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Upcoming changes to malariaverse

Upcoming-changes.Rmd

📢 Advance notice of a major update

This page gives advance notice of a significant update to the malariaverse site files and several of the supporting packages. We’re flagging it ahead of time because the changes will affect — and in some cases break — existing workflows.

⚙️ What’s changing

The malariaverse packages and site files are being substantially updated (full detail in site PR #56 and postie PR #8). The headline changes include:

  • 🌍 Population and demography methods updated to the latest WorldPop outputs.
  • 🌧️ Monthly rainfall estimates updated to CHIRPS v3.0.
  • 🗺️ Updated to the latest MAP rasters.
  • 📊 WHO figures updated to the 2025 World Malaria Report.
  • 💉 Updated UNICEF malaria vaccine dose-delivery data.
  • ✨ New functionality: the option to specify a parameter draw, a Plasmodium vivax model, and within-year (sub-year) intervention specification.
  • 🛏️ Refined intervention implementation — net modelling now aligns more closely with the MAP net model, IRS trial-to-implementation downscaling, and corrected SMC/PMC round timing.
  • ⚠️ itn_model_dist is now a required input (with helper functions and a detailed error message to guide you if it’s missing).
  • 🏥 The previous fixed shortcut (malaria deaths taken as a constant multiple of hospitalised severe incidence) is replaced by an explicit calculation that splits severe cases into hospital and community streams, each with its own case-fatality ratio.
  • 🏥 In postie, a new ft_sev input lets you set and vary over time the proportion of severe cases that reach hospital. It defaults to 0.8, which reproduces the previous behaviour.
  • 🧾 New disaggregated output columns (hospital vs community severe streams) and case-fatality-ratio arguments are available.

Importantly, alongside these data and methods updates, the structure of the site files themselves is changing, and the supporting malariaverse packages are being updated in step. Taken together, this means code written against the current site files and packages will likely not run unchanged once the update lands.

🔁 Reproducing existing work

Many of you will need to re-run or reproduce earlier analyses. Two things make that possible:

  1. Older site files will remain available through fetch_site(), so you can continue to retrieve the previous data.
  2. We have frozen the current versions of the malariaverse packages as a coordinated snapshot under the tag malariaverse_01_2025. Pairing the older site files with this tagged set of packages reproduces the environment your existing workflows were built for.

To install the frozen package set, e.g. with pak:

pak::pak(c(
  "mrc-ide/site@malariaverse_01_2025",
  "mrc-ide/postie@malariaverse_01_2025",
  "mrc-ide/[other-pkg]@malariaverse_01_2025"
))

Remember, you can see al available site-files and versions by calling site::available_sites()

🗓️ Timing

We expect to merge these changes in the next month or so. If you have analyses in progress, we’d recommend noting which package versions you’re currently using (or installing the tagged snapshot above) before then.

❓ Questions

If you have any questions or run into problems, please open an issue on the site package issue page or contact us at .

🙏 Huge thanks to the many individuals who have contributed to these changes.