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Estimating the time-varying reproduction number of COVID-19 with a state-space method
Fig 3
Synthetic daily cases generated by simulating the Hawkes-type count process and the estimated reproduction number.
(A) Rapid increase followed by a slow decrease. (B) Increase followed by a rapid decrease, and then an increase. (C) Slow increase followed by a decrease, and then another large increase. In the upper panel plotting the number of daily cases (purple line), the rate estimated by the state-space method 
is also plotted (blue line). In the lower panel, the reproduction number 
estimated with the state-space method is plotted in reference to the true reproduction number Ri (purple line). The blue solid line and the shaded area represent the median and 95% range of the posterior distribution, respectively. The reproduction numbers estimated by Wallinga and Teunis (WT: orange line) and by Cori et al. (EpiEstim: green line) are also plotted for reference.
doi: https://doi.org/10.1371/journal.pcbi.1008679.g003