Statistics used to evaluate model performance under scenarios 1, 2, and 3 for analyses using case incidence only (epi), phylogenetic tree only (phylo), and both data sources combined (combo).

The best or joint-best result for each statistic for each scenario is highlighted in bold. Trajectory RMSE: root-mean-squared error. Calibrated Trajectory Coverage: proportion of true trajectory that falls within the 95% HPD, scaled by 0.95. Scaled HPD Width: mean width of the 95% highest posterior density interval, scaled by the true value. Continuous Ranked Probability Score: mean CRPS across the trajectory time series. Brier Score: Classification accuracy for transmission phase (Rt) being above or below 1. Further details on the calculation of these statistics are included in the Supplementary Information (S5 Table).