TLFs).
+
+![](collaboration.png)
+
+_Open-Source Collaboration in standardizing Clinical Trial analyses and Submissions. Broadening ways to bring treatments to Patients._
+
+## Pilot 3 Timeline
+
+The initial submission was submitted through the eCTD gateway on Aug 28, 2023. FDA verbal responses were received from Jan-July 2024 during R submission working group meetings. Documentation of this initial feedback and response can be found at [response-FDA-IR-pilot3.pdf](https://github.com/RConsortium/submissions-pilot3-adam-to-fda/blob/main/m1/us/response-FDA-IR-pilot3.pdf). The updated submission package addressed reported issues and was re-submitted on Apr 19, 2024. The final response letter from FDA was received on Aug 8, 2024.
+
+## Pilot 3 Scope
+
+The Pilot 3 test submission exemplifies an all-R submission package for ADaMs and TLFs, adhering to electronic Common Technical Document (eCTD) specifications. This comprehensive package not only includes ADaMs and TLGs, but it emulates a full study submission package including the source Study Data Tabulation Models (SDTMs) used to generate the Pilot 3 ADaMs. It also encompasses the installation and loading of the proprietary {pilot3utils} R package, various open-source R packages, R scripts for the Analysis Data Model (ADaM) datasets derived from Pilot 3, and Tables, Listings, and Figures (TLFs) from Pilot 1. In addition to other requisite eCTD components, the Pilot 3 package also includes the Analysis Data Reviewer’s Guide (ADRG) providing detailed steps leading to the execution of the analysis R scripts to re-produce the ADaMs and TLFs from a FDA reviewers perspective. These Pilot 3 submission materials are linked above.
+
+Pilot 3 serves as a complement to Pilots [1](https://github.com/RConsortium/submissions-pilot1-to-fda) and [2](https://github.com/RConsortium/submissions-pilot2-to-fda), which demonstrated the feasibility of submitting TLF R scripts and R Shiny code, respectively. Furthermore, Pilot 3 successfully validated the submission of proprietary R packages in compressed file formats, serving as another alternative to {pkglite} or installation directly from github.
+
+If you have any questions about this Pilot 3 submission, we would love to hear from you. Feel free to submit any questions you may have as a [new issue](https://github.com/RConsortium/submissions-pilot3-adam-to-fda/issues/new/choose) in our Pilot 3 github repository or you may find any of the Pilot 3 team members in [Pharmaverse slack](https://pharmaverse.slack.com/archives/C030EB2M4GM).
+
+## Learnings from Pilots 1 through 3
+
+In the three pilots, for various TLFs, the working group members intentionally created different tables in different formats using various open-source R packages. The FDA staff successfully accepted and reproduced the results generated from these different open-source packages. However, though not in scope of these Pilots, we want to share awareness that sponsors are responsible for selecting open-source packages that demonstrate sufficient reliability. Further information on this can be found in the [R Validation Hub](https://www.pharmar.org/), formed in 2018 by the PSI AIMS Special Interest Group and supported by the R Consortium. It offers tools like [{riskmetric}](https://www.pharmar.org/posts/news/updates-aug-2024/) to quantify the “risk” of R packages and a user-friendly R Shiny app, [{riskassessment}](https://www.pharmar.org/riskassessment/), to evaluate package reliability.
+
+The majority of FDA staff feedback falls under the following themes :
+
+1.  Clear ADRG documentation on computing environment, package dependencies, and expected warnings
+2.  Clear documentation on data processing rules and statistical method implementation
+3.  Good statistical practice in confirmatory trials, such as avoiding the possibility of “p-hacking” 
+
+For future submissions using open-source languages, it is recommended to give special attention to recommendation theme 1. Recommendation themes 2 and 3 are language-agnostic and should always be followed, regardless of the programming language used. All of these themes fall in line with the FDA’s [Statistical Software Clarifying Statement](https://rconsortium.github.io/submissions-pilot3-adam/main/articles/statistical-software-clarifying-statement.html).
+
+## Upcoming Pilots
+
+As a next step, the R Consortium R Submission Working Group initiated [submission pilot 4](https://rconsortium.github.io/submissions-pilot4/), to explore the use of novel technologies such as Linux containers and web assembly to bundle a Shiny application into a self-contained package, facilitating a smoother process of both transferring and executing the application.
+
+## The R Consortium R Submission Working Group
+
+The [R Consortium R Submissions Working Group](https://rconsortium.github.io/submissions-wg/) is focused on improving practices for R-based clinical trial regulatory submissions.
+
+To bring an experimental clinical product to market, electronic submission of data, computer programs, and relevant documentation is required by health authority agencies from different countries. In the past, submissions have been mainly based on the SAS language. 
+
+In recent years, the use of open source languages, especially the R language, has become very popular in the pharmaceutical industry and research institutions. Although the health authorities accept submissions based on open source programming languages, sponsors may be hesitant to conduct submissions using open source languages due to a lack of working examples.
+
+Therefore, the R Submissions Working Group aims at providing R-based submission examples and identifying potential gaps during submission of these example packages. All materials, including submission examples and communications, are publicly available on the R consortium Github page: [https://github.com/RConsortium](https://github.com/RConsortium) .
+
+The R consortium R submission working group includes members from more than 10 pharmaceutical companies, as well as regulatory agencies. More details of the working group can be found at: [https://rconsortium.github.io/submissions-wg/](https://rconsortium.github.io/submissions-wg/) .
+
+The R consortium R submission working group is open to anyone who is interested in joining. If interested, please contact Joseph Rickert at [email protected]. 
+
+## Pilot 3 FDA Reviewers
+
+FDA reviewers included  
+
+[Hye Soo Cho](https://www.linkedin.com/in/hye-soo-cho/),  [Paul Schuette](https://www.linkedin.com/in/paul-schuette-40aa838/), and [Youn Kyeong Chang](https://www.linkedin.com/in/youn-kyeong-chang-885785159/).  
+
+## Pilot 3 Developers
+
+The Pilot 3 development team included [Joel Laxamana](https://www.linkedin.com/in/jlaxamana/) (Project Lead, Roche), [Robert Devine](https://www.linkedin.com/in/robert-devine-50b0b931/) (J&J) , [Benjamin Straub](https://www.linkedin.com/in/ben-straub/) (GSK) , [Kangjie Zhang](https://www.linkedin.com/in/kaz462/) (Bayer) , [Thomas Neitmann](https://www.linkedin.com/in/thomas-neitmann/) (Roche), [Phanikumar Tata](https://www.linkedin.com/in/tataphani/) (Syneos), [Steven Haesendonckx](https://www.linkedin.com/in/stevenhaesendonckx/) (J&J), [Yutong Liu](https://www.linkedin.com/in/yutong-liu-a25b68a8/) (Moderna), Lei Zhao (Roche), [Nicole Jones (Merck)](https://www.linkedin.com/in/nicolekjonesmph/), [Benjamin Wang (Merck),](https://www.linkedin.com/in/bingjun-wang-2b9783147/) [Dadong Zhang (Illumina)](https://www.linkedin.com/in/dadong-zhang-48b937201/), [Declan Hodges (GSK)](https://www.linkedin.com/in/declan-hodges/).

posts/r-ladies-bariloche-in-argentina-fostering-a-different-approach/index.qmd

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+---
+title: "R-Ladies Bariloche in Argentina: Fostering a Different Approach to  Leadership"
+description: "Lina Moreno, founder and organizer of the R-Ladies Bariloche chapter in Argentina, recently shared her journey with the R Consortium."
+author: "R Consortium"
+date: "09/06/2024"
+---
+
+![](lina.jpg)
+
+[Lina Moreno](https://www.linkedin.com/in/lina-moreno-azocar-81a5aa276/?originalSubdomain=ar), founder and organizer of the [R-Ladies Bariloche](https://www.meetup.com/es/rladies-bariloche/) chapter in Argentina, recently shared her journey with the R Consortium. A biologist focusing on evolutionary ecology, she discussed her experience building a local R community, the challenges of maintaining engagement post-pandemic, and her efforts to foster discussions on leadership and gender equity within academia. Through her work, she aims to create an inclusive space for women in data science and strengthen the R community in Bariloche.
+
+**Please share your background and involvement with the RUGS group.**
+
+I am a biologist working on evolutionary ecology, I did a bachelor in Sciences in another Argentinian province and then moved to Bariloche to start my PhD. (That was 16 years ago!) I spent a couple of years working in the field (I study reptiles, mainly lizards, and their adaptations to cold environments), and then I had to analyze the data. When I started my main analysis, I could only do it in R. At that time, my boss told me to start with R immediately, so I started searching online. I am doing this kind of work in my home country, so finding resources was complex. I had to work on a comparative analysis and phylogenies, which was difficult initially. However, I started studying and meeting people who taught me, which was awesome. 
+
+After several years, I encountered a problem I couldn’t resolve. I turned to Google and found a helpful community of ladies. They assisted me a lot and saved me from a tight spot. After some communication, they suggested starting an R-Ladies community in Bariloche. I met with them in person when I traveled to Buenos Aires. They convinced me to start a Bariloche chapter, and by the end of 2019, a few of my colleagues and I, mainly biologists working in the same area, created the Bariloche chapter.
+
+![](chapter.jpg)
+
+**What are some challenges you have faced in organizing this group?**
+
+We are currently facing some difficulties as people seem unwilling to get involved. As a result, we are exploring new strategies such as combined meetups (online and in person), and together with other R-Ladies groups. We also plan to organize three or four meetups this year. Despite our efforts, we are getting discouraged by the lack of response, but we will see how it goes.
+
+During the pandemic, there were five organizers, three of us with young children, so it was pretty difficult. We started a study group for the [R for Data Science](https://r4ds.hadley.nz/) book, which had recently been translated into [Spanish](https://es.r4ds.hadley.nz/). We also organized meetups, mainly led by us. Surprisingly, there was good attendance during the pandemic, with around 40 people each time, similar to before the pandemic. However, after returning to in-person meetups, the attendance dropped significantly. The most crowded meetup had only 15 people, whereas before, we used to have two meetups on the same subject, both with 40 attendees.
+
+![](meetup.png)
+
+We are attempting to integrate virtual and in-person components, which has proven challenging. We aim to introduce a beginner’s course in R through a meetup to help attendees gain confidence for future meetups. Our meetups typically have a good turnout, but there is a lack of interest in specific topics, particularly those related to gender bias and women’s issues. Despite this, we are putting in a significant effort. Last year, we participated in a round table during a conference in Bariloche, focusing on gender bias and the difficulties of being a woman in Academia, and it received a lot of support, especially from women. The rest of the group is currently working on documenting our experience at that round table. I am not participating as I have been busy with other responsibilities.
+
+Last year we surveyed people on how they feel R-Ladies is contributing to their careers, its influence on leadership abilities, their reasons for abandoning our events, or why they were too busy to attend. We have received some responses, but not as many as we expected.
+
+However, we have enough data to write a paper about it. We’re also looking into the topic of leadership. We are opening our minds and exploring the possibilities of supporting the R community here in Bariloche, but it’s quite challenging at the moment.
+
+**Can you share what the R community is like in Argentina?** 
+
+The field of artificial intelligence and machine learning is rapidly evolving, which greatly helps incorporate knowledge in R. The leading software used for this purpose is R and Python. R is more popular than Python, as it has been around longer and is more user-friendly. Many people from academia with expertise in machine learning are transitioning to private industries. Regarding statistical analysis in biology, tools such as the [Vegan](https://cran.r-project.org/web/packages/vegan/vegan.pdf) package and those incorporating [GAM (Generalized Additive Models)](https://m-clark.github.io/generalized-additive-models/application.html) are commonly used. Tools that can handle multiple effects simultaneously are in high demand in ecology.
+
+![](community.jpg)
+
+**Would you like to talk about any recent activity from the group?**
+
+It was exciting what happened after the conference we participated in. As women, we are trying to maintain an open community. Initially, the organizers needed to learn how to manage an open group without a leader or a head, where everyone is considered equal. The participants ranged from students to established researchers, which ignited discussions about leadership and how women and minority groups navigate the world. We are accustomed to a robust and assertive leadership style, often associated with being at the top. However, as women, we wanted a different kind of leadership. This led to discussions on creating a new type of leadership that doesn’t adhere to the traditional patriarchal model. The manuscript the group is working on currently revolves around creating a new style of leadership that focuses on nurturing individuals to become better persons, researchers, or workers. 
+
+The topics discussed in the manuscript revolve around how we can lead differently. These discussions were not limited to our group; we engaged with several groups from Argentina and Spain who also expressed a similar desire for a different kind of leadership. It is interesting to note that as women and minority groups, we want to be in positions to make meaningful decisions, especially given that our work as biologists primarily tackles environmental issues. Despite historically shying away from more traditional forms of leadership, we are now advocating for different styles. This shared sentiment has brought us closer to other minority groups, and we believe it’s an important topic that needs further discussion. It’s important to recognize that women have a different approach, and it doesn’t make us weaker than men; it simply signifies that we have a unique way of contributing.
+
+## How do I Join?
+
+R Consortium’s R User Group and Small Conference Support Program (RUGS) provides grants to help R groups organize, share information, and support each other worldwide. We have given grants over the past four years, encompassing over 68,000 members in 33 countries. We would like to include you! Cash grants and meetup.com accounts are awarded based on the intended use of the funds and the amount of money available to distribute.
+
+[Learn more](../../all-projects/rugsprogram.qmd)