Exact Bayesian Inference and Model Selection for Stochastic Models of Epidemics Among a Community of Households

Abstract.  Much recent methodological progress in the analysis of infectious disease data has been due to Markov chain Monte Carlo (MCMC) methodology. In this paper, it is illustrated that rejection sampling can also be applied to a family of inference problems in the context of epidemic models, avoiding the issues of convergence associated with MCMC methods. Specifically, we consider models for epidemic data arising from a population divided into households. The models allow individuals to be potentially infected both from outside and from within the household. We develop methodology for selection between competing models via the computation of Bayes factors. We also demonstrate how an initial sample can be used to adjust the algorithm and improve efficiency. The data are assumed to consist of the final numbers ultimately infected within a sample of households in some community. The methods are applied to data taken from outbreaks of influenza.     

A case study in non-centering for data augmentation: Stochastic epidemics

In this paper, we introduce non-centered and partially non-centered MCMC algorithms for stochastic epidemic models. Centered algorithms previously considered in the literature perform adequately well for small data sets. However, due to the high dependence inherent in the models between the missing data and the parameters, the performance of the centered algorithms gets appreciably worse when larger data sets are considered. Therefore non-centered and partially non-centered algorithms are introduced and are shown to out perform the existing centered algorithms.     

Cross-infection in epidemics spread by carriers

A block-structured transient Markov process is introduced to describe an epidemic spreading within two linked populations, of carriers and susceptibles. The epidemic terminates as soon as there are no more carriers or susceptibles present in the population. Our purpose is to determine the distribution of the final susceptible and carrier states, and of any integral path for the susceptible process. The transient epidemic state is also briefly discussed. Then, the model is extended to allow the recovery of infected individuals. Finally, several particular models, some known, are used for illustration.     

Bayesian inference for stochastic multitype epidemics in structured populations via random graphs

Summary.  The paper is concerned with new methodology for statistical inference for final outcome infectious disease data using certain structured population stochastic epidemic models. A major obstacle to inference for such models is that the likelihood is both analytically and numerically intractable. The approach that is taken here is to impute missing information in the form of a random graph that describes the potential infectious contacts between individuals. This level of imputation overcomes various constraints of existing methodologies and yields more detailed information about the spread of disease. The methods are illustrated with both real and test data.     

Stochastic differential equation systems for an SIS epidemic model with vaccination and immigration

Two Itô stochastic differential equation (SDE) systems are constructed for a Susceptible-Infected-Susceptible epidemic model with temporary vaccination. A constant number of new members enter the population and total size of the population is variable. Some conditions for disease extinction in the stochastic models are established and compared with conditions in deterministic one. It is shown that the two stochastic models are equivalent in the sense that their solutions come from same distribution. In addition, the SDE models are simulated and the equivalence of the two stochastic models is confirmed by numerical examples. The probability distribution for extinction is also obtained numerically, provided there exists a probability for disease persistence whereas the expected duration of epidemic is acquired when extinction occurs with probability 1.     

Collapsing of Non‐centred Parameterized MCMC Algorithms with Applications to Epidemic Models

Data augmentation is required for the implementation of many Markov chain Monte Carlo (MCMC) algorithms. The inclusion of augmented data can often lead to conditional distributions from well‐known probability distributions for some of the parameters in the model. In such cases, collapsing (integrating out parameters) has been shown to improve the performance of MCMC algorithms. We show how integrating out the infection rate parameter in epidemic models leads to efficient MCMC algorithms for two very different epidemic scenarios, final outcome data from a multitype SIR epidemic and longitudinal data from a spatial SI epidemic. The resulting MCMC algorithms give fresh insight into real‐life epidemic data sets.     

Spatial measurement error in infectious disease models

Individual-level models (ILMs) for infectious disease can be used to model disease spread between individuals while taking into account important covariates. One important covariate in determining the risk of infection transfer can be spatial location. At the same time, measurement error is a concern in many areas of statistical analysis, and infectious disease modelling is no exception. In this paper, we are concerned with the issue of measurement error in the recorded location of individuals when using a simple spatial ILM to model the spread of disease within a population. An ILM that incorporates spatial location random effects is introduced within a hierarchical Bayesian framework. This model is tested upon both simulated data and data from the UK 2001 foot-and-mouth disease epidemic. The ability of the model to successfully identify both the spatial infection kernel and the basic reproduction number (R ₀) of the disease is tested.     

Bayesian penalized B-spline estimation approach for epidemic models

Ordinary differential equations (ODEs) are normally used to model dynamic processes in applied sciences such as biology, engineering, physics, and many other areas. In these models, the parameters are usually unknown, and thus they are often specified artificially or empirically. Alternatively, a feasible method is to estimate the parameters based on observed data. In this study, we propose a Bayesian penalized B-spline approach to estimate the parameters and initial values for ODEs used in epidemiology. We evaluated the efficiency of the proposed method based on simulations using the Markov chain Monte Carlo algorithm for the Kermack–McKendrick model. The proposed approach is also illustrated based on a real application to the transmission dynamics of hepatitis C virus in mainland China.     

Recent developments in nonlinear stochastic modelling of social processes

After a brief review of social applications of Markov chains, the paper discusses nonlinear (“interactive”) Markov models in discrete and continuous time. The rather subtle relationship between the deterministic and stochastic versions of such models is explored by means of examples. It is shown that the behaviour of nonlinear systems over time periods of practical interest depends critically on the total size as well as on the system parameters. Particular attention is paid to strong and weak forms of quasi-stationarity exhibited by stochastic systems.     

Forward Simulation Markov Chain Monte Carlo with Applications to Stochastic Epidemic Models

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.     

Perfect simulation for Reed-Frost epidemic models

The Reed-Frost epidemic model is a simple stochastic process with parameter q that describes the spread of an infectious disease among a closed population. Given data on the final outcome of an epidemic, it is possible to perform Bayesian inference for q using a simple Gibbs sampler algorithm. In this paper it is illustrated that by choosing latent variables appropriately, certain monotonicity properties hold which facilitate the use of a perfect simulation algorithm. The methods are applied to real data.     

Bayesian inference for partially observed stochastic epidemics

The analysis of infectious disease data is usually complicated by the fact that real life epidemics are only partially observed. In particular, data concerning the process of infection are seldom available. Consequently, standard statistical techniques can become too complicated to implement effectively. In this paper Markov chain Monte Carlo methods are used to make inferences about the missing data as well as the unknown parameters of interest in a Bayesian framework. The methods are applied to real life data from disease outbreaks.     

Analyses of infectious disease data from household outbreaks by Markov chain Monte Carlo methods

The analysis of infectious disease data presents challenges arising from the dependence in the data and the fact that only part of the transmission process is observable. These difficulties are usually overcome by making simplifying assumptions. The paper explores the use of Markov chain Monte Carlo (MCMC) methods for the analysis of infectious disease data, with the hope that they will permit analyses to be made under more realistic assumptions. Two important kinds of data sets are considered, containing temporal and non-temporal information, from outbreaks of measles and influenza. Stochastic epidemic models are used to describe the processes that generate the data. MCMC methods are then employed to perform inference in a Bayesian context for the model parameters. The MCMC methods used include standard algorithms, such as the Metropolis–Hastings algorithm and the Gibbs sampler, as well as a new method that involves likelihood approximation. It is found that standard algorithms perform well in some situations but can exhibit serious convergence difficulties in others. The inferences that we obtain are in broad agreement with estimates obtained by other methods where they are available. However, we can also provide inferences for parameters which have not been reported in previous analyses.     

A stochastic graph process for epidemic modelling

A stochastic graph process with a Markov property is introduced to model the flow of an infectious disease over a known contact network. The model provides a probability distribution over unobserved infectious pathways. The basic reproductive number in compartmental models is generalized to a dynamic reproductive number based on the sequence of outdegrees in the graph process. The cumulative resistance and threat associated with each individual is also measured based on the cumulative indegree and outdegree of the graph process. The model is applied to the outbreak data from the 2001 foot‐and‐mouth (FMD) outbreak in the United Kingdom. The Canadian Journal of Statistics 40: 55–67; 2012 © 2012 Statistical Society of Canada     

Terminating markov renewal processes

Several kinds of terminating Markov Renewal Processes are defined. Of interest in these processes are the time T until termination and the number of transitions N_T until termination. For several kinds of terminating processes, the distribution and moments of T and N_T are obtained along with their covariance. The distributions of associated cumulative processes are also considered. A Markov Renewal model is compared with results of Markov Chains used to model epidemics, and other examples are examined in compartmental modeling and competing risks.     

Final outcome probabilities for SIR epidemic model

Abstract

We consider an SIR stochastic epidemic model in which new infections occur at rate f(x, y), where x and y are, respectively, the number of susceptibles and infectives at the time of infection and f is a positive sequence of real functions. A simple explicit formula for the final size distribution is obtained. Some efficient recursive methods are proved for the exact calculation of this distribution. In addition, we give a Gaussian approximation for the final distribution using a diffusion process approximation.     

A Test to Detect Within-family Infectivity when the Whole Epidemic Process is Observed

An epidemic model for the spread of an infectious disease in a population of families is considered. The score test of the hypothesis that there is no higher infectivity between family members is constructed under the assumption that the epidemic process is observed continuously up to some time t . The score process is a martingale as a function of t and by letting the number of families tend to infinity, a central limit theorem for the process can be proved. The central limit theorem not only justifies a normal approximation of the test statistic—it also suggests a smaller variance estimator than expected.     

Computing the distribution of sequential Hölder norms of the Brownian motion

ABSTRACT

In this article, we give explicit formulas and study practical computations for the distribution function of sequential Hölder norms of a Brownian motion and of a Brownian bridge. We also discuss some statistical applications in the detection of some short “epidemic” changes in a sample.     

Retrospective change detection in categorical time series

The aim of this paper is to propose methods of detecting change in the coefficients of a multinomial logistic regression model for categorical time series offline. The alternatives to the null hypothesis of stationarity can be either the hypothesis that it is not true, or that there is a temporary change in the sequence. We use the efficient score vector of the partial likelihood function. This has several advantages. First, the alternative value of the parameter does not have to be estimated; hence, we have a procedure that has a simple structure with only one parameter estimation using all available observations. This is in contrast with the generalized likelihood ratio-based change point tests. The efficient score vector is used in various ways. As a vector, its components correspond to the different components of the multinomial logistic regression model’s parameter vector. Using its quadratic form a test can be defined, where the presence of a change in any or all parameters is tested for. If there are too many parameters one can test for any subset while treating the rest as nuisance parameters. Our motivating example is a DNA sequence of four categories, and our test result shows that in the published data the distribution of the four categories is not stationary.     

Analytic computation of nonparametric Marsan–Lengliné estimates for Hawkes point processes

In 2008, Marsan and Lengliné presented a nonparametric way to estimate the triggering function of a Hawkes process. Their method requires an iterative and computationally intensive procedure which ultimately produces only approximate maximum likelihood estimates (MLEs) whose asymptotic properties are poorly understood. Here, we note a mathematical curiosity that allows one to compute, directly and extremely rapidly, exact MLEs of the nonparametric triggering function. The method here requires that the number q of intervals on which the nonparametric estimate is sought equals the number n of observed points. The resulting estimates have very high variance but may be smoothed to form more stable estimates. The performance and computational efficiency of the proposed method is verified in two disparate, highly challenging simulation scenarios: first to estimate the triggering functions, with simulation-based 95% confidence bands, for earthquakes and their aftershocks in Loma Prieta, California, and second, to characterise triggering in confirmed cases of plague in the United States over the last century. In both cases, the proposed estimator can be used to describe the rate of contagion of the processes in detail, and the computational efficiency of the estimator facilitates the construction of simulation-based confidence intervals.