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Capturing the time-varying drivers of an epidemic using stochastic dynamical systems

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  • Joseph Dureau
  • Konstantinos Kalogeropoulos
  • Marc Baguelin

Abstract

Epidemics are often modeled using non-linear dynamical systems observed through partial and noisy data. In this paper, we consider stochastic extensions in order to capture unknown influences (changing behaviors, public interventions, seasonal effects, etc.). These models assign diffusion processes to the time-varying parameters, and our inferential procedure is based on a suitably adjusted adaptive particle Markov chain Monte Carlo algorithm. The performance of the proposed computational methods is validated on simulated data and the adopted model is applied to the 2009 H1N1 pandemic in England. In addition to estimating the effective contact rate trajectories, the methodology is applied in real time to provide evidence in related public health decisions. Diffusion-driven susceptible exposed infected retired-type models with age structure are also introduced.

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File URL: http://eprints.lse.ac.uk/41749/
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Bibliographic Info

Paper provided by London School of Economics and Political Science, LSE Library in its series LSE Research Online Documents on Economics with number 41749.

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Date of creation: Jul 2013
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Publication status: Published in Biostatistics, July, 2013, 14(3), pp. 541-555. ISSN: 1465-4644
Handle: RePEc:ehl:lserod:41749

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Keywords: Bayesian inference; particle MCMC; population epidemic model; time-varying parameters;

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  1. Yvo Pokern & Andrew M. Stuart & Petter Wiberg, 2009. "Parameter estimation for partially observed hypoelliptic diffusions," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 71(1), pages 49-73.
  2. Konstantinos Kalogeropoulos, 2007. "Likelihood-based inference for a class of multivariate diffusions with unobserved paths," LSE Research Online Documents on Economics 31423, London School of Economics and Political Science, LSE Library.
  3. Golightly, A. & Wilkinson, D.J., 2008. "Bayesian inference for nonlinear multivariate diffusion models observed with error," Computational Statistics & Data Analysis, Elsevier, vol. 52(3), pages 1674-1693, January.
  4. Christophe Andrieu & Arnaud Doucet & Roman Holenstein, 2010. "Particle Markov chain Monte Carlo methods," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 72(3), pages 269-342.
  5. David J. Spiegelhalter & Nicola G. Best & Bradley P. Carlin & Angelika van der Linde, 2002. "Bayesian measures of model complexity and fit," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 64(4), pages 583-639.
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