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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!

femR: Bridging Physics and Statistics in R with Support from the R Consortium

By Blog

Laura M. Sangalli is a professor of Statistics at Politecnico di Milano, Italy. Her research interests include functional data analysis, high-dimensional and complex data, spatial data analysis, and biostatistics. With a team composed by Aldo Clemente, Alessandro Palummo and Luca Formaggia at Politecnico di Milano, and Eleonora Arnone at the University of Turin, Laura created the femR, a package for applying Finite Element Methods to solve second-order linear elliptic Partial Differential Equations over two-dimensional spaces. A grant from the R Consortium supported this project.

“femR: Finite Element Method for Solving PDEs in R” was funded by the R Consortium in 2022. What is the current status?

The femR project, generously supported last year by the R Consortium, aimed to develop a package implementing Finite Element Methods (FEM) for solving simple yet flexible forms of Partial Differential Equations (PDEs), specifically second-order linear elliptic PDEs across general two-dimensional spatial domains. This goal has been successfully achieved, and the project is now complete. However, development on the femR package continues, extending beyond the original proposal funded by the R Consortium. 

The femR package is accessible in its GitHub repository at https://github.com/fdaPDE/femR. It includes documentation and initial vignettes. Key functionalities of femR, as outlined in the proposal, are:

  • Providing an interface with the RTriangle package, enabling users to build two-dimensional triangular meshes from the boundaries of spatial domains.
  • Constructing finite element bases over these triangulations.
  • Solving elliptic PDEs using finite element discretization.

The project’s broader objective was to introduce the R community to a foundational tool for applying Finite Element Methods to certain PDE problems. This is especially relevant considering the R community’s prevalent use of the deSolve package, which employs finite differences for discretization in differential problems.

During the development of femR, the team engaged with Karline Soetaert and Thomas Petzoldt, the authors of deSolve. These interactions led to the realization that the deSolve community had a keen interest in space-time PDE problems—a domain femR had not initially planned to address in its original proposal. Responding to this need, the team began developing capabilities within femR for solving time-dependent PDE problems, expanding the package’s scope and utility beyond its original mandate.

In summary, the femR project has not only achieved its primary goal of providing a tool for solving specific types of PDEs using FEM in the R environment but has also adapted and grown in response to community feedback and evolving scientific needs, particularly in the realm of space-time PDE problems.

What is your background, and why did you decide to propose this project?

My main research interest lies in developing Physics-Informed statistical models for spatial and functional data observed over complex multidimensional domains, such as the brain’s surface, the gray matter’s volume, a spatial region with a complex conformation, or a road network. In regularizing terms, these Physics-Informed statistical models use PDEs to embed knowledge of the Physics of the underlying phenomenon and the geometry of the domain into the statistical models. 

I love these methods since they bind together two of the richest and most powerful modeling frameworks, from statistics and mathematics. On the one hand, the regression/maximum likelihood framework for the empirical model, and on the other hand, PDEs are the most powerful mathematical tool to model complex phenomena and behaviors. 

The Physics-Informed statistical models we develop leverage on Finite Elements discretizations of the estimation problems, and they are implemented in the R package fdaPDE, which is available from CRAN for almost ten years now. This package fills a significant gap in R’s capabilities, as there was a notable absence of direct implementations of FE methods for solving PDEs, as also highlighted in the CRAN Task View on Differential Equations.

As we already discussed, deSolve enables solving some simple forms of PDEs through finite differences. However, finite differences work over regular tensorized domains (rectangular domains) and are not the natural choice to solve PDEs on more complex domains. Moreover, they cannot achieve the same level of accuracy of FEM.

Therefore, the need for an R package capable of solving PDEs using the FEM to complement deSolve. The development of femR addresses this need. It provides solutions for PDEs on complex domains and enhances accuracy, aligning perfectly with my research interests in advancing sophisticated, Physics-Informed statistical models.

Finite Element Methods (FEM) are used to solve partial differential equations (PDEs). In what situations is it used most often? Can you give some basic examples of when you would use R and FEM to solve a PDE?

Partial Differential Equations (PDEs) are extensively used in all sciences and engineering fields to model complex phenomena behaviors. However, PDEs do not usually possess closed form solutions and are typically solved numerically through discretization methods. 

The Finite Element Method stands out as one of the most popular, computationally efficient, 

and versatile approaches for discretizing and solving PDEs. (Editor’s note: In applied mathematics, discretization is the process of transferring continuous functions, models, variables, and equations into discrete counterparts.) This method enables the solution of PDEs on multidimensional domains with complex shapes and various boundary conditions with high accuracy.

The femR package I’ve been discussing exemplifies the application of FEM in addressing a range of partial differential problems. It can handle both spatial and spatiotemporal diffusion-transport-reaction problems. A common and straightforward example is heat conduction, modeled by the well-known heat equation. This capability finds numerous applications in various fields.

In environmental sciences, for instance, femR can be utilized to study the dispersion of pollutants released in water or air, which are transported by currents or winds. It is also adept at modeling temperature variations and pressure. In biomedicine, femR could be used to study electrophysiology and the mechanics of organs, including tumor growth dynamics.

These examples demonstrate the wide-ranging applicability of femR in solving complex PDEs across diverse scientific disciplines. The package’s ability to handle simple forms of elliptic and parabolic PDEs and more complex PDE scenarios makes it a valuable tool in the scientific community. Moving forward, there are plans to continually enhance femR, expanding its scope to address increasingly complex differential problems and applying it to additional fields of study.

Since FEM implementations were not available in R in the past, statisticians had to use external software. Now you can do this using R. Can you explain what the before and after looks like for a statistician who is using R? How big of a change is it?

Including PDEs in data analysis methods allows us to incorporate problem-specific information that may come from the problems in physics, chemistry, mechanics, or morphology of the problem into the statistical model. These physics-informed methods are gaining increasing attention from the scientific community. For example, Physics-informed Neural Networks represent a cutting-edge research direction in Artificial Intelligence. 

PDEs are not only pivotal in advanced fields like AI but are also fundamental components of epidemiological models. Additionally, they are being increasingly used in spatial data analysis and functional data analysis. These applications are particularly useful for modeling data observed over complex domains and addressing issues like anisotropy and non-stationarity.

As the complexity of data analysis challenges our community faces grows, there is an escalating need for new data analytics methods that effectively combine empirical and physical models. It’s becoming increasingly important for statisticians to be familiar with PDEs as a fundamental tool for modeling complex phenomena.

In this evolving landscape, the femR package plays a crucial role. It offers a built-in toolbox within the R environment for solving PDEs using Finite Element Methods (FEM), thus eliminating the need for users to depend on external environments. We have invested significant effort in creating an intuitive R interface. This interface simplifies formulating differential problems, making it as easy as writing them down on paper. We are confident that the availability of femR, a native and user-friendly package, will greatly aid and assist the statistical community in developing new physics-informed models.

FemR complements deSolve (https://desolve.r-forge.r-project.org/). Are there examples and documentation to help users with femR?

We have already prepared documentation and created initial vignettes for our package, available on the GitHub repository at https://fdapde.github.io/femR/.  We plan to continue enriching these vignettes with more content.

We aim to offer a tool that may complement deSolve. As mentioned earlier, we have been discussing with the authors of deSolve to understand the needs of the deSolve community. We decided to delay the release of the package on CRAN to enable a testing period in which interested users may start using the package, and we may get feedback. These are crucial as they may help us tailor the package in the most convenient way to the community. This testing period will help us avoid potential backward compatibility issues that we might otherwise encounter and ensure better integration with deSolve. 

As I mentioned, we are also actively working on incorporating other functionalities that interest the deSolve community. In particular, as part of the future development of the package, we will aim to introduce non-linear PDE terms, such as logistic terms. Indeed, adding non-linear forcing terms will enable the modeling of various biologically relevant problems, that cannot currently be tackled within femR, perhaps within the next year.

How was it working with the R Consortium? Would you recommend it to other people who work with the R programming language? Will you continue to develop femR?

We’ve had a great experience with the R Consortium, and we would recommend applying for funding to anyone who has the potential to develop packages that can benefit the R community. 

Furthermore, the grant enabled us to fund young collaborators, offering them the opportunity to gain research experience and encouraging them to pursue a Ph.D. In particular, through the grant, we supported two graduated students, Aldo Clemente and Alessandro Palummo, co-authors of femR. Aldo and Alessandro are already enrolled in a Ph.D. here at Politecnico di Milano, so we will keep working on femR and enlarge the scope of this new toolbox in several different directions toward more complex PDEs to model phenomena over different domains. We believe this may support the R community in developing new cutting-edge data analysis methods, interfacing statistical methodology and physical models. This will facilitate exploring new avenues of research.

There is a new frontier here in science! Seeds of something big! 

About ISC Funded Projects

A major goal of the R Consortium is to strengthen and improve the infrastructure supporting the R Ecosystem. We seek to accomplish this by funding projects that will improve both technical infrastructure and social infrastructure.

R Implementation in China’s Pharmaceutical Industry in 2023

By Blog

Guest blog contributed by Wenlan Pan, Statistical Programmer Analyst, Johnson & Johnson

Transforming the Landscape – The Rise of R in the China Pharmaceutical Industry

In recent years, the China Pharmaceutical Industry has undergone a significant transformation in data analysis practices, driven by the growing interest in utilizing R, a powerful statistical programming language, as an alternative to SAS. This article aims to delve into the significant strides made in R implementation within the industry in 2023, focusing on key meetings, notable examples of R implementation, and panel discussions surrounding the utilization of sharing R-generated reports and the harmonious development of open-source packages. 

Key Meetings – Driving R Implementation in 2023

Several influential meetings and discussions in 2023 played a pivotal role in promoting the widespread adoption of R within the China Pharmaceutical Industry. Two meetings were specifically focused on R, while the other two had a broader scope with a growing emphasis on R-related topics. These meetings provided platforms for professionals to exchange knowledge, foster collaboration, and present innovative ideas:

1. The first China Pharma R User Group (RUG) Meeting

It was the first conference of its kind. This groundbreaking event brought together over 300 participants from Shanghai, Beijing, and online on March 31st. With 13 presentations from nine leading companies, the meeting served as a platform for professionals to share knowledge and explore innovative solutions with R for the pharmaceutical industry. It highlighted the growing importance of R in this field and allowed participants to delve into the latest developments, powerful R packages, and breakthrough methodologies that benefit the industry.

2. Open Source Clinical Reporting SummeR 2023 workshop

Hosted by Roche on August 29, this workshop emphasized the importance of open-source solutions and collaboration for clinical data reporting. Through interactive sessions, industry experts shared their experiences using open-sourced R packages like Admiral, NEST, and tidytlg, for tasks such as SDTM mapping, ADaM data creation, and TLG creation. The workshop featured eight presentations, demonstrated the effectiveness of R in generating clinical reports, and provided valuable insights into the successful utilization of open-source R packages for efficient clinical reporting.

3. Pharma Software Users Group (Pharma SUG) 2023 and PHUSE Single Day Events

These two meetings had a boarder focus, each centered around a specific theme. The first meeting focused on “New Policy, New Technology & New Opportunity”, while the second had a theme of “Standardisation-Driven End-to-End Automation”. Coincidentally, these events witnessed a surge in the number of papers and presentations dedicated to R implementation. During these meetings, professionals presented their research and experiences, highlighting how R, when coupled with domain-specific knowledge and standards, contributed to advanced analytics and navigation of complex challenges. It is worth noting that PharmaSUG 2023 also offered pre-conference training on R titled “Deep Dive into Tidyverse, ggplot2, and Shiny with Real Case Applications in Drug Development.” This training provided participants with practical skills for leveraging R’s powerful data visualization and analysis capabilities.

Exemplifying R’s Potential – Notable Examples of R Implementation

R has found wide-ranging applications in the pharmaceutical industry. Here are notable examples:

1. Regulatory Submissions and Reporting

R’s open-code nature enables the development and utilization of open-source projects focused on implementing or developing CDISC standards. In addition to writing R open codes, open-source packages are leveraged. For instance, OAK automates the mapping of CDASH to SDTM and generates raw synthetic data. Admiral, a modularized toolbox, facilitates the development of ADaM datasets in R. R packages like tidytlg make it easier to create tables, listings, and graphs (TLG) for clinical study reports. Notably, several R-based tools have already been officially recognized by the CDISC Open-Source Alliance (COSA) as open-source projects focused on implementing or developing CDISC standards. Another example is Dataset-JSON – R Package Implementation, which allows users to read and write JSON files while also providing functions to update metadata on the dataset. This could help meet the requirements of regulatory submission and other data exchange scenarios. Valuable experience in the development and implementation of such packages in practice had been shared during the meetings.

2. Statistical Analysis and modelling

R could be extensively used for statistical analysis and modeling in clinical trials since it provides a wide range of statistical functions and packages for efficacy and safety analysis. It offers alternative approaches of SAS like mixed-effect models for repeated measures (MMRM) and negative binomial regression, which may require a combination use of multiple packages but also indicate the flexibility of R considering that users can freely choose any packages as they prefer. Furthermore, R allows for the development of custom packages tailored to specific analysis needs, providing specialized functionalities, and enhancing overall data analysis processes.

3. Quality Control and Validation

R offers comprehensive tools and functions for ensuring stringent quality control and validation processes in data analysis and reporting. This is particularly useful during the transition period when validating the outputs produced by SAS using R. R’s built-in validation functions, combined with customized scripts, provide confidence in the accuracy and consistency of results. For example, R allows for the comparison of data frames and reports, offering a fast and efficient way to execute validation checks and generate a summary report, which is user-friendly and flexible.

4. Data Visualization and Interactivity 

R’s Shiny package has revolutionized data visualization in the pharmaceutical industry.  Going beyond traditional methods, Shiny enables the development of interactive dashboards. This empowers stakeholders to dynamically explore and interpret data, facilitating timely, data-driven decision-making. There are several examples of R shiny apps shared during the meetings, such as those for Prostate-Specific Antigen (PSA) navigation, baseline shiny framework for standard safety tables and figures as well as efficacy modules, and support popPK analysis even for users without known any programming knowledge.

Panel Discussion – Report Sharing and Open-Source Package Development

During the meetings, concerns were also proposed, and panel discussions were conducted with the joined experts from various companies. 

Concerns were expressed about the direct use of R for internal and external sharing of reports.  Multinational pharmaceuticals and regulators are exploring and attempting to use the new R language written programs to make submissions, marking a shift from submissions that were mainly based on the SAS language in the past. The industry actively engaged in this process and expected the results of pilot studies to evaluate the feasibility and effectiveness of this transition.

Balancing the development of open-source packages and utilizing packages from other companies is another concern within the industry. Organizations are better off adopting an ecosystem-driven approach, evaluating the strengths and weaknesses of different solutions. Active participation in the open-source community empowers organizations to contribute to the development of packages, thereby advancing the industry’s collective knowledge and capabilities.

Embracing a Data-Driven Future in the China Pharmaceutical Industry

The pharmaceutical industry in China is rapidly adopting R for data analysis. Key meetings and discussions have forested collaboration, knowledge-sharing, and innovation. Examples have showcased the vast array of applications, illustrating how R has been implemented in regulatory submissions and reporting, statistical analysis and modeling, quality control, and validation, as well as data visualization and interactivity. Concerns also arise and have been discussed regarding report sharing and the balance between the development and utilization of open-source packages. Embracing R as an essential tool ensures competitiveness and positions organizations at the forefront of scientific progress in the evolving pharmaceutical landscape.

About the Author 

Wenlan Pan is a Statistical Programmer Analyst at Johnson & Johnson with over two years of programming experience in the pharmaceutical industry, currently supporting neuroscience studies. She has been using R for seven years and received a Master of Science degree in Biostatistics from the University of California, Los Angeles.

R Validation Hub Community Meeting – December Recap

By Blog

After a brief hiatus, the R Validation Hub recently reconvened for its community meeting, celebrating a year of remarkable achievements and setting the stage for future endeavors.

In 2023, the R Validation Hub was present at these top conferences: useR!, Posit:conf, and R/Pharma. And riskassessment was awarded the title for “Best App” at Shiny Conf 2023

If you want to connect with us in 2024, please do so! The Regulatory R Repository workstream supports a transparent, cross-industry approach of establishing and maintaining a repository of validated R packages. Join us! 

Meeting Notes

 

In 2023, a new R Validation Hub structure, including Head, Executive Committee, and workstreams, was established. Doug Kelkhoff is taking over for Andy Nicholls as Head. The executive committee governs the R Validation Hug. Here are the committee members, as of August 2023:

  • Doug Kelkhoff (Chair)
  • Joe Rickert (R Consortium)
  • Preetham Palukuru (R Consortium)
  • Juliane Manitz (Communications Workstream Lead)
  • Coline Zeballos (Repositories Workstream Lead)
  • Eric Milliman (riskmetric Workstream Lead)
  • Aaron Clark (riskassessment App Workstream Lead)

Full Meeting Slides available here!

Additional Resources

R Validation website: https://www.pharmar.org/  

Thank you!

Thank you from the R Validation Hub and R Consortium Community for your support and interest in 2023. Welcome 2024!

Be Part of the Global R community!

By Announcement, Blog

Contributed post by Mike Smith, Senior Director Statistics at Pfizer

There’s likely a group of people meeting fairly near where you are right now, regardless of where you are in the globe, discussing how they use R in their work, research, or just for fun. If you feel like you’re the only person using R and struggling to keep up with latest developments or are feeling “stuck” and needing some advice or input, that’s where the growing network of R communities comes in. 

R Communities are great places to learn, share, or just meet up with like-minded people. Local and regional R community meetings like R User Groups and R Ladies tend to be smaller in size than conferences, so you are less likely to feel overwhelmed by numbers or a mismatch between your level of comfort and expertise in R compared to others. 

If you can’t make it in person, there are also online communities and groups and huge array of video content on sites like YouTube where videos of webinars and meetups are shared. So come along, sign up,and see what the global R community has to offer.

Resources

You can find local R User Groups listed here: https://www.meetup.com/pro/r-user-groups/

R Ladies groups are listed here: https://www.meetup.com/pro/rladies/ 

R Consortium YouTube channel: https://www.youtube.com/@RConsortium

R User Groups and R Ladies are sponsored through the R Consortium grants.

R in Action: Madrid R Users Group on Trends and Insights Navigating R’s Evolution and Future Trends in Madrid’s Dynamic Industry

By Blog

Madrid R Users Group (RUG) is a community of industry professionals from a diverse range of backgrounds that provides a learning and networking platform. The organizing committee of the Madrid RUG recently engaged in a conversation with the R Consortium regarding the use of R in their respective industries. The organizers, Carlos Ortega, Pedro Concejero, Francisco Rodriguez, and José Luis Cañadas shared their valuable insights about the industry’s evolving landscape of R applications.

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

Francisco: I began learning the R programming language in 1999 when I started my Ph.D. program. R was primarily used for command-line programming, but I did not use it seriously until 2012, 16 years later. Since then, I have used R in various enterprise settings, including insurance companies and banks. I have used R to process data and build models, and I continue to use it in my current role in the financial sector.

Carlos: I began my career at AT&T Microelectronics, a semiconductor plant in Madrid. We collaborated with Bell Labs, who invented R and used it heavily in the manufacturing plant. We collaborated with many colleagues, including John Chambers and his team. Some of their team members in the statistical group at Bell Labs laboratories were in our plant, sharing their code. When they started using R, we also started using it. However, the factory has since closed.

I transitioned to the consulting industry, working independently without formal affiliation to a particular sector. I analyzed data in various industries, including finance, manufacturing, and telecommunications. I worked in consulting for several years, and later with Francisco at a Spanish telecommunications company called Orange, and previously in the banking sector. We applied various models, analyses, and algorithms using distributed computing on servers and clusters. 

I am currently employed in the service sector for a multinational human resources company. We place thousands of people into employment. Since the 1990s, I have used R to model, analyze, and clean data for many years.

Jose Luis: I am a statistician employed by Telco in Orange, Spain. I have been working in Orange for approximately five years. My primary job is to work with a Spark cluster using “sparklyr”, and the H2O library “sparkling.” I am a big fan of “sparklyr,” tidyverse, and dplyr. dplyr and sparklyr are the most useful tools for my work. 

Pedro: My academic background is in psychometrics, and I have used nearly all the major statistics software, including SAS and BMDP. I came to R when I started working in data science for my previous company, Telefonica. In 2011, I began learning R on my own, and I enjoyed it immensely. I then met some people I am working with now when I started teaching psychometrics with R at the university. They thought I was crazy, but I enjoyed it, and it was a success. I then worked on many projects at Telefonica, including social network analysis with iGraph. I particularly enjoyed making prototypes with Shiny.When Shiny first appeared, it was a marvel, especially for those of us in data science who wanted to create systems, web pages, and prototypes. It was quite successful. I left Telefónica four years ago, and I miss it sometimes. Now I teach text mining and artificial intelligence at the university. I use Python for artificial intelligence, as I find it a bit easier. But I teach the rest of the machine learning and text mining with R. 

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

Carlos: As I mentioned before, we meet monthly. We work in different sectors: Francisco in insurance and finance, Jose Luis in telecommunications, me in services, and Pedro in education. Pedro previously worked in telecommunications as well. Most of the people we invite to our sessions are from industry. We invite a few people from academia from time to time, but most of our activities and recent developments are from industry. Therefore, industry is currently the focus of our group.

I joined this group because of its diversity, especially in the applied world. Many people are working on different projects, and their diverse ideas can be inspiring. In this sense, I believe that academics sometimes become too engrossed in their circles. The real-world applications of R are found by meeting people with diverse backgrounds.

Pedro: All of our meetings are recorded and uploaded on our website since 2010 or 2011. The credit for this goes entirely to Carlos who has consistently maintained this website. 

Why do industry professionals come to your user group? What is the benefit for attending?

Carlos: The most important part of the meeting is the social events that take place afterward. The meeting itself typically lasts 40-45 minutes, during which we present new things, such as applying the Spark package or H2O library. Recently, Francisco presented how to apply a scorecard method for risk models in banking. Pedro presented how to use Shiny or Shiny mixed with GLMs or other types of models. Many people attend these meetings to see how effective R is in the real world. After the meetings, we discuss the state of the industry, such as which companies are betting on R and where the good projects are. This is a great way to socialize and discuss our issues.

Pedro: Now that Carlos has introduced the topic, I believe that the debate between Python and R is pointless. In my experience, both languages can be used seamlessly, and there is no difficulty in switching between them. My experience at Telefonica has shown that the choice of language can depend on the background of the project team, but ultimately, the results are the same. However, I must mention that the documentation available for R is excellent. I believe that R has a significant advantage over any other framework in the industry for statistical modeling.

The vignettes for packages are particularly helpful, as they provide detailed information on how to use the packages. Additionally, I believe that it is much easier and faster to start doing data science in R than in Python. Python is chaotic, with different versions of the language and packages being released frequently. R is more homogenous, with backward compatibility being a priority for the R Foundation. This makes it much easier to maintain a consistent environment in R.

While Python may be easier to use for some tasks, I believe that R is the better choice for professional data science work. It is more stable, has better documentation, and is more widely used in the industry.

Shiny in Python was released this year. However, when I teach about Shiny in Python, I tell my students to read the documentation in R. This is because the two languages are very similar, with only minor differences. For example, ggplot and Shiny are both available in both languages. As a result, students can simply copy and paste code from the R documentation and use it in Python. This will allow them to quickly and easily create powerful applications.

Francisco: The process of creating training, connecting to a database, extracting data, viewing the data loosely, creating a button, and distributing all the applications to all the people in your enterprise is relatively straightforward. However, the security of the data must be taken into account. If the data is compliant with GDPR and can be shared, then it can be quickly made into an application that can be viewed on a mobile phone. This can be done in Python, but it is more difficult. I prefer to use R for training.

Jose Luis: The use of plumber or other API packages has made it easier than ever to deploy R models in production. Kubernetes and Docker have made this possible. 

Carlos: The approach to production is changing significantly with PosIt (former RStudio). Rather than having packages isolated, the focus is shifting to how to produce models in the enterprise. This means bringing R and Python closer to a real environment. These packages are making things much easier.

Pedro: For example, when I teach machine learning, I often use Python. However, when I get to mixed models, which I know José Luis is interested in, I have to recommend that students install an R library. This is because no Python library for mixed models is as comprehensive or well-developed as the ones available in R. At least two years ago, this was the case. I believe that R is currently years ahead of Python environments for statistical analysis.

What trends do you currently see in R language and your industry? Any trends you see developing in the near future?

Francisco:In my sector, banking, I remember that 15 years ago, SAS totally dominated the modeling part. Before 2010, it was the best option. It was not only a language but also a solution that allowed you to create a core model easily without coding. However, it was very expensive. Nowadays, I have noticed that R methods have been appearing in the industry since around 2015 or 2016. For example, in 2017, I was a consultant and taught a course to the regulator here in Spain. The Central European Bank wanted to use R to inspect bank entities, which was surprising to me, as I had not expected another country to use software other than SAS. Currently, we are testing R using a library created in 2020 called “scorecard,” which I believe is a powerful library.

This library, with only a few lines of code, enables building a complex model step-by-step and putting it into production easily. In my current job, I can use SAS or R. Here, given the choice, I use the easier and faster one, which is R. You can access data quickly with R, without any issues with the network. You use your computer’s memory, which gives you a lot of freedom to use the data you want.

I believe that the flexibility of this library in particular is causing many data scientists to transition to open-source. It includes people who use Python since Python has copied this library, “scorecard.” Formerly, one had to pay to use it. The quality of the model is comparable, if not better. What you are using here is a logistic regression.

Carlos: In the service sector, the use of dashboards has been on the rise. Power BI, in particular, has seen a significant increase in popularity, surpassing Tableau. QlikView has all but disappeared from the market. Now, the two leading dashboarding platforms are Power BI and Tableau. However, I believe that the industry is poised for a major change. R is a powerful tool, but it requires a machine with the R engine installed. Imagine being able to use R in a serverless mode, like in WebR, even through a web browser. This would revolutionize the industry by eliminating the need to pay for licenses. Dashboards could be published and shared with colleagues for free.

In essence, the way we expand will change significantly, as we will use R or Python to make it very easy to create and distribute dashboards at no cost. I believe this change, as well as the things that are working now at Posit, could have a major impact on our industry but especially in the service sector, where we use a lot of different dashboards.

Jose Luis: I agree with Carlos, but I must point out that QlikView is still in operation. As you know, I worked with you at Orange, and I can assure you that Qlik is alive and well. Recently, I have been using Quarto to create reports for my customers and business owners. I have found Quarto to be an effective tool for communicating my results. I have used Quarto to create slides, reports, and interactive documents. I am very pleased with Quarto’s ability to help me share my analysis. I may also use “conflr” library to create analyses in R markdown and publish them directly to Confluence. This would allow me to create an analysis and immediately publish the documentation, which would be a great time-saver.

Pedro:You inquired about what we miss or would like to see in the R environment. I am not familiar with the web services provided by Posit or RStudio. However, I would like to see something similar to Google Colab. Google Colab for universities is a marvel. You have access to really powerful machines and a lot of RAM for free. It is a freemium service, but you can still use it. I am not aware of an equivalent in the R sector.

Carlos: Posit Cloud’s free tier provides a very small account with only one gigabyte of storage. This is insufficient for many users, especially those who need to use GPUs for machine learning or data science. Posit is not as powerful as the Google Colab Platform. It would be beneficial for Posit to offer a GPU-enabled tier for users who need more powerful hardware.

Carlos: The use of GPUs in deep learning is a topic that is open to debate. Python dominates the field, and has a wide range of packages and libraries available for deep learning, such as PyTorch. R has an older library for deep learning, but it is not as widely used as Python. Many of the latest developments in deep learning, such as generative AI, are primarily done in Python. Therefore, for R to be used more widely for deep learning, it needs to have faster and more compatible libraries, as well as a more user-friendly interface.

Pedro: The development of R is progressing at a rapid pace, perhaps too quickly for the requirements of R libraries. This is because the libraries are constantly changing, with major changes occurring every six months. As a result, users must keep a close eye on the third number in the library versions to ensure that they are using the latest and greatest version. This can be a bit messy, but it is also exciting to see the language evolving so quickly.

Jose Luis: I used iGraph and visNetwork to conduct social network analysis on mobile phones in order to communicate my findings. I also used Spark to perform social network analysis (library Graphframes), but I presented the results to my customers using R. It was a large project.

Any upcoming projects that you might want to discuss?

Jose Luis: I have an upcoming talk planned in which I will discuss the use of R in production. You have seen API, Docker, and other technologies. Perhaps sharing Azure in AWS and Google Cloud. I believe I attempted to teach too much. However, it may be beneficial to teach others how to use R in production. I would start with simple automation, such as using the cronR R Package and taskscheduleR in Windows. The next step would be to use an API. Then Docker. Then Kubernetes. Finally, publish and deploy on a cloud platform.

Carlos:In my case, I calculate projections for different types of time series on a monthly basis. This can involve up to 3,000 to 4,000 different time series, which are calculated automatically and in a distributed manner. These projections are already in production, and I use them to track different KPIs for different economic sectors in Spain. This is of great importance to my industry, as it allows us to identify which sectors are growing and which are declining so that we can invest in the right areas. This is a live system that is of great value to us.

Francisco: In my case, I am working on the first level of the problem that Jose Luis mentioned. My objective is to predict which customers are likely to default on their payments. After a customer makes a purchase online, they have to pay the first installment. My goal is to predict the probability that the second installment will not be paid.

I have developed a fully automated process that collects all the data from a SAS database. The process extracts the data, loads it into a model, applies the model, and then prepares the data for another application. The other application uses a model to prioritize customers who are likely to pay, and then selects a subset of customers to send SMS or email reminders to.

This process is fully automated and runs every day between 10am and 6pm. It takes only five minutes to complete. 

Pedro: In my case, I will be presenting a paper on psychometrics at the Barcelona Congress. Psychometrics is a niche area of statistics that focuses on psychological measurement. R is the only software that offers advanced psychometrics models. I will be using one of the oldest but still classical models. I have prepared a table of the current status of psychometrics models in R, which I may include in my presentation. This is because R is the only option for psychometricians nowadays. The big suites do not offer this software. This is another example of why R is the only way to go for these niche areas. 

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 65,000 members in 35 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.

deposits R Package Delivers a Common Workflow for R Users

By Blog

Mark Padgham, a Software Research Scientist for rOpenSci, has decades of experience in R, C, and C++, and maintains many packages on CRAN. Mark is leading the development of the deposits R package. Mark has been supported throughout this project by rOpenSci staff.

Publicly depositing datasets associated with published research is becoming more common, partly due to journals increasingly requiring data sharing and partly through more general and ongoing cultural changes with data sharing. Yet data sharing is often seen as time-consuming, particularly to meet the expectations of individual data repositories. While documentation and training can help familiarize users with data-sharing processes, browser-based data, and metadata submission workflows can only be so fast, are not easily reproduced, and do not facilitate regular or automated data and metadata updates. Better programmatic tools can transform data sharing from a mountainous climb into a pit of success.

deposits is a universal client for depositing and accessing research data in online deposition services. It provides a unified interface to many different research data repositories, which functions like dplyr, through “verbs” that work identically across many backend data repositories. 

Currently supported services are Zenodo and Figshare. These two systems have fundamentally different APIs and access to deposition services has traditionally been enabled through individual software clients. The deposits package aims to be a universal client offering access to a variety of deposition services, without users having to know any specific details of the APIs for each service.

The deposits package works seamlessly with the “frictionless” data workflow, to enable unified documentation of all aspects of datasets in one place. 

Outside of his work at rOpenSci, Mark has a passion for urban environments and understanding how cities can be improved. He is the lead developer of the Urban Analyst platform, ‘a platform for open-source, open-access interactive visualizations of urban structure and function.’ Mark says, “Cities cannot learn; therefore, I built a data platform for cities to learn from one another.”

RC: Doesn’t data sharing take too much time and too much effort? What is Deposits and what does it do? What problem are you solving?

Data sharing takes time and effort; everyone sharing from different places makes it hard to sync up. However, the deposits R package creates a common workflow for R users. It aims to streamline the data-sharing process. 

It addresses the issue of disparate data-sharing locations by creating a standardized workflow, simplifying the process for researchers. All deposits are initiated on the nominated services as “private” deposits, meaning they can only be viewed by the deposit owner until the owner decides. A deposit can only be publicly viewed once it has been published. The process of using deposits to prepare one or more datasets for publication involves multiple stages of editing and updating.

RC: How far along are you on the project? Currently supported services are zenodo and figshare. Will you be adding more?

Currently, the project provides support for Zenodo (CERN’s Data Centre) and Figshare (Open Data) as the initial services. There are plans to expand and include more repositories in the future. 

The team is working on integrating additional services, and there is a possibility of securing further funding for the Harvard Dataverse system, which operates as a federated rather than a centralized system. Integrating the DataVerse system presents additional complexities due to its federated nature, requiring more intricate API handling with greater flexibility but potentially posing challenges in adopting the workflow. 

RC: Have users contributed their own plugins to extend functionality to other repositories?

deposits is implementing a modular/plugin system to enable users to contribute their own plugins to extend functionality to other repositories. Users will be able to authenticate, prepare data and metadata, and finally submit, fetch, and browse data.

Actual activity around plugins has been a little slow so far. We are writing a JSON Schema for the system which will improve the process. We will be seeking people to build plugins after more adaptations are done and documented. Actually, I would not recommend regular users try to extend deposits to other repositories yet. But that is coming soon!

Preparing the data is a barrier, mainly during preparation. deposits is made to run workflows, documenting all the columns in a data table. By using deposits, there will be a completely painless, single update function. 

RC: What was your experience working with the R Consortium? Would you recommend applying for a grant to others?

Yes! The application process was painless and straightforward. In fact, I got a second grant recently. I’m very thankful for the support.

The only off-putting part of the process was no guidance on how much to ask for. You are fully enabled to submit it on your own. This is good, and I appreciate the outcome, getting financial support. But giving applicants better overall guidance would be very helpful. The R Consortium should make the application process more inclusive with more consultation. 

2023 : A Year of Progress for PHUSE CAMIS Working Group.

By Blog

This blog post contributed by PHUSE CAMIS

As we draw towards the end of 2023, the PHUSE CAMIS Working Group reflect on their key progress and successes this year.

The CAMIS repository went live in January 2023, drawing on the content from the PHUSE CSRMLW project.  This searchable repository compares analysis method implementations in software (CAMIS) such as SAS, R and python. 

The White Paper was published in June, which highlighted the importance of clearly specifying your analysis, such that it can be replicated in different software, and isn’t relying on default options which can be different.

For more complex analyses, it can still be hard to understand what defaults and algorithms your software is using, so the team focused 2023 on expanding our repo content, comparing SAS vs R methods.  By August, we had covered the following topics in the repo: quartiles, rounding, anova, mmrm, cmh, log-rank, cox-ph, mcnemar’s test, kruskal-wallis test and logistic. October saw the launch of the sub-working group: CAMIS-Oncology, led by Somasekhar Sriadibhatla (AstraZeneca).  This team will focus specifically on oncology endpoints and analyzing them in SAS, R and Python.  The CAMIS team have expanded in membership during 2023 presenting at numerous conferences around the world. In November, we welcomed Harshal Khanolkar (NovoNordisk), to join the leadership team alongside Christina Fillmore (GSK) and Lyn Taylor (PAREXEL).  Our focus for 2024, will be on the creation of additional content for the repo, and sharing awareness of the project across the medical research and wider community.  We’d like to take this opportunity to thank all of our team members and contributors, and encourage everyone to check out the repository and help us to grow our content CAMIS (psiaims.github.io).  If you would like to join the team please get in touch through the repo.

Igniting Innovation: Bilikisu Wunmi Olatunji’s Journey with Abuja’s Thriving R User Community

By Blog

The R Consortium recently caught up with Bilikisu Wunmi Olatunji, founder of the Abuja R User Group and R-Ladies Abuja. Bilikisu shared they began conducting in-person meetups last month by adding new types of gatherings, such as focus groups, quarterly workshops, and more. The October event was a success, as the group now has members from diverse fields, including a lawyer. Currently, the group is planning more exciting events for the upcoming year. 

We interviewed you in September 2021 and published Creating Successful R User Groups in Abuja, Nigeria. It’s nice to connect with you again! What’s new?

It’s great to reconnect with you too! Since our last interview in September 2021, our local meetup group has seen some exciting developments. We’ve continued to grow our community with members from within and outside our local community, and we have had both local and international speakers who have supported us by honoring our invitation to speak during our meetups, which led to more engaging and beneficial experiences for our members.

Last month, we had our first in-person meetups since the COVID-19 lockdown. This has led to some significant changes to the expansion of our event offerings. We’ve added new types of gatherings, such as focused groups (Data science and analytics with R, Epidemiology, Econometrics), quarterly workshops, and hybrid meetups, to cater to our community’s broader range of interests. These additions have received a very positive response, and we’re looking forward to increased participation and impact for our members.

To maintain momentum, we’ve utilized WhatsApp groups and established focused subgroups for Data Science and Analytics, Physiology, and Economics, allowing continuous engagement and specialized discussions.

We’re piloting an on-site group starting today and plan to expand access in January. The next six weeks, leading up to Christmas, are a trial period for this new approach. Beginning in January, we aim to scale this prototype, enhancing our support for the community.

We also appreciate the grant we got from R Consortium this year to support our group. Thank you, R Consortium.

In summary, we’re moving towards study groups, quarterly hybrid meetups, and workshops that will continue to serve our local community effectively. We’re excited about what’s ahead and look forward to the positive changes these plans will bring.

We want to get to know you more on the personal side. Can you please tell me about yourself? For example, hobbies/interests or anything you want to share about yourself. 

Sure, I’d be happy to share a bit about myself. I am Bilikisu Wunmi Olatunji. I’m happily married and blessed with wonderful children, both sons and daughters. Although my work often keeps me very busy, in my downtime, I have a passion for the arts — I particularly enjoy drawing. Another one of my pleasures is savoring delicious food. I’m not much of a cook, so I relish the opportunity to dine out with my family and explore different cuisines.

When relaxing at home, I love spending quality time with my kids, often watching cartoons or movies. These moments are special to me as they allow us to laugh and enjoy each other’s company.

These are aspects of my life that I usually keep private. Professionally, I’m a data scientist and the founder of Abuja R User Group and R-Ladies Abuja. I work closely with other co-organizers to help develop and expand our community.

You held a Meetup on Abuja R User Group Meet & Greet on Oct 28th, 2023. Can you share how the event went? What kind of topics were covered? Why those topics?

Yes, we had our first in-person meetup since the COVID-19 lockdown. The primary goal of the meetup is to meet each other and know what the members want from the group moving forward. We had new members who attended the meetup, and most of our old members also called in to show their support. We discussed the challenges the group and the members face, e.g., attending in-person meetups. I found the event to be a positive experience that will motivate me and others to help improve the groups’ meet-up attendance. A fun suggestion from our members was to involve dancing and more enjoyment in our meetups. 

Who was the target audience for attending this event? 

Our focus is on academics, particularly those in statistics and computer science, which aligns well with our area’s abundance of educational institutions. However, integrating our work with schools has been challenging due to bureaucratic hurdles, making it time-consuming and stressful.

Despite these obstacles, we’ve made some progress. We managed to have academic participation in our events—for instance, Muhammed Tahir Muhammed, a statistics lecturer from our network. We also had a representative from the field of epidemiology named Isaac Joseph, the department director. 

We’re excited about the potential for collaboration with these academics and professionals. At a recent event, we were pleased to see participation from three professionals from different fields, a new record for us. Among them was a lawyer, Michael Ezeh, who has experience with data visualization tools like Power BI and Tableau. He’s keen to expand his programming knowledge, starting with R, which is encouraging. We also had the following new members: Obaniyi Fidelis (Economics), Mafiana Ifechi (Data Analyst), and Benedicta Amarachukwu (New to R Data Analyst).

We’re running small focus groups as a pilot, which we hope to launch by January. The diverse backgrounds of our attendees are promising, and they will likely attract even more participants to our community.

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 unable to attend physical events in the future?  

I recommend Zoom meetings and Github. They are both easy to help regarding collaboration and resource sharing.

When is your next event? Please give details!

We will be starting our focus groups in January. We are currently using the remaining days of this year to plan for 2024.

Please share any additional details you would like included in the blog. 

We’re excited and hopeful that we will be able to impact the community with much more coming next year. We’ll be able to reach out to more people. As shown in our pictures, we have a fun time. I can also say that our numbers on the Meetup group are growing, which makes me happy. 

How do I Join?

R Consortium’s R User Group and Small Conference Support Program (RUGS) provides grants to help R groups worldwide organize, share information, and support each other. We have given grants over the past four years, encompassing over 65,000 members in 35 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.

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)