Which reproduction number for which decision? Code, simulated data and results

Code, simulated datasets and results supporting a study that compares genome-based and case-based estimates of the reproduction number (R) in the 2026 Bundibugyo virus disease outbreak in the Democratic Republic of the Congo. The package contains (1) a simulator and 20 simulated outbreaks with known growth rates, sampled with homogeneous or dense-site genome sampling, with ground truth and checksums; (2) Colab notebooks to calibrate Delphy and BEAST X on them, with the acceptance rules, including a rerun of the homogeneous datasets at 8,000 cells; (3) scripts for a hierarchical Bayesian case-based backtest by health zone, a prediction test, and a simulation of the case-based estimator; (4) the written analysis plans with SHA-256 fingerprints; (5) result tables, convergence diagnostics and chain logs for every analysis reported; and (6) the manuscript figures. No real or restricted-use sequence data are included or were used. Situation-report case counts are public and are not redistributed; instructions to obtain them are in the README.