This fall, the R Consortium’s support for advancing data science in medicine continues with the third of three exceptional events, pulling together experts in their fields, including the Covid-19 Data Forum, R/Medicine, and R/Pharma.
What is R/Pharma?
R/Pharma is an ISC working group under the R Consortium. The entire event is a community-lead effort and 100% volunteer run. R/Pharma is vendor neutral and very much an academic conference. Harvard has been very helpful in hosting the event.
August 27-29, 5:30am PDT / 8:30am EDT / 2:30pm CEST – Register now!
Brought to you by the Children’s Hospital of Philadelphia, Yale School of Public Health, and the R Consortium, the R/Medicine conference encourages the adoption of statistical modeling and reproducible data processing in clinical practice.
R is the gold standard in reproducible research in academia and industry and has powerful capabilities to create highly-customizable interactive analytic dashboards, as well as predictive models that employ machine learning, deep learning, and artificial intelligence.
Presentations will showcase how the R ecosystem is currently leveraged in medical applications including clinical trial design and analysis, personalized medicine, the development of machine learning models using laboratory and patient record data, and reproducible research.
Hosted by the COVID-19 Data Forum/Stanford Data Science Initiative/R Consortium
COVID-19 is the first pandemic to occur in the age of open data. Public health agencies around the world are releasing case counts to the public, and scientists are providing analyses and forecasts in real-time. However, the content of this data has so far been limited to simple metrics like cases, deaths, and hospitalizations at coarse geographic and demographic scales. To drive the next phase of COVID-19, scientists need access to higher-dimensional patient-level data, so we can understand how the virus causes disease, why are some more at risk than others, when and how is transmission occurring, what therapeutics are more likely to work, and what healthcare resources are being used. But sharing such data brings up tremendous challenges in terms of patient privacy and data standardization. The COVID-19 Data Forum, a collaboration between Stanford University and the R Consortium, is hosting the event “Beyond case counts: Making COVID-19 clinical data available and useful” to push the conversation forward on these issues. The event will include talks by representatives from international collaborative teams who are working to collect and share detailed clinical and biological data from individuals with COVID-19. The event will be open to the public, and is part of a continuing series focusing on data-related aspects of the scientific response to the pandemic.
Jenna Reps, Observational Health Data Sciences & Informatics (OHDSI) Consortium /Janssen R&D
Andrea Ganna, COVID-19 Host Genetics Initiative/Harvard Medical School/Finland Institute for Molecular Medicine
Ken Massey, EndPandemic National Data Consortium/Saama Technologies
Ryan Tibshirani, DELPHI epidemic forecasting group/Dept of Statistics, Carnegie Mellon University
Thank you to Carlos Ortega, Principal Data Scientist, Teradata, for providing this summary and pictures from the conference
The XI Conference of R Users (XI Jornadas de Usuarios de R), held November 14 – 16, Madrid, Spain, was organized by the Asociación Comunidad R Hispano. The ambitious program and the invited international speakers made the participation massive, exceeding 200 attendees. The Conference was divided into two locations, Repsol (Spanish Gas and Oil company) and UNED (Spanish Distance Learning University), highlighting the university-business combination that has been one of the key factors in the success of the conference.
On Thursday, November 14, the opening ceremony was held at the Repsol Campus auditorium and attended by Emilio López Cano (president of the Asociación Hispano R Community), Julio Gonzalo (deputy vice chancellor for research at UNED), Enrique Dameno (Director of Digitalization and Integrated Customer Management of Repsol), and Teresa García (Repsol).
Max Kuhn (R Studio) gave a lecture on “Modeling in the Tidyverse,” and after that, in the round table “R in business,” the crucial role of data scientists in solving problems in diverse areas was covered. Raúl Vaquerizo (Pont Group), Noelia Ruiz (Mutua Madrileña), Jorge Ayuso (Telefónica España), Enrique Lasso (Repsol) and Carlos Ortega (Teradata) participated in the round table.
On the 15th and 16th, at the School of Education of the UNED, an extensive and vibrant program was developed with workshops, communications sessions, “lightning sessions,” poster sessions, round tables and invited conferences. Bernd Bischl (University of Munich) gave a lecture on MLR3, Jo-Fai Chow (H2O.ai) presented “Automatic and explainable machine learning in R,” and Max Kuhn gave a workshop on “Designing R modeling packages.”
Following the multidisciplinary philosophy of using R to handle any kind of data, communications sessions dealt with applications in genetics, data analysis, model and project management, society and culture, surveys and education, medicine and veterinary and economics and company. In addition to these monographic sessions, the “lightning sessions” dealt with many different topics.
A round table on Data Journalism was held to close the conference, moderated by Leonardo Hansa (R-Hispano) in which Virginia Peón (Indigitall), Alba Martín (Newtral), Antonio Delgado (Datadista) and Carmen Aguilar (Sky News) participated. The importance of knowing how to treat the data in an appropriate and honest way was highlighted, so that information that reaches the public is truthful.
In the closing ceremony, the prize for the Best Young Work of the Conference was announced, which went to Rocío Aznar Gimeno (Technological Institute of Aragon) for the work “Multilevel mixed models: An application of the lme4 library to estimate the fetal weight percentile in twin pregnancies.”
Michael: My first exposure to medicine using R came from my internship at Revolution Computing (now Microsoft R). At the time most companies used SAS and Revolution had started providing validated versions of R and some packages, similar to SAS’s validation process, which would allow R to be used in submissions to the FDA. Since then, the rules have changed, and R sees a lot more use in this space because it provides inexpensive access to powerful tools for designing and analyzing health, genetic, and clinical data.
We are currently using and developing these tools to find subtypes in immunotherapy studies for treating cancer. Patients can respond very differently to cancer therapies depending which stage of cancer they have, how many previous treatments they’ve had, and the diversity of the tumor environment. By understanding how factors like these are related to prognostic heterogeneity, we can do a better job prescribing people with cancer the most effective possible treatments.
What drove you to create an event to bring together the R medicine community?
Michael: This conference was inspired by R/Finance. The committee does a fantastic job of providing an entertaining and informative conference. The richness and diversity of the talk subjects show how vast finance is and, at the same time, the speakers and other attendees are completely accessible. We want to bring that same sense of inclusiveness and collaboration to medicine, where sometimes practices become siloed. We hope people realize that we, in medicine, are also part of a rich large and rich area of research and we hope the conference helps to jell the community.
What is the organizing committee’s goals and measures of success for this first event?
Michael: Our goal for the first year to better understand the community as a whole. We are expecting submissions from the clinical trials community, the genetics and omics community, and the epidemiology community. We are hoping we get submissions from both academia and industry. We want to see how people are using R to advance human health. I’ll consider the conference a success if attendees find at least one talk where they are surprised, entertained, and delighted by a use of R that hadn’t occurred to them.
Our other goal is to reinvest in the conference. If we are successful, and we are able to secure enough sponsorship, then we would like to make it easier for people to attend the conference. This would include providing more awards for travel, particularly for students.
How do you see working with R Consortium as critical for driving consensus and critical mass in the medicine community?
Michael: The R Consortium has become the umbrella for the entire R community. Their approval lets the community know that this is the conference to go to if you are using R in Medicine.
We thank Micheal for his time, and hope that if you are in the medical community using R that you look to attend this event.
End of August here in North America means summer is winding down, kids are headed back to school, and the annual Open Source Summit hosted by the Linux Foundation is happening. For those not familiar with the event, Open Source Summit North America is the leading conference for developers, architects and other technologists – as well as open source community and industry leaders – to collaborate, share information, learn about the latest technologies and gain a competitive advantage by using innovative open solutions.
Open Source Summit, being held this year in Vancouver from August 29th – 31st, 2018, connects the open source ecosystem under one roof. It covers cornerstone open source technologies; helps ecosystem leaders to navigate open source transformation with the Diversity Empowerment Summit and tracks on business and compliance; and delves into the newest technologies and latest trends touching open source, including networking, cloud-native, edge computing, AI and much more. It is an extraordinary opportunity for cross-pollination between the developers, sysadmins, DevOps professionals and IT architects driving the future of technology.
R Consortium is excited to participate in this event in two key ways:
An explicit goal of the R Consortium is to help create a welcoming space for everyone, no matter their race, ethnicity, gender, gender identity and expression, socio-economic status, nationality, citizenship, religion, sexual orientation, ability, or age. Diversity and inclusion are essential to foster true collaboration, move ideas forward, and create long-term sustainable community.
R Consortium recently sponsored R/Finance 2018, where it was found that there were insufficient diversity and inclusion practices, including the absence of a prominently displayed Code of Conduct. This illuminated shortcomings with our existing processes for sponsoring conferences. We are troubled and disappointed to have sponsored a conference that does not reflect our core beliefs in diversity and inclusion.
The Infrastructure Steering Committee (ISC) has approved the creation of a new working group to address diversity and inclusion issues in the R community. The R Community Diversity and Inclusion Working Group (RCDI-WG), which will include members from R Community groups that promote diversity, such as R-Ladies and FORWARDS, event organizers, and key industry members, will focus on three areas:
Work with conferences organizers to ensure diversity is addressed as a priority in both their program committees and speaker lineups.
Establish recommended Code of Conduct and Diversity Guidelines for R Community events, which will be adopted by the R Consortium and required for any event that the R Consortium participates in.
Have an ongoing conversation on opportunities to drive diversity and inclusion across the R Community.
This group is open to any member of the R community, and you can join by signing up for the mailing list. The group plans to have a kickoff meeting soon to work on the Code of Conduct and Diversity Guidelines, with the goal to have them established later in summer 2018. Look for updates on progress on the R Consortium blog.
In just one year, the R Consortium through the R User Group Support program sponsored 76 R user groups and 3 small conferences with cash grants totaling just under $30,000. This program aligns with the R Consortium mission of fostering the continued growth of R community and the data science ecosystem, and has already helped bring more people to using R and contributing to the community.
Coming off a successful 2017, we are pleased to announce the opening of the 2018 program today. While the structure of the 2018 program is similar to last year’s program with the multiple levels of support, we have enhanced the program based on feedback from last year’s funded user groups.
Complimentary Meetup.com Pro Account
After a year of supporting user groups, we’ve found that the primary cost for each group is having a page on meetup.com or thier own website ( though the majority prefer the meetup.com platform ). This leaves less funds available things like meetup space, food, or even swag, and thus put more of a burden on the group leaders to attract people to the group.
This year we’ve leveraged our relationship with the Linux Foundation, and now will provide each user group a complimentary meetup.com Pro account. Leveraging this not removes one less cost concern for group leaders, but it will also better enable us to promote user groups through the many features the platform provides for groups. For all the details of the program, eligibility requirements for the three levels of user group grants, the schedule of grants and the details of signing up for the meetup.com pro account please see the R Consortium’s R User Group Support Program webpage.
Small Conference Support
We’ve also seen an increase in the number of smaller, regional focused R conferences happening around the world. Grassroots events like this are critical for sustainability in the R community, but need financial support and community awareness to be successful. Several reached out last year and we provided funding with excess funds in the program with greatresults.
These events perfectly align with the mission of the R User Group Support program, we’re formally expanding it this year to provide cash grants in the $500 to $1,000 range to continue to encourage small, R-focused conferences and meetings organized by non-profit or volunteer groups are the world. You can find out more about this new piece of the program on the R Consortium’s R User Group Support Program webpage.
Length of Program
R Consortium will begin taking applications for both R User Group Support and Small Conference Support today. Applications will be accepted through September 30, 2018.
The R Consortium was happy to be a sponsor rOpenSci’s ozunconf last October in Melbourne. You can read about the “unconference” on rOpenSci’s blog and follow some of the projects begun at the event here.
Through the RUGS program, R Consortium was honored to be a sponsor for this event. If you have an smaller event you would like support for, stay tuned for the official program announcement in early 2018.
Editor’s Note: This post comes from Nicoleta Caragea, uRos2017 conference organizer. uRos2017 is a conference held in November 2017 for collaboration around the use of R in Romania. Through the RUGS program, R Consortium was honored to be a sponsor for this event. If you have an smaller event you would like support for, stay tuned for the official program announcement in early 2018.
The International Conference New Challenges for Statistical Software – The Use of R in Official Statistics – uRos2017, the fifth in a series of events, organized at Romanian NIS dedicated to the use of R Project in Romania, was held between 6-7 of November 2017. The conference, which provides a public forum for researchers from academia and institutes of statistics, brought together over 60 participants from 20 countries (Austria, Canada, Columbia, Croatia, France, Deutschland, Italy, Irak, Japan, Lithuania, Luxembourg, Morocco, Netherlands, Norway, Poland, Romania, Spain, Switzerland and Turkey). Moreover, representatives from Eurostat and other international organizations (United Nations/UNIDO and FAO) attended as guests.
Not only was uRos2017 an opportunity to develop new ideas and cooperation in the field of official statistics, the event once again demonstrated the significant role played by National Institute of Statistics in the official statistics and gives Romania a prominent spot on the map of useRs.
Throughout the five editions of the event, the international participation has increased exponentially.
The event hosted, besides the presentations, eight workshops lectured by prestigious professionals from official statistics and academia:
Valentin Todorov (United Nations Industrial Development Organization), R in the statistical office: the UNIDO experience
Bernhard Meindl (Statistics Austria), Current developments in R-packages sdcMicro and sdcTable for statistical disclosure control
Marcello D’Orazio (Food and Agriculture Organization of The United Nations), Outlier detection in R: some remarks
Camelia Goga (Institut de Mathématiques de Bourgogne, Université de Bourgogne, France), Survey sampling techniques with R
Hervé Cardot (Institut de Mathématiques de Bourgogne, Université de Bourgogne, France), Fast robust center estimation, clustering and Principal Components Analysis with large samples in high dimension with R
Bogdan Oancea (National Institute of Statistics/University of Bucharest, Romania) and Ciprian Alexandru (National Institute of Statistics/Ecological University of Bucharest, Romania), From unstructured data to structured data – Web scraping for Official Statistics
Elena Druică (University of Bucharest, Department of Economic and Administrative Sciences, Romania), Working with the ‘pglm’ package in R. Explaining the number of nosocomial infections in Romanian hospitals
The proceedings of the conference, which took place in parallel sections and included 22 presentations and 8 thematic workshops, will be published in two issues of Romanian Statistical Review: no. 4/2017 and no. 1/2018. The first one has already been published and handed to the participants during the conference, and the second one will be released in March 2018.
A novelty of this year’s edition is that the conference joined with “International Conference On Computing, Mathematics And Statistics 2017” (iCMS2017), held in Langkawi Island, Malaysia. Nicolaas Jan Dirk Nagelkerke, Matthias Templ and Martin Everett delivered keynote talks at uRos2017 Asia Pacific/iCMS2017.
As a satellite event of uRos2017, a meeting between Japan’s, Austria’s (UN/UNIDO) and Romanian NIS representatives took place on November 8. The meeting was an opportunity to exchange ideas and knowledge. The discussions regarded the following subjects:
Modernization of Romanian Official Statistics
The use of R in statistical surveys
Data editing (outlier detection, imputation etc.)
Generation of statistical reports using R with Sweave/knitr
Online data collection for business statistics surveys