Fig. 2. Effective reproduction number R_e estimates using the proposed method (ϕ) and phylodynamics (BEAST2).

a–d Piecewise constant median $R_e^{\mathrm{BEAST}}\left(\tau \right)$ estimates (green solid lines) were calculated using the BDSKY model for the indicated intervals, as described in the “Methods” section. Daily estimates $R_e^{\varphi }\left(t\right)$ (blue dots) were directly calculated from the incidence correlates ϕ using the Wallinga-Teunis method³⁰. The median of these values for the indicated intervals $R_e^{\varphi }\left(\tau \right)$ is shown as solid blue lines. The 95% confidence interval is specified by the shaded areas. Justifications of the intervals are found in Supplementary Note 2.