title: INFERENCE FOR INDIVIDUAL-LEVEL MODELS OF INFECTIOUS DISEASES IN LARGE POPULATIONS.
abstract: Individual Level Models (ILMs), a new class of models, are being applied to infectious epidemic data to aid in the understanding of the spatio-temporal dynamics of infectious diseases. These models are highly flexible and intuitive, and can be parameterised under a Bayesian framework via Markov chain Monte Carlo (MCMC) methods. Unfortunately, this parameterisation can be difficult to implement due to intense computational requirements when calculating the full posterior for large, or even moderately large, susceptible populations, or when missing data are present. Here we detail a methodology that can be used to estimate parameters for such large, and/or incomplete, data sets. This is done in the context of a study of the UK 2001 foot-and-mouth disease (FMD) epidemic.
authors.affiliation: Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
authors.forename: Rob
authors.initials: R
authors.lastname: Deardon
authors.affiliation: Statistical Laboratory, University of Cambridge, Cambridge, CB3 0WB, U.K.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Brooks
authors.affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544- 2016, U.S.A.
authors.forename: Bryan T
authors.initials: BT
authors.lastname: Grenfell
authors.affiliation: Mathematics Institute, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Keeling
authors.affiliation: Mathematics Institute, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Tildesley
authors.affiliation: Centre for Infectious Diseases, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh, EH9 3JF, U.K.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Savill
authors.affiliation: Veterinary Clinical Sciences, R(D)SVS, University of Edinburgh, Easter Bush Veterinary Centre, Roslin, Midlothian, EH25 9RG, U.K.
authors.forename: Darren J
authors.initials: DJ
authors.lastname: Shaw
authors.affiliation: Centre for Infectious Diseases, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh, EH9 3JF, U.K.
authors.forename: Mark E J
authors.initials: ME
authors.lastname: Woolhouse
keywords: Bayesian inference; Markov chain Monte Carlo; Spatio-temporal epidemic modelling; computational methodology; foot-and- mouth disease; missing data