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A comparison of inferential methods for highly nonlinear state space models in ecology and epidemiology

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Fasiolo_2016_SS_InferentialMethods_FinalPubVersion.pdf (923.3Kb)
Date
2016
Author
Fasiolo, Matteo
Pya, Natalya
Wood, Simon N.
Funder
EPSRC
Grant ID
EP/I000917/1
Keywords
Approximate bayesian computation
Nonlinear dynamics
Particle filters
State space models
Statistical ecology
QA Mathematics
Statistics and Probability
Mathematics(all)
Statistics, Probability and Uncertainty
NDAS
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Abstract
Highly nonlinear, chaotic or near chaotic, dynamic models are important in fields such as ecology and epidemiology: for example, pest species and diseases often display highly nonlinear dynamics. However, such models are problematic from the point of view of statistical inference. The defining feature of chaotic and near chaotic systems is extreme sensitivity to small changes in system states and parameters, and this can interfere with inference. There are twomain classes ofmethods for circumventing these difficulties: information reduction approaches, such as Approximate Bayesian Computation or Synthetic Likelihood, and state space methods, such as Particle Markov chain Monte Carlo, Iterated Filtering or Parameter Cascading. The purpose of this article is to compare the methods in order to reach conclusions about how to approach inference with such models in practice. We show that neither class of methods is universally superior to the other. We show that state space methods can suffer multimodality problems in settings with low process noise or model misspecification, leading to bias toward stable dynamics and high process noise. Information reduction methods avoid this problem, but, under the correct model and with sufficient process noise, state space methods lead to substantially sharper inference than information reduction methods. More practically, there are also differences in the tuning requirements of different methods. Our overall conclusion is that model development and checking should probably be performed using an information reduction method with low tuning requirements, while for final inference it is likely to be better to switch to a state space method, checking results against the information reduction approach.
Citation
Fasiolo , M , Pya , N & Wood , S N 2016 , ' A comparison of inferential methods for highly nonlinear state space models in ecology and epidemiology ' , Statistical Science , vol. 31 , no. 1 , pp. 96-118 . https://doi.org/10.1214/15-STS534
Publication
Statistical Science
Status
Peer reviewed
DOI
https://doi.org/10.1214/15-STS534
ISSN
0883-4237
Type
Journal article
Rights
© Institute of Mathematical Statistics, 2016. This work is made available online in accordance with the publisher’s policies. This is the final published version of the work, which was originally published at: https://doi.org/10.1214/15-STS534
Description
Most of this work was undertaken at the University of Bath, where M.F. was a Ph.D. student, and it was supported in part by EPSRC Grants EP/I000917 and EP/K005251/1.
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  • University of St Andrews Research
URL
https://arxiv.org/abs/1411.4564
URI
http://hdl.handle.net/10023/16250

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