Fig. 1: Schematic of the methodology.
A parametric relationship between transmission and mobility is assumed and allows to link the effective reproduction number at time of infection (Rt,i) to mobility (mt,i).We obtain the delayed effective reproduction number at time of death (\(R_{t,i}^D\)) as a weighted average of Rt,i’s, relying on the delay between infection and death (see Methods section). Inference relies on the likelihood of observed vs predicted deaths, with predicted deaths being a function the \(R_{t,i}^D\) (see Methods section). To estimates how much variations in transmission can be explained by variations in mobility, we estimate a non-parametric and delayed reproduction number relying on EpiEstim framework23 (\(R_{t,i}^{D,EpiEstim}\)) and compare it to \(R_{t,i}^D\).
