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 class of maximum-entropy multivariate distributions

This paper characterizes a class of multivariate distributions that includes the multinormal and is contained in the exponential family. The wide range of possible applications of these distributions is suggested by some of hte characteristics germane to them: First, they maximize Shannon's entropy among all distributions that have finite moments of given orders. As such, they constitute a class of distributions that includes the multinormal and some likely alternatives. Second, they can exhibit several modes, and, further-more, they do so with a relatively small number of parameters (compared to mixtures of multinormals). Third, they are the stationary distributions of certain diffusion processes. Fourth, they approximate, near the multinormal, the multivariate Pearson family. And fifth, the maximum likelihood estimators of their population moments are the sample moments. Two possible methods of estimating the distributions are studied in this paper: maximum likelihood estimation, and a fast procedure that can be used to find consistent estimators of the parameters via sample moments. A FORTTAN subroutine that implements the latter method is also provided.     

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.     

A conditionally-unbiased estimator of population size based on plant-capture in continuous time

This paper proposes an estimator of the unknown size of a target population to which has been added a planted population of known size. The augmented population is observed for a fixed time and individuals are sighted according to independent Poisson processes. These processes may be time-inhomogeneous, but, within each population, the intensity function is the same for all individuals. When the two populations have the same intensity function, known results on factorial series distributions suggest that the proposed estimator is approximately unbiased and provide a useful estimator of standard deviation. Except for short sampling times, computational results confirm that the proposed population-size estimator is nearly unbiased, and indicate that it gives a better overall performance than existing estimators in the literature. The robustness of this performance is investigated in situations in which it cannot be assumed that the behaviour of the plants matches that of individuals from the target population.     

On the integrated maximum likelihood estimators for a closed population capture–recapture model with unequal capture probabilities

Nuisance parameter elimination is a central problem in capture–recapture modelling. In this paper, we consider a closed population capture–recapture model which assumes the capture probabilities varies only with the sampling occasions. In this model, the capture probabilities are regarded as nuisance parameters and the unknown number of individuals is the parameter of interest. In order to eliminate the nuisance parameters, the likelihood function is integrated with respect to a weight function (uniform and Jeffrey's) of the nuisance parameters resulting in an integrated likelihood function depending only on the population size. For these integrated likelihood functions, analytical expressions for the maximum likelihood estimates are obtained and it is proved that they are always finite and unique. Variance estimates of the proposed estimators are obtained via a parametric bootstrap resampling procedure. The proposed methods are illustrated on a real data set and their frequentist properties are assessed by means of a simulation study.     

More flexible sequential and non-sequential designs in long-term clinical trial

In this paper, we describe decision making procedures as they exist in most clinical trials,review some recently suggested approaches to monitoring and clarify how these methods allow greater flexibility in monitoring and explicit specification of data monitoring methods in the protocol.     

A Bootstrap Likelihood Approach to Bayesian Computation

There is an increasing amount of literature focused on Bayesian computational methods to address problems with intractable likelihood. One approach is a set of algorithms known as Approximate Bayesian Computational (ABC) methods. One of the problems with these algorithms is that their performance depends on the appropriate choice of summary statistics, distance measure and tolerance level. To circumvent this problem, an alternative method based on the empirical likelihood has been introduced. This method can be easily implemented when a set of constraints, related to the moments of the distribution, is specified. However, the choice of the constraints is sometimes challenging. To overcome this difficulty, we propose an alternative method based on a bootstrap likelihood approach. The method is easy to implement and in some cases is actually faster than the other approaches considered. We illustrate the performance of our algorithm with examples from population genetics, time series and stochastic differential equations. We also test the method on a real dataset.     

A Bayesian analysis of the Conway–Maxwell–Poisson cure rate model

The purpose of this paper is to develop a Bayesian analysis for the right-censored survival data when immune or cured individuals may be present in the population from which the data is taken. In our approach the number of competing causes of the event of interest follows the Conway–Maxwell–Poisson distribution which generalizes the Poisson distribution. Markov chain Monte Carlo (MCMC) methods are used to develop a Bayesian procedure for the proposed model. Also, some discussions on the model selection and an illustration with a real data set are considered.     

The generalized log-gamma mixture model with covariates: local influence and residual analysis

In a sample of censored survival times, the presence of an immune proportion of individuals who are not subject to death, failure or relapse, may be indicated by a relatively high number of individuals with large censored survival times. In this paper the generalized log-gamma model is modified for the possibility that long-term survivors may be present in the data. The model attempts to separately estimate the effects of covariates on the surviving fraction, that is, the proportion of the population for which the event never occurs. The logistic function is used for the regression model of the surviving fraction. Inference for the model parameters is considered via maximum likelihood. Some influence methods, such as the local influence and total local influence of an individual are derived, analyzed and discussed. Finally, a data set from the medical area is analyzed under the log-gamma generalized mixture model. A residual analysis is performed in order to select an appropriate model. The authors would like to thank the editor and referees for their helpful comments. This work was supported by CNPq, Brazil.     

倒向随机微分方程中非参数估计的核函数选择

比较了多种类型的核函数下倒向随机微分方程（BSDE）中生成元z的非参数估计方法,利用不同的核函数估计BSDE中的生成元z的非参数估计,在均方误差意义下比较了8种不同的核函数下得到的BSDE的生成元z的非参数估计的精度,统计分析结果显示Gaussian核函数下的估计效果最好。     

Testing equality of survival distributions when the population marks are missing

This paper introduces a nonparametric approach for testing the equality of two or more survival distributions based on right censored failure times with missing population marks for the censored observations. The standard log-rank test is not applicable here because the population membership information is not available for the right censored individuals. We propose to use the imputed population marks for the censored observations leading to fractional at-risk sets that can be used in a two sample censored data log-rank test. We demonstrate with a simple example that there could be a gain in power by imputing population marks (the proposed method) for the right censored individuals compared to simply removing them (which also would maintain the right size). Performance of the imputed log-rank tests obtained this way is studied through simulation. We also obtain an asymptotic linear representation of our test statistic. Our testing methodology is illustrated using a real data set.     

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.     

Some stochastic properties of conditionally dependent frailty models

The frailty approach is commonly used in reliability theory and survival analysis to model the dependence between lifetimes of individuals or components subject to common risk factors; according to this model the frailty (an unobservable random vector that describes environmental conditions) acts simultaneously on the hazard functions of the lifetimes. Some interesting conditions for stochastic comparisons between random vectors defined in accordance with these models have been described in the literature; in particular, comparisons between frailty models have been studied by assuming independence for the baseline survival functions and the corresponding environmental parameters. In this paper, a generalization of these models is developed, which assumes conditional dependence between the components of the random vector, and some conditions for stochastic comparisons are provided. Some examples of frailty models satisfying these conditions are also described.     

Distance sampling: estimating animal density

All too often we hear in the news statements like "there are, at most, a few hundred individuals left of this endangered species" or "there is small hope for the persistence of this population given that so few are left". How do scientists count animals to make such statements? Tiago Marques explains the concepts and pitfalls of distance sampling—one of the most widely used methods for estimating animal populations.     

Analysis of reliability characteristics in the acceptance sampling tests

Until now, various acceptance reliability sampling plans have been developed based on different life tests of items. However, the statistical effect of the acceptance sampling tests on the reliability characteristic of the lots accepted in the test has not been appropriately addressed. In this paper, we deal with an acceptance reliability sampling plan under a ‘general framework’ and discuss the corresponding statistical effect of the acceptance sampling tests. The lifetime of the population before the acceptance test and that of population ‘conditional on the acceptance’ in the sampling test are stochastically compared. The improvement of reliability characteristics of the population conditional on the acceptance in the sampling test is precisely analyzed.     

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.     

Modeling attainment of steady state of drug concentration in plasma by means of a Bayesian approach using MCMC methods

The approach of Bayesian mixed effects modeling is an appropriate method for estimating both population-specific as well as subject-specific times to steady state. In addition to pure estimation, the approach allows to determine the time until a certain fraction of individuals of a population has reached steady state with a pre-specified certainty. In this paper a mixed effects model for the parameters of a nonlinear pharmacokinetic model is used within a Bayesian framework. Model fitting by means of Markov Chain Monte Carlo methods as implemented in the Gibbs sampler as well as the extraction of estimates and probability statements of interest are described. Finally, the proposed approach is illustrated by application to trough data from a multiple dose clinical trial.     

蒙特卡罗方法下线性模型的异方差性检验方法

在已有的异方差性检验方法的基础上,运用蒙特卡罗方法,借助permutation检验思想,在不假定随机扰动项服从同一分布族的条件下,通过从大样本中提取大量的子样本,不断对线性模型进行拟合和检验,根据异方差为真的频率大小,给出了一种新的异方差检验方法。随机模拟表明本检验方法优于传统方法。     

A Note on the Inverse Birthday Problem With Applications

The classical birthday problem considers the probability that at least two people in a group of size N share the same birthday. The inverse birthday problem considers the estimation of the size N of a group given the number of different birthdays in the group. In practice, this problem is analogous to estimating the size of a population from occurrence data only. The inverse problem can be solved via two simple approaches including the method of moments for a multinominal model and the maximum likelihood estimate of a Poisson model, which we present in this study. We investigate properties of both methods and show that they can yield asymptotically equivalent Wald-type interval estimators. Moreover, we show that these methods estimate a lower bound for the population size when birth rates are nonhomogenous or individuals in the population are aggregated. A simulation study was conducted to evaluate the performance of the point estimates arising from the two approaches and to compare the performance of seven interval estimators, including likelihood ratio and log-transformation methods. We illustrate the utility of these methods by estimating: (1) the abundance of tree species over a 50-hectare forest plot, (2) the number of Chlamydia infections when only the number of different birthdays of the patients is known, and (3) the number of rainy days when the number of rainy weeks is known. Supplementary materials for this article are available online.     

Semiparametric estimation of moment condition models with weakly dependent data

This paper develops the asymptotic theory for the estimation of smooth semiparametric generalized estimating equations models with weakly dependent data. The paper proposes new estimation methods based on smoothed two-step versions of the generalised method of moments and generalised empirical likelihood methods. An important aspect of the paper is that it allows the first-step estimation to have an effect on the asymptotic variances of the second-step estimators and explicitly characterises this effect for the empirically relevant case of the so-called generated regressors. The results of the paper are illustrated with a partially linear model that has not been previously considered in the literature. The proofs of the results utilise a new uniform strong law of large numbers and a new central limit theorem for U-statistics with varying kernels that are of independent interest.