A farewell to R: time series models for tracking and forecasting epidemics


Type
Article
Change log
Authors
Harvey, A 
Abstract

The time-dependent reproduction number, Rt, is a key metric used by epidemiologists to assess the current state of an outbreak of an infectious disease. This quantity is usually estimated using time series observations on new infections combined with assumptions about the distribution of the serial interval of transmissions. Bayesian methods are often used with the new cases data smoothed using a simple, but to some extent arbitrary, moving average. This paper describes a new class of time series models, estimated by classical statistical methods, for tracking and forecasting the growth rate of new cases and deaths. Estimates of Rt, together with their standard deviations, are obtained as a by-product. Very few assumptions are needed and those that are made can be tested.

Description
Keywords
COVID-19, Gompertz curve, Kalman filter, state-space model, stochastic trend, waves, Bayes Theorem, COVID-19, Epidemics, Forecasting, Humans, Models, Statistical, SARS-CoV-2
Journal Title
Journal of the Royal Society Interface
Conference Name
Journal ISSN
1742-5662
1742-5662
Volume Title
Publisher
The Royal Society
Rights
All rights reserved