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 Stochastic Epidemics in Populations with Random Social Structure

A single-population Markovian stochastic epidemic model is defined so that the underlying social structure of the population is described by a Bernoulli random graph. The parameters of the model govern the rate of infection, the length of the infectious period, and the probability of social contact with another individual in the population. Markov chain Monte Carlo methods are developed to facilitate Bayesian inference for the parameters of both the epidemic model and underlying unknown social structure. The methods are applied in various examples of both illustrative and real-life data, with two different kinds of data structure considered.     

Statistical Inference on a Stochastic Epidemic Model

In this work, we develop statistical inference for the parameters of a discrete-time stochastic SIR epidemic model. We use a Markov chain for describing the dynamic behavior of the epidemic. Specifically, we propose estimators for the contact and removal rates based on the maximum likelihood and martingale methods, and establish their asymptotic distributions. The obtained results are applied in the statistical analysis of the basic reproduction number, a quantity that is useful in establishing vaccination policies. In order to evaluate the population size for which the results are useful, a numerical study is carried out. Finally, a comparison of the maximum likelihood and martingale estimators is conducted by means of Monte Carlo simulations.     

Likelihood estimation for stochastic compartmental models using Markov chain methods

This paper presents a method for estimating likelihood ratios for stochastic compartment models when only times of removals from a population are observed. The technique operates by embedding the models in a composite model parameterised by an integer k which identifies a switching time when dynamics change from one model to the other. Likelihood ratios can then be estimated from the posterior density of k using Markov chain methods. The techniques are illustrated by a simulation study involving an immigration-death model and validated using analytic results derived for this case. They are also applied to compare the fit of stochastic epidemic models to historical data on a smallpox epidemic. In addition to estimating likelihood ratios, the method can be used for direct estimation of likelihoods by selecting one of the models in the comparison to have a known likelihood for the observations. Some general properties of the likelihoods typically arising in this scenario, and their implications for inference, are illustrated and discussed.     

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.     

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.     

Statement of Withdrawal: Statistical analysis of an endemic disease from a capture–recapture experiment

There are a number of statistical techniques for analysing epidemic outbreaks. However, many diseases are endemic within populations and the analysis of such diseases are complicated by changing population demography. Motivated by the spread of cowpox among rodent populations, a combined mathematical model for population and disease dynamics is introduced. An MCMC algorithm is then constructed to make statistical inference for the model based on data being obtained from a capture–recapture experiment. The statistical analysis is used to identify the key elements in the spread of the cowpox virus.     

Statistical analysis of an endemic disease from a capture–recapture experiment

There are a number of statistical techniques for analysing epidemic outbreaks. However, many diseases are endemic within populations and the analysis of such diseases is complicated by changing population demography. Motivated by the spread of cowpox amongst rodent populations, a combined mathematical model for population and disease dynamics is introduced. A Markov chain Monte Carlo algorithm is then constructed to make statistical inference for the model based on data being obtained from a capture–recapture experiment. The statistical analysis is used to identify the key elements in the spread of the cowpox virus.     

Asymptotic distribution of martingale estimators for a class of epidemic models

This article is a contribution to the asymptotic inference on the parameters of a quite general class of stochastic models for the spread of epidemics developing in closed populations. Various epidemic models are contained within our framework, for instance, a stochastic version of the Kermack and McKendrick model and the SIS epidemic model. Each model belonging to this class, which consists in a family of discrete-time stochastic process, contains certain parameters to be estimated by means of martingale estimators. Some particular cases defined by means of Markov chains are included in our setting. The main aim of this work is to prove consistency and asymptotic normality of these estimators. Some hypothesis tests based on the main results are also shown.     

Local sensitivity approximations for selectivity bias

Observational data analysis is often based on tacit assumptions of ignorability or randomness. The paper develops a general approach to local sensitivity analysis for selectivity bias, which aims to study the sensitivity of inference to small departures from such assumptions. If M is a model assuming ignorability, we surround M by a small neighbourhood N defined in the sense of Kullback–Leibler divergence and then compare the inference for models in N with that for M . Interpretable bounds for such differences are developed. Applications to missing data and to observational comparisons are discussed. Local approximations to sensitivity analysis are model robust and can be applied to a wide range of statistical problems.     

A Partial Likelihood Estimator of Vaccine Efficacy

A partial likelihood method is proposed for estimating vaccine efficacy for a general epidemic model. In contrast to the maximum likelihood estimator (MLE) which requires complete observation of the epidemic, the suggested method only requires information on the sequence in which individuals are infected and not the exact infection times. A simulation study shows that the method performs almost as well as the MLE. The method is applied to data on the infectious disease mumps.     

Bayesian diffusion process models with time-varying parameters

The diffusion process is a widely used statistical model for many natural dynamic phenomena but its inference is very complicated because complete data describing the diffusion sample path is not necessarily available. In addition, data is often collected with substantial uncertainty and it is not uncommon to have missing observations. Thus, the observed process will be discrete over a finite time period and the marginal likelihood given by this discrete data is not always available. In this paper, we consider a class of nonstationary diffusion process models with not only the measurement error but also discretely time-varying parameters which are modeled via a state space model. Hierarchical Bayesian inference for such a diffusion process model with time-varying parameters is applied to financial data.     

A network epidemic model for online community commissioning data

A statistical model assuming a preferential attachment network, which is generated by adding nodes sequentially according to a few simple rules, usually describes real-life networks better than a model assuming, for example, a Bernoulli random graph, in which any two nodes have the same probability of being connected, does. Therefore, to study the propagation of “infection” across a social network, we propose a network epidemic model by combining a stochastic epidemic model and a preferential attachment model. A simulation study based on the subsequent Markov Chain Monte Carlo algorithm reveals an identifiability issue with the model parameters. Finally, the network epidemic model is applied to a set of online commissioning data.     

Avoiding 'data snooping' in multilevel and mixed effects models

Summary.  Multilevel or mixed effects models are commonly applied to hierarchical data. The level 2 residuals, which are otherwise known as random effects, are often of both substantive and diagnostic interest. Substantively, they are frequently used for institutional comparisons or rankings. Diagnostically, they are used to assess the model assumptions at the group level. Inference on the level 2 residuals, however, typically does not account for 'data snooping', i.e. for the harmful effects of carrying out a multitude of hypothesis tests at the same time. We provide a very general framework that encompasses both of the following inference problems: inference on the 'absolute' level 2 residuals to determine which are significantly different from 0, and inference on any prespecified number of pairwise comparisons. Thus, the user has the choice of testing the comparisons of interest. As our methods are flexible with respect to the estimation method that is invoked, the user may choose the desired estimation method accordingly. We demonstrate the methods with the London education authority data, the wafer data and the National Educational Longitudinal Study data.     

Sequential Bayesian inference in hidden Markov stochastic kinetic models with application to detection and response to seasonal epidemics

We study sequential Bayesian inference in stochastic kinetic models with latent factors. Assuming continuous observation of all the reactions, our focus is on joint inference of the unknown reaction rates and the dynamic latent states, modeled as a hidden Markov factor. Using insights from nonlinear filtering of continuous-time jump Markov processes we develop a novel sequential Monte Carlo algorithm for this purpose. Our approach applies the ideas of particle learning to minimize particle degeneracy and exploit the analytical jump Markov structure. A motivating application of our methods is modeling of seasonal infectious disease outbreaks represented through a compartmental epidemic model. We demonstrate inference in such models with several numerical illustrations and also discuss predictive analysis of epidemic countermeasures using sequential Bayes estimates.     

Inference for Epidemics with Three Levels of Mixing: Methodology and Application to a Measles Outbreak

Abstract. A stochastic epidemic model is defined in which each individual belongs to a household, a secondary grouping (typically school or workplace) and also the community as a whole. Moreover, infectious contacts take place in these three settings according to potentially different rates. For this model, we consider how different kinds of data can be used to estimate the infection rate parameters with a view to understanding what can and cannot be inferred. Among other things we find that temporal data can be of considerable inferential benefit compared with final size data, that the degree of heterogeneity in the data can have a considerable effect on inference for non‐household transmission, and that inferences can be materially different from those obtained from a model with only two levels of mixing. We illustrate our findings by analysing a highly detailed dataset concerning a measles outbreak in Hagelloch, Germany.     

Nonparametric estimation of the sojourn time distributions for a multipath model

Summary. We use a multipath (multistate) model to describe data with multiple end points. Statistical inference based on the intermediate end point is challenging because of the problems of nonidentifiability and dependent censoring. We study nonparametric estimation for the path probability and the sojourn time distributions between the states. The methodology proposed can be applied to analyse cure models which account for the competing risk of death. Asymptotic properties of the estimators proposed are derived. Simulation shows that the methods proposed have good finite sample performance. The methodology is applied to two data sets.     

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.     

Inference with a contrast-based posterior distribution and application in spatial statistics

The likelihood function is often used for parameter estimation. Its use, however, may cause difficulties in specific situations. In order to circumvent these difficulties, we propose a parameter estimation method based on the replacement of the likelihood in the formula of the Bayesian posterior distribution by a function which depends on a contrast measuring the discrepancy between observed data and a parametric model. The properties of the contrast-based (CB) posterior distribution are studied to understand what the consequences of incorporating a contrast in the Bayes formula are. We show that the CB-posterior distribution can be used to make frequentist inference and to assess the asymptotic variance matrix of the estimator with limited analytical calculations compared to the classical contrast approach. Even if the primary focus of this paper is on frequentist estimation, it is shown that for specific contrasts the CB-posterior distribution can be used to make inference in the Bayesian way.The method was used to estimate the parameters of a variogram (simulated data), a Markovian model (simulated data) and a cylinder-based autosimilar model describing soil roughness (real data). Even if the method is presented in the spatial statistics perspective, it can be applied to non-spatial data.     

Inference With Dyadic Data: Asymptotic Behavior of the Dyadic-Robust t-Statistic

ABSTRACT

This article is concerned with inference in the linear model with dyadic data. Dyadic data are indexed by pairs of “units;” for example, trade data between pairs of countries. Because of the potential for observations with a unit in common to be correlated, standard inference procedures may not perform as expected. We establish a range of conditions under which a t-statistic with the dyadic-robust variance estimator of Fafchamps and Gubert is asymptotically normal. Using our theoretical results as a guide, we perform a simulation exercise to study the validity of the normal approximation, as well as the performance of a novel finite-sample correction. We conclude with guidelines for applied researchers wishing to use the dyadic-robust estimator for inference.