Meeting the Stars of the R-Universe: The R-Universe Against Diseases.

A new post of our interview series “Meeting the stars of the R-universe”. We aim to introduce the teams and people behind the development of software and packages many of us use and which are available through the R-Universe. We want to highlight and explore different teams and projects around the world, the work they do, their processes and users. This stop is at the United Kingdom to talk with members of the Centre for Global Infectious Disease Analysis. Be sure to watch the video at the end with excerpts from the interview.

Infectious diseases continue to generate multiple problems in human health. The pandemic experience taught us the importance of research to fight epidemics. Today we will meet a team of developers who use the R-Universe to host packages that help in this work.

The chat begins with Rich FitzJohn, who leads the research software engineering team at the MRC Centre for Global Infectious Disease Analysis. This center works on the global analysis of infectious diseases. It is a center for research and development of tools for epidemiological analysis and modeling of infectious diseases to collaborate with the work of national and international agencies to plan public policy responses to potential infectious disease threats.

This team was one of the first to use our R-Universe and we’re interested in understanding and sharing their reasons for joining the platform.

As Rich explains, their work consists of providing answers to general and specific epidemiology problems and responding to more than 200 different companies. Within this framework, they use the R-Universe as a way to distribute and present packages they develop and use in their work.

Rob Ashton, a software engineer who works with Rich, adds that these packages are important as they allow them to deliver the work to all the users in a simple, useful, and responsible way. Especially if you consider that it is very collaborative work and often they are working against the clock. That is why they try to all work at the same time on the same code with a permanent development and revision cycle to meet the needs of the researchers. This work will then be used by researchers worldwide, and that is where the R-Universe becomes a fundamental tool.

Multiple users can access the MRC R-Universe at the same time to use the packages and have the necessary material available for their research. However, it is likely that they will need some training or knowledge to be able to use these packages because of the level of specificity, and the R-Universe helps there too by hosting documentation such as vignettes and articles.

Recalling how they first entered the R-universe, Rich says it was by being invited to try out a new project that rOpenSci was working on. They then quickly realized that it represented the possibility of saving hours of work in different tasks. Over time the features and functionalities of the R-Universe changed and expanded as the project matured.

It was at this point in the interview that Rich and Rob discussed possible future features that could be useful in the R-Universe; from archiving different versions of the binaries of each package according to a researcher’s reproducibility needs, to automatic generation of package documentation, to different ideas for increasing the R-Universe’s package search and discovery capabilities.

Some of these features are currently under development and others have already been implemented. For example: Downloading snapshots and creating stable R packages repositories using R-Universe and Discovering and learning everything there is to know about R packages using R-Universe.

In the following video, Rich and Rob share more details of their work in the MRC and with the rOpenSci R-Universe.