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Analyses of infectious disease data from household outbreaks by Markov chain Monte Carlo methods
Author(s) -
O'Neill Philip D.,
Balding David J.,
Becker Niels G.,
Eerola Mervi,
Mollison Denis
Publication year - 2000
Publication title -
journal of the royal statistical society: series c (applied statistics)
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.205
H-Index - 72
eISSN - 1467-9876
pISSN - 0035-9254
DOI - 10.1111/1467-9876.00210
Subject(s) - markov chain monte carlo , gibbs sampling , computer science , inference , bayesian probability , context (archaeology) , markov chain , bayesian inference , econometrics , monte carlo method , data mining , algorithm , statistics , machine learning , artificial intelligence , mathematics , geography , archaeology
The analysis of infectious disease data presents challenges arising from the dependence in the data and the fact that only part of the transmission process is observable. These difficulties are usually overcome by making simplifying assumptions. The paper explores the use of Markov chain Monte Carlo (MCMC) methods for the analysis of infectious disease data, with the hope that they will permit analyses to be made under more realistic assumptions. Two important kinds of data sets are considered, containing temporal and non‐temporal information, from outbreaks of measles and influenza. Stochastic epidemic models are used to describe the processes that generate the data. MCMC methods are then employed to perform inference in a Bayesian context for the model parameters. The MCMC methods used include standard algorithms, such as the Metropolis–Hastings algorithm and the Gibbs sampler, as well as a new method that involves likelihood approximation. It is found that standard algorithms perform well in some situations but can exhibit serious convergence difficulties in others. The inferences that we obtain are in broad agreement with estimates obtained by other methods where they are available. However, we can also provide inferences for parameters which have not been reported in previous analyses.