Most of our work at Epiverse TRACE involves either developing an R package from scratch or adopting and maintaining an existing R package. In the former case, decision-making during development is guided by internal policies documented in the Epiverse-TRACE blueprints. However, a less common scenario for us has been taking on the maintenance of an existing package — a situation we recently encountered with the bpmodels R package.

Note This is a follow-up blog post to the Dual licensing R packages with code and data post published in September 2024. It contains learnings from submitting epiparameter to CRAN with a dual license. Overview of previous blog post on R package licensing We previously published a post on the Epiverse-TRACE blog discussing the importance of licensing code and data for open source.

Licenses are an important topic within open source. Without licenses, information or code can be publicly available but not legally available for reuse or redistribution. The open source software community’s most common licenses are the MIT license or the GNU GPLv3. When you read the MIT or GNU license, you can see they are rather specific: and They aim to cover primarily software, not other forms of information such as, for example, data.

GitHub recently previewed ‘Copilot Workspace’, which aims to use generative AI to assist software developers. Rather than just giving in-line suggestions, as GitHub copilot does, workspace allows users to map out and execute entire projects. We got early preview access to the tool, so decided to see how well it performed for our needs in Epiverse-TRACE.

We are continuing our post series on S3 object orientation and interoperability in R. We have previously discussed what makes a good S3 class and how to choose a good parent for it, as well as when to write or not write a custom method. We have highlighted in particular how classes inheriting from data.frames can simplify user experience because of familiarity, and reduce developer workload due to the pre-existing S3 methods.

There are ongoing outbreaks of mpox globally. The Democratic Republic of Congo (DRC) is so far the worst hit with a total of 7,851 cases and 384 deaths reported between January 1 and May 26, 2024 ¹ . Before 2022, there were few reports of sustained mpox transmission globally.

I have recently published a series of blog posts on the reasons why one may want to start using object-oriented programming (and more specifically R S3 classes) to improve interoperability with other tools from the ecosystem. But there are still questions I have not addressed directly, even if they may have been implicitly included sometimes: what makes a good object class? What good practices in class &

Throughout the Epiverse project, we use the renv R package to ensure reproducibility of the training materials and the pipelines we are providing. But we sometimes get reports from users who struggle to rebuild the environment and run the code. In this post, we dissect the source of these issues, explain why in reality renv is not at fault, and how this is caused by the inherent complexity of reproducibility.