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

Accepted version
Peer-reviewed

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