Case count tree#73
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Add phylogenetic/workflows/bdbv-2026-epi/collect-cases.py, which consults a local clone of the INRB-UMIE/Ebola_DRC_2026 data repo and emits a single tidy TSV of case counts per MoH health zone over time. It reads the four per-zone metric files under data/insp_sitrep/processed/ (new_/cumulative_ x confirmed_/suspected_cases) and merges them on (nom, date) into columns: nom, date, new_confirmed_cases, new_suspected_cases, cumulative_confirmed_cases, cumulative_suspected_cases. The "nom" field is the canonical health-zone name that joins to the shapefile; dates are the raw sitrep calendar dates. National-total rows are excluded. We add a cumulative_confirmed_cases_clamped column to guard against presumptive data errors where a subsequent timepoint's case count decreases. Health zones are corrected via the INRB-UMIE/Ebola_DRC_2026's aliases CSV Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Add phylogenetic/workflows/bdbv-2026-epi/make-tree.py, which assembles a custom Auspice v2 dataset JSON for the 2026 Bundibugyo ebolavirus outbreak directly from the collected epi TSVs. Most dataset metadata is hardcoded. Because we have no transmission information each case is a child of a root polytomy, with a branch length which defaults to 7 days - this allows us to visualise cases over time on the tree & map. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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See added README
Dataset at https://next.nextstrain.org/staging/ebola/bdbv/drc-uganda-2026-cases