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.

Our team’s work relies a lot on GitHub Actions. Besides the usual workflows to check our code for errors after each push ¹ , we also have many workflows set up to run on a schedule.

31 March, in just under a weeks time, will mark the last day we are producing global national and subnational Rt estimates and nowcasts at https://epiforecasts.io/covid/posts/global/ - more than 2 years after we published the first set of estimates. This is a good opportunity to reflect on what we have learned from this, what went well and what went wrong, and what we would aim to do better next time.

On 10th November, 2017, a suspected case of diphtheria was reported at a Médecins Sans Frontières (MSF) clinic in Cox’s Bazar district, Bangladesh (Finger et al. 2019). A bacterial infection, diphtheria was a major cause of childhood illness and death in the early 20th Century, before a vaccine was developed in the 1920s, then included in the WHO’s Expanded Programme on Immunization in the 1970s.