Key Concepts in Infectious Disease Epidemiology

Authored by: Nicholas P. Jewell

Handbook of Infectious Disease Data Analysis

Print publication date:  November  2019
Online publication date:  November  2019

Print ISBN: 9781138626713
eBook ISBN: 9781315222912
Adobe ISBN:


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In this chapter space-time analysis of surveillance count data is considered. Such data are ubiquitous and a number of approaches have been proposed for their analysis. We first describe the aims of a surveillance endeavor, before reviewing and critiquing a number of common models. The focus is on models in which time is discretized to the timescale of the latent and infectious periods of the disease under study. In particular, the focus is on the time series SIR (TSIR) models originally described in Finkenstädt and Grenfell (2000) and the epidemic/endemic models first proposed in Held et al (2005). Both of these models are implemented in the Stan software and their performance illustrated by analyses of measles data collected over a 2-year period in 17 regions in the Weser-Ems region of Lower Saxony, Germany.

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