Bayesian nonparametrics for stochastic epidemic models

The vast majority of models for the spread of communicable diseases are parametric in nature and involve underlying assumptions about how the disease spreads through a population. In this article we consider the use of Bayesian nonparametric approaches to analysing data from disease outbreaks. Specifically we focus on methods for estimating the infection process in simple models under the assumption that this process has an explicit time-dependence

Bayesian model choice via mixture distributions with application to epidemics and population process models

We consider Bayesian model choice for the setting where the observed data are partially observed realisations of a stochastic population process. A new method for computing Bayes factors is described which avoids the need to use reversible jump approaches. The key idea is to perform inference for a hypermodel in which the competing models are components of a mixture distribution. The method itself has fairly general applicability. The methods are illustrated using simple population process models and stochastic epidemics

Bayesian model choice via mixture distributions with application to epidemics and population process models

We consider Bayesian model choice for the setting where the observed data are partially observed realisations of a stochastic population process. A new method for computing Bayes factors is described which avoids the need to use reversible jump approaches. The key idea is to perform inference for a hypermodel in which the competing models are components of a mixture distribution. The method itself has fairly general applicability. The methods are illustrated using simple population process models and stochastic epidemics

Estimating vaccine effects on Transmission of Infection from Household Data

This article is concerned with a method for making inferences about various measures of vaccine efficacy. These measures describe reductions in susceptibility and in the potential to transmit infection. The method uses data on household outbreaks; it is based on a model that allows for transmission of infection both from within a household and from the outside. The use of household data is motivated by the hope that these are informative about vaccine-induced reduction of the potential to transmit infection, as household outbreaks contain some information about the possible source of infection. For illustration, the method is applied to observed data on household outbreaks of smallpox. These data are of the form needed and the number of households is of a size that can be managed in a vaccine trial. It is found that vaccine effects, such as the mean reduction in susceptibility and the mean reduction in the potential to infect others, per infectious contact, can be estimated with precision. However, a more specific parameter reflecting the reduction in infectivity for individuals partially responding to vaccination is not estimated well in the application. An evaluation of the method using artificial data shows that this parameter can be estimated with greater precision when we have outbreak data on a large number of small households

Bayesian model choice via mixture distributions with application to epidemics and population process models

We consider Bayesian model choice for the setting where the observed data are partially observed realisations of a stochastic population process. A new method for computing Bayes factors is described which avoids the need to use reversible jump approaches. The key idea is to perform inference for a hypermodel in which the competing models are components of a mixture distribution. The method itself has fairly general applicability. The methods are illustrated using simple population process models and stochastic epidemics

Bayesian non-parametric inference for stochastic epidemic models using Gaussian Processes

This paper considers novel Bayesian non-parametric methods for stochastic epidemic models. Many standard modeling and data analysis methods use underlying assumptions (e.g. concerning the rate at which new cases of disease will occur) which are rarely challenged or tested in practice. To relax these assumptions, we develop a Bayesian non-parametric approach using Gaussian Processes, specifically to estimate the infection process. The methods are illustrated with both simulated and real data sets, the former illustrating that the methods can recover the true infection process quite well in practice, and the latter illustrating that the methods can be successfully applied in different settings

Bayes Factors for Partially Observed Stochastic Epidemic Models

We consider the problem of model choice for stochastic epidemic models given partial observation of a disease outbreak through time. Our main focus is on the use of Bayes factors. Although Bayes factors have appeared in the epidemic modelling literature before, they can be hard to compute and little attention has been given to fundamental questions concerning their utility. In this paper we derive analytic expressions for Bayes factors given complete observation through time, which suggest practical guidelines for model choice problems. We adapt the power posterior method for computing Bayes factors so as to account for missing data and apply this approach to partially observed epidemics. For comparison, wealso explore the use of a deviance information criterion for missing data scenarios. The methods are illustrated via examples involving both simulated and real data

Modelling, Bayesian inference, and model assessment for nosocomial pathogens using whole?genome?sequence data

Whole genome sequencing of pathogens in outbreaks of infectious disease provides the potential to reconstruct transmission pathways and enhance the information contained in conventional epidemiological data. In recent years there have been numerous new methods and models developed to exploit such high-resolution genetic data. However, corresponding methods for model assessment have been largely overlooked. In this paper we develop both new modelling methods and new model assessment methods, specifically by building on the work of Worby et al. 1 Although the methods are generic in nature, we focus specifically on nosocomial pathogens, and analyse a data set collected during an outbreak of MRSA in a hospital setting