A numerical framework for estimating the effective reproduction number of infectious diseases from compartmental epidemic models

Abstract

We present a numerical framework for estimating the effective reproduction number of infectious diseases from compartmental epidemic models. The idea is to augment the reproduction number as an extended state variable in the model. We assume the reproduction number is a piece-wise constant function with jumps every new data are recorded. The numerical framework is written in discrete-time and is combined with estimation algorithms. Simulation results using epidemiological data from Denmark and Germany show our approach is comparable with existing method such as methods based on Bayesian statistical inference.