Estimating the epidemic reproduction number from temporally aggregated incidence data: A statistical modelling approach and software tool.

ABSTRACT: The time-varying reproduction number (Rt) is an important measure of epidemic transmissibility that directly informs policy decisions and the optimisation of control measures. EpiEstim is a widely used opensource software tool that uses case incidence and the serial interval (SI, time between symptoms in a case and their infector) to estimate Rt in real-time. The incidence and the SI distribution must be provided at the same temporal resolution, which can limit the applicability of EpiEstim and other similar methods, e.g. for contexts where the time window of incidence reporting is longer than the mean SI. In the EpiEstim R package, we implement an expectation-maximisation algorithm to reconstruct daily incidence from temporally aggregated data, from which Rt can then be estimated. We asse

SUBMITTER: Nash RK 

PROVIDER: S-EPMC10491397 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature