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).

各场景下的各项统计指标的最优结果或并列最优结果均以粗体标注。
轨迹均方根误差（Trajectory RMSE）：即均方根误差（root-mean-squared error）。
校准轨迹覆盖率（Calibrated Trajectory Coverage）：指真实轨迹落在95%最高后验密度区间（95% HPD）内的比例，按0.95进行缩放后的值。
缩放后的HPD宽度（Scaled HPD Width）：指95%最高后验密度区间的平均宽度，按真实值进行缩放后的值。
连续排名概率得分（Continuous Ranked Probability Score，简称CRPS）：指轨迹时间序列上的平均CRPS值。
布里尔得分（Brier Score）：用于评估传播阶段（Rt）高于或低于1的分类准确率。
上述各项统计指标的详细计算方法见补充材料（S5表）。