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Interview Jeroen Ooms OpenCPU #rstats

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Below an interview with Jeroen Ooms, a pioneer in R and web development. Jeroen contributes to R by developing packages and web applications for multiple projects.

jeroen

Ajay- What are you working on these days?
Jeroen- My research revolves around challenges and opportunities of using R in embedded applications and scalable systems. After developing numerous web applications, I started the OpenCPU project about 1.5 year ago, as a first attempt at a complete framework for proper integration of R in web services. As I work on this, I run into challenges that shape my research, and sometimes become projects in their own. For example, the RAppArmor package provides the security framework for OpenCPU, but can be used for other purposes as well. RAppArmor interfaces to some methods in the Linux kernel, related to setting security and resource limits. The github page contains the source code, installation instructions, video demo’s, and a draft of a paper for the journal of statistical software. Another example of a problem that appeared in OpenCPU is that applications that used to work were breaking unexpectedly later on due to changes in dependency packages on CRAN. This is actually a general problem that affects almost all R users, as it compromises reliability of CRAN packages and reproducibility of results. In a paper (forthcoming in The R Journal), this problem is discussed in more detail and directions for improvement are suggested. A preprint of the paper is available on arXiv: http://arxiv.org/abs/1303.2140.

I am also working on software not directly related to R. For example, in project Mobilize we teach high school students in Los Angeles the basics of collecting and analyzing data. They use mobile devices to upload surveys with questions, photos, gps, etc using the ohmage software. Within Mobilize and Ohmage, I am in charge of developing web applications that help students to visualize the data they collaboratively collected. One public demo with actual data collected by students about snacking behavior is available at: http://jeroenooms.github.com/snack. The application allows students to explore their data, by filtering, zooming, browsing, comparing etc. It helps students and teachers to access and learn from their data, without complicated tools or programming. This approach would easily generalize to other fields, like medical data or BI. The great thing about this application is that it is fully client side; the backend is simply a CSV file. So it is very easy to deploy and maintain.

Ajay-What’s your take on difference between OpenCPU and RevoDeployR ?
Jeroen- RevoDeployR and OpenCPU both provide a system for development of R web applications, but in a fairly different context. OpenCPU is open source and written completely in R, whereas RevoDeployR is proprietary and written in Java. I think Revolution focusses more on a complete solution in a corporate environment. It integrates with the Revolution Enterprise suite and their other big data products, and has built-in functionality for authentication, managing privileges, server administration, support for MS Windows, etc. OpenCPU on the other hand is much smaller and should be seen as just a computational backend, analogous to a database backend. It exposes a clean HTTP api to call R functions to be embedded in larger systems, but is not a complete end-product in itself.

OpenCPU is designed to make it easy for a statistician to expose statistical functionality that will used by web developers that do not need to understand or learn R. One interesting example is how we use OpenCPU inside OpenMHealth, a project that designs an architecture for mobile applications in the health domain. Part of the architecture are so called “Data Processing Units”, aka DPU’s. These are simple, modular I/O units that do various sorts of data processing, similar to unix tools, but then over HTTPS. For example, the mobility dpu is used to calculate distances between gps coordinates via a simple http call, which OpenCPU maps to the corresponding R function implementing the harversine formula.

Ajay- What are your views on Shiny by RStudio?
Jeroen- RStudio seems very promising. Like Revolution, they deliver a more full featured product than any of my projects. However, RStudio is completely open source, which is great because it allows anyone to leverage the software and make it part of their projects. I think this is one of the reasons why the product has gotten a lot of traction in the community, which has in turn provided RStudio with great feedback to further improve the product. It illustrates how open source can be a win-win situation. I am currently developing a package to run OpenCPU inside RStudio, which will make developing and running OpenCPU apps much easier.

Ajay- Are you still developing excellent RApache web apps (which IMHO could be used for visualization like business intelligence tools?)
Jeroen-   The OpenCPU framework was a result of those webapps (including ggplot2 for graphical exploratory analysis, lme4 for online random effects modeling, stockplot for stock predictions and irttool.com, an R web application for online IRT analysis). I started developing some of those apps a couple of years ago, and realized that I was repeating a large share of the infrastructure for each application. Based on those experiences I extracted a general purpose framework. Once the framework is done, I’ll go back to developing applications :)

Ajay- You have helped  build web apps, openCPU, RAppArmor, Ohmage , Snack , mobility apps .What’s your thesis topic on?
Jeroen- My thesis revolves around all of the technical and social challenges of moving statistical computing beyond the academic and private labs, into more public, accessible and social places. Currently statistics is still done to mostly manually by specialists using software to load data, perform some analysis, and produce results that end up in a report or presentation. There are great opportunities to leverage the open source analysis and visualization methods that R has to offer as part of open source stacks, services, systems and applications. However, several problems need to be addressed before this can actually be put in production. I hope my doctoral research will contribute to taking a step in that direction.

Ajay- R is RAM constrained but the cloud offers lots of RAM. Do you see R increasing in usage on the cloud? why or why not?
Jeroen-   Statistical computing can greatly benefit from the resources that the cloud has to offer. Software like OpenCPU, RStudio, Shiny and RevoDeployR all provide some approach of moving computation to centralized servers. This is only the beginning. Statisticians, researchers and analysts will continue to increasingly share and publish data, code and results on social cloud-based computing platforms. This will address some of the hardware challenges, but also contribute towards reproducible research and further socialize data analysis, i.e. improve learning, collaboration and integration.

That said, the cloud is not going to solve all problems. You mention the need for more memory, but that is only one direction to scale in. Some of the issues we need to address are more fundamental and require new algorithms, different paradigms, or a cultural change. There are many exciting efforts going on that are at least as relevant as big hardware. Gelman’s mc-stan implements a new MC method that makes Bayesian inference easier and faster while supporting more complex models. This is going to make advanced Bayesian methods more accessible to applied researchers, i.e. scale in terms of complexity and applicability. Also Javascript is rapidly becoming more interesting. Performance of Google’s javascript engine V8 outruns any other scripting language at this point, and the huge Javascript community provides countless excellent software libraries. For example D3 is a graphics library that is about to surpass R in terms of functionality, reliability and user base. The snack viz that I developed for Mobilize is based largely on D3. Finally, Julia is another young language for technical computing with lots of activity and very smart people behind it. These developments are just as important for the future of statistical computing as big data solutions.

About-
You can read more on Jeroen and his work at  http://jeroenooms.github.com/ and reach out to him here http://www.linkedin.com/in/datajeroen


2 Comments

  1. Everything I always wanted to ask Jeroen Ooms but was afraid to ask!

    Actually, there’s one additional question I’d like to ask him, or anyone else here:
    I could be wrong but none of the R web tools described in this interview includes a REPL console, i.e. the command-line R interface that is the data scientist’s bread and butter in RStudio or Linux terminal. (This doesn’t count the browser version of RStudio, but I’m pretty sure it has low adoption.) What are your thoughts on adding an R command-line interface to the suite of web-based tools? Would the capabilities of OpenCPU extend to that kind of app, or are they different animals?

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