We develop a health informatics toolbox that enables timely analysis and evaluation of the timecourse dynamics of a range of infectious disease epidemics. As a case study, we examine the novel coronavirus (COVID-19) epidemic using the publicly available data from the China CDC. This toolbox is built upon a hierarchical epidemiological model in which two observed time series of daily proportions of infected and removed cases are generated from the underlying infection dynamics governed by a Markov Susceptible-Infectious-Removed (SIR) infectious disease process. We extend the SIR model to incorporate various types of time-varying quarantine protocols, including government-level ‘macro’ isolation policies and community-level ‘micro’ social distancing (e.g. self-isolation and self-quarantine) measures. We develop a calibration procedure for underreported infected cases. This toolbox provides forecasts, in both online and offline forms, as well as simulating the overall dynamics of the epidemic. An R software package is made available for the public, and examples on the use of this software are illustrated. Some possible extensions of our novel epidemiological models are discussed.
We propose a varying coefficient Susceptible-Infected-Removal (vSIR) model that allows changing infection and removal rates for the latest corona virus (COVID-19) outbreak in China. The vSIR model together with proposed estimation procedures allow one to track the reproductivity of the COVID-19 through time and to assess the effectiveness of the control measures implemented since Jan 23 2020 when the city of Wuhan was lockdown followed by an extremely high level of self-isolation in the population. Our study finds that the reproductivity of COVID-19 had been significantly slowed down in the three weeks from January 27th to February 17th with 96.3% and
95.1% reductions in the effective reproduction numbers R among the 30 provinces and 15 Hubei cities, respectively. Predictions to the ending times and the total numbers of infected are made under three scenarios of the removal rates. The paper provides a timely model and associated estimation and prediction methods which may be applied in other countries to track, assess and predict the epidemic of the COVID-19 or other infectious diseases