BVDOutbreakSize

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Release notes for BVDOutbreakSize. Major versions of the report are kept as GitHub Releases; each push to main also republishes the rendered analysis and the output/ artifacts.

v1.1.0 ​

Modelling ​

  • Bound the seeding time T from below with a soft prior on the genetic time to the most recent common ancestor (TMRCA), following a suggestion from Neil Ferguson to combine the genetic signal with the other data streams as a seeding bound.

  • Switched the export deaths to a daily (time-resolved binned) Poisson process: a continuous survival weight for the no-death stretch before the first dated death, then a per-day Poisson from that day to the cut-off.

  • Bound T with export-death timing through that survival weight, and with case-export detection timing through a first-export-detection survival term on the Uganda admission date. Dates supplied in data/observations.toml.

  • Death-convolution quadrature adapted to the sampled delay scale.

  • Added a clock-rate sensitivity: refit the joint model under the faster 1.9e-3 early-epidemic TMRCA estimate and compare the impact on outbreak size, seeding time and growth rate against the 1.2e-3 baseline.

  • Sped up the deaths-among-exports likelihood: precompute the onset-to-death CDF once and reuse it across bin edges (ExportDeathDelay), replacing the per-node nested quadrature.

  • Removed hardcoded death and case constants that diverged from the observations in data/observations.toml.

  • Added a forecast validation: fit the joint model to the original report's data, project it forward to the current cut-off, and compare the predicted cumulative and new counts per stream against the counts observed since, as a table and a 2×3 coverage plot.

Data ​

  • Updated to the McCabe et al. 20 May 2026 report, comparing both report versions.

  • Sourced the genetic TMRCA seeding bound from the BEAST temporal-tree estimate in the 2026-05-21 virological.org update (mean 2026-03-25, 95% HPD 2026-02-20 to 2026-04-20, at the 1.2e-3 EBOV clock rate this analysis assumes).

Infrastructure ​

  • Dropped MCMCChains for FlexiChains and prepared for registry release.

  • CI docs preview PR comments and version-bump automation.

Docs ​

  • Added a scope note to the README and analysis report framing the work as an external view built on our understanding of real-time infectious disease dynamics, and inviting feedback, reuse and adaptation.

  • Surfaced results from the README and analysis landing page, added stable and dev docs badges.

  • Plotting and labelling fixes: surveillance dispersion on the 1/√k scale, predictive histograms labelled as frequency, and coarser (four-weekly) start-date axis ticks so the labels stay readable.

  • Reworked the headline summary to report the credible intervals as sentences rather than leading with a median, defined the prior-IQR shift, and explained the reported-case scaling in terms of the DRC reporting fraction with a link to the pair plot.

  • Replaced the model-structure diagram with a parameter-to-observation table.

  • Culled promotional register in the analysis report.

v1.0.0 ​

First release. A joint Bayesian re-analysis of the McCabe et al. report that fits all data streams together in a single Turing model over the latent cumulative case count.

  • Conditions on the exported cases and DRC deaths the report uses, plus reported DRC cases (with an ascertainment component) and deaths among exported cases.

  • Adds a no-onward-transmission projected-deaths counterfactual, a one-week-ahead forecast of newly reported cases, deaths and exports, and an onset-to-death delay sensitivity analysis.

  • Replaces the deaths-convolution and small-growth-rate exports closed-form approximations with their exact forms.

  • Maths-first analysis page with code folded behind dropdowns and a diagram of the model build-up.

  • Compares against a joint reimplementation of the report's approach and its original published estimates.