Bayesian estimation for percolation models of disease spread in plant populations


Gibson, GJ; Otten, W; Filipe, JAN; Cook, A; Marion, G; Gilligan, CA; (2006) Bayesian estimation for percolation models of disease spread in plant populations. Statistics and computing, 16 (4). pp. 391-402. ISSN 0960-3174 DOI: https://doi.org/10.1007/s11222-006-0019-z

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Abstract

Statistical methods are formulated for fitting and testing percolation-based, spatio-temporal models that are generally applicable to biological or physical processes that evolve in spatially distributed populations. The approach is developed and illustrated in the context of the spread of Rhizoctonia solani, a fungal pathogen, in radish but is readily generalized to other scenarios. The particular model considered represents processes of primary and secondary infection between nearest-neighbour hosts in a lattice, and time-varying susceptibility of the hosts. Bayesian methods for fitting the model to observations of disease spread through space and time in replicate populations are developed. These use Markov chain Monte Carlo methods to overcome the problems associated with partial observation of the process. We also consider how model testing can be achieved by embedding classical methods within the Bayesian analysis. In particular we show how a residual process, with known sampling distribution, can be defined. Model fit is then examined by generating samples from the posterior distribution of the residual process, to which a classical test for consistency with the known distribution is applied, enabling the posterior distribution of the P-value of the test used to be estimated. For the Rhizoctonia-radish system the methods confirm the findings of earlier non-spatial analyses regarding the dynamics of disease transmission and yield new evidence of environmental heterogeneity in the replicate experiments.

Item Type: Article
Keywords: spatio-temporal modeling, stochastic modelling, fungal pathogens, Bayesian inference, Markov chain Monte Carlo, SPATIOTEMPORAL MODELS, EPIDEMICS, TRANSMISSION, THRESHOLDS, INVASION, DYNAMICS, SYSTEMS
Faculty and Department: Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology
Web of Science ID: 241260600006
URI: http://researchonline.lshtm.ac.uk/id/eprint/10596

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