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  • fsMCMC_sjs_final

    Rights statement: ‘This is the peer reviewed version of the following article: Neal, P., and Terry Huang, C. L. (2015), Forward Simulation Markov Chain Monte Carlo with Applications to Stochastic Epidemic Models. Scand J Statist, 42, 378–396. doi: 10.1111/sjos.12111. which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/sjos.12111/abstract. This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving'.

    Accepted author manuscript, 499 KB, PDF document

  • sjos12111

    Rights statement: © 2014 The Authors. Scandinavian Journal of Statistics published by John Wiley & Sons Ltd on behalf of The Board of the Foundation of the Scandinavian Journal of Statistics. The copyright line of this article has been subsequently changed [30 March 2015]. This article is made OnlineOpen. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Final published version, 601 KB, PDF document

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Forward simulation MCMC with applications to stochastic epidemic models

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<mark>Journal publication date</mark>06/2015
<mark>Journal</mark>Scandinavian Journal of Statistics
Issue number2
Volume42
Number of pages19
Pages (from-to)378-396
Publication StatusPublished
Early online date8/08/14
<mark>Original language</mark>English

Abstract

For many stochastic models, it is difficult to make inference about the model parameters because it is impossible to write down a tractable likelihood given the observed data. A common solution is data augmentation in a Markov chain Monte Carlo (MCMC) framework. However, there are statistical problems where this approach has proved infeasible but where simulation from the model is straightforward leading to the popularity of the approximate Bayesian computation algorithm. We introduce a forward simulation MCMC (fsMCMC) algorithm, which is primarily based upon simulation from the model. The fsMCMC algorithm formulates the simulation of the process explicitly as a data augmentation problem. By exploiting non-centred parameterizations, an efficient MCMC updating schema for the parameters and augmented data is introduced, whilst maintaining straightforward simulation from the model. The fsMCMC algorithm is successfully applied to two distinct epidemic models including a birth–death–mutation model that has only previously been analysed using approximate Bayesian computation methods.

Bibliographic note

© 2014 The Authors. Scandinavian Journal of Statistics published by John Wiley & Sons Ltd on behalf of The Board of the Foundation of the Scandinavian Journal of Statistics. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. The copyright line of this article has been subsequently changed [30 March 2015]. This article is made OnlineOpen.