Fig. 2: Effective reproduction number Re estimates using the proposed method (ϕ) and phylodynamics (BEAST2). | Nature Communications

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

From: Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020

Fig. 2

a–d Piecewise constant median \({R}_{e}^{{{{{{{{\rm{BEAST}}}}}}}}}(\tau )\) estimates (green solid lines) were calculated using the BDSKY model for the indicated intervals, as described in the “Methods” section. Daily estimates \({R}_{e}^{\phi }(t)\) (blue dots) were directly calculated from the incidence correlates ϕ using the Wallinga-Teunis method30. The median of these values for the indicated intervals \({R}_{e}^{\phi }(\tau )\) 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.

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