Inferences for Mixtures of Distributions for Centrally Censored Data with Partial Identification

In this article, several methods to make inferences about the parameters of a finite mixture of distributions in the context of centrally censored data with partial identification are revised. These methods are an adaptation of the work in Contreras-Cristán, Gutiérrez-Peña, and O'Reilly (2003 Contreras-Cristán , A. , Gutiérrez-Peña , E. , O'Reilly , F. ( 2003 ). Inferences using latent variables for mixtures of distributions for censored data with partial identification . Comm. Stat. Theor. Meth. 32 ( 4 ): 749 – 774 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) in the case of right censoring. The first method focuses on an asymptotic approximation to a suitably simplified likelihood using some latent quantities; the second method is based on the expectation-maximization (EM) algorithm. Both methods make explicit use of latent variables and provide computationally efficient procedures compared to non-Bayesian methods that deal directly with the full likelihood of the mixture appealing to its asymptotic approximation. The third method, from a Bayesian perspective, uses data augmentation to work with an uncensored sample. This last method is related to a recently proposed Bayesian method in Baker, Mengersen, and Davis (2005 Baker , P. , Mengersen , K. , Davis , G. ( 2005 ). A Bayesian solution to reconstructing centrally censored distributions . J. Agr. Biol. Environ. Stat. 1 : 61 – 84 . [Google Scholar]). Our proposal of the three adapted methods is shown to provide similar inferential answers, thus offering alternative analyses.     

Higher order asymptotic computation of Bayesian significance tests for precise null hypotheses in the presence of nuisance parameters

The full Bayesian significance test (FBST) was introduced by Pereira and Stern for measuring the evidence of a precise null hypothesis. The FBST requires both numerical optimization and multidimensional integration, whose computational cost may be heavy when testing a precise null hypothesis on a scalar parameter of interest in the presence of a large number of nuisance parameters. In this paper we propose a higher order approximation of the measure of evidence for the FBST, based on tail area expansions of the marginal posterior of the parameter of interest. When in particular focus is on matching priors, further results are highlighted. Numerical illustrations are discussed.     

Application of a predictive distribution formula to Bayesian computation for incomplete data models

We consider exact and approximate Bayesian computation in the presence of latent variables or missing data. Specifically we explore the application of a posterior predictive distribution formula derived in Sweeting And Kharroubi (2003), which is a particular form of Laplace approximation, both as an importance function and a proposal distribution. We show that this formula provides a stable importance function for use within poor man’s data augmentation schemes and that it can also be used as a proposal distribution within a Metropolis-Hastings algorithm for models that are not analytically tractable. We illustrate both uses in the case of a censored regression model and a normal hierarchical model, with both normal and Student t distributed random effects. Although the predictive distribution formula is motivated by regular asymptotic theory, it is not necessary that the likelihood has a closed form or that it possesses a local maximum.     

Approximate Bayesian Inference for Survival Models

Abstract. Bayesian analysis of time‐to‐event data, usually called survival analysis, has received increasing attention in the last years. In Cox‐type models it allows to use information from the full likelihood instead of from a partial likelihood, so that the baseline hazard function and the model parameters can be jointly estimated. In general, Bayesian methods permit a full and exact posterior inference for any parameter or predictive quantity of interest. On the other side, Bayesian inference often relies on Markov chain Monte Carlo (MCMC) techniques which, from the user point of view, may appear slow at delivering answers. In this article, we show how a new inferential tool named integrated nested Laplace approximations can be adapted and applied to many survival models making Bayesian analysis both fast and accurate without having to rely on MCMC‐based inference.     

Extended Bayesian model averaging for heritability in twin studies

Family studies are often conducted to examine the existence of familial aggregation. Particularly, twin studies can model separately the genetic and environmental contribution. Here we estimate the heritability of quantitative traits via variance components of random-effects in linear mixed models (LMMs). The motivating example was a myopia twin study containing complex nesting data structures: twins and siblings in the same family and observations on both eyes for each individual. Three models are considered for this nesting structure. Our proposal takes into account the model uncertainty in both covariates and model structures via an extended Bayesian model averaging (EBMA) procedure. We estimate the heritability using EBMA under three suggested model structures. When compared with the results under the model with the highest posterior model probability, the EBMA estimate has smaller variation and is slightly conservative. Simulation studies are conducted to evaluate the performance of variance-components estimates, as well as the selections of risk factors, under the correct or incorrect structure. The results indicate that EBMA, with consideration of uncertainties in both covariates and model structures, is robust in model misspecification than the usual Bayesian model averaging (BMA) that considers only uncertainty in covariates selection.     

Generalized multiple-point Metropolis algorithms for approximate Bayesian computation

It is well known that the approximate Bayesian computation algorithm based on Markov chain Monte Carlo methods suffers from the sensitivity to the choice of starting values, inefficiency and a low acceptance rate. To overcome these problems, this study proposes a generalization of the multiple-point Metropolis algorithm, which proceeds by generating multiple-dependent proposals and then by selecting a candidate among the set of proposals on the basis of weights that can be chosen arbitrarily. The performance of the proposed algorithm is illustrated by using both simulated and real data.     

Monte Carlo Methods for Bayesian Inference on the Linear Hazard Rate Distribution

The Bayesian estimation and prediction problems for the linear hazard rate distribution under general progressively Type-II censored samples are considered in this article. The conventional Bayesian framework as well as the Markov Chain Monte Carlo (MCMC) method to generate the Bayesian conditional probabilities of interest are discussed. Sensitivity of the prior for the model is also examined. The flood data on Fox River, Wisconsin, from 1918 to 1950, are used to illustrate all the methods of inference discussed in this article.     

Laplace approximations for censored linear regression models

We consider approximate Bayesian inference about scalar parameters of linear regression models with possible censoring. A second-order expansion of their Laplace posterior is seen to have a simple and intuitive form for logconcave error densities with nondecreasing hazard functions. The accuracy of the approximations is assessed for normal and Gumbel errors when the number of regressors increases with sample size. Perturbations of the prior and the likelihood are seen to be easily accommodated within our framework. Links with the work of DiCiccio et al. (1990) and Viveros and Sprott (1987) extend the applicability of our results to conditional frequentist inference based on likelihood-ratio statistics.     

A Case Study for Modelling Cancer Incidence Using Bayesian Spatio‐Temporal Models

Researchers familiar with spatial models are aware of the challenge of choosing the level of spatial aggregation. Few studies have been published on the investigation of temporal aggregation and its impact on inferences regarding disease outcome in space–time analyses. We perform a case study for modelling individual disease outcomes using several Bayesian hierarchical spatio‐temporal models, while taking into account the possible impact of spatial and temporal aggregation. Using longitudinal breast cancer data from South East Queensland, Australia, we consider both parametric and non‐parametric formulations for temporal effects at various levels of aggregation. Two temporal smoothness priors are considered separately; each is modelled with fixed effects for the covariates and an intrinsic conditional autoregressive prior for the spatial random effects. Our case study reveals that different model formulations produce considerably different model performances. For this particular dataset, a classical parametric formulation that assumes a linear time trend produces the best fit among the five models considered. Different aggregation levels of temporal random effects were found to have little impact on model goodness‐of‐fit and estimation of fixed effects.     

Bayesian quantile regression for longitudinal data models

In this paper, we discuss a fully Bayesian quantile inference using Markov Chain Monte Carlo (MCMC) method for longitudinal data models with random effects. Under the assumption of error term subject to asymmetric Laplace distribution, we establish a hierarchical Bayesian model and obtain the posterior distribution of unknown parameters at τ-th level. We overcome the current computational limitations using two approaches. One is the general MCMC technique with Metropolis–Hastings algorithm and another is the Gibbs sampling from the full conditional distribution. These two methods outperform the traditional frequentist methods under a wide array of simulated data models and are flexible enough to easily accommodate changes in the number of random effects and in their assumed distribution. We apply the Gibbs sampling method to analyse a mouse growth data and some different conclusions from those in the literatures are obtained.     

Simple and accurate inference for the mean of the gamma model

The two-parameter gamma model is widely used in reliability, environmental, medical and other areas of statistics. It has a two-dimensional sufficient statistic, and a two-dimensional parameter which can be taken to describe shape and mean. This makes it closely comparable to the normal model, but it differs substantially in that the exact distribution for the minimal sufficient statistic is not available. Some recently developed asymptotic theory is used to derive an approximation for observed levels of significance and confidence intervals for the mean parameter of the model. The approximation is as easy to apply as first-order methods, and substantially more accurate.     

Inference Using Latent Variables for Mixtures of Distributions for Censored Data with Partial Identification

Abstract

In this article two methods are proposed to make inferences about the parameters of a finite mixture of distributions in the context of partially identifiable censored data. The first method focuses on a mixture of location and scale models and relies on an asymptotic approximation to a suitably constructed augmented likelihood; the second method provides a full Bayesian analysis of the mixture based on a Gibbs sampler. Both methods make explicit use of latent variables and provide computationally efficient procedures compared to other methods which deal directly with the likelihood of the mixture. This may be crucial if the number of components in the mixture is not small. Our proposals are illustrated on a classical example on failure times for communication devices first studied by Mendenhall and Hader (Mendenhall, W., Hader, R. J. (1958 Mendenhall, W. and Hader, R. J. 1958. Estimation of parameters of mixed exponentially distributed failure time distributions from censored life test data. Biometrika, 45: 504–520. [Crossref], [Web of Science ®] , [Google Scholar]). Estimation of parameters of mixed exponentially distributed failure time distributions from censored life test data. Biometrika 45:504–520.). In addition, we study the coverage of the confidence intervals obtained from each of the methods by means of a small simulation exercise.     

On implementing Jeffreys' substitution likelihood for Bayesian inference concerning the medians of unknown distributions

When statisticians are uncertain as to which parametric statistical model to use to analyse experimental data, they will often resort to a non-parametric approach. The purpose of this paper is to provide insight into a simple approach to take when it is unclear as to the appropriate parametric model and plan to conduct a Bayesian analysis. I introduce an approximate, or substitution likelihood, first proposed by Harold Jeffreys in 1939 and show how to implement the approach combined with both a non-informative and an informative prior to provide a random sample from the posterior distribution of the median of the unknown distribution. The first example I use to demonstrate the approach is a within-patient bioequivalence design and then show how to extend the approach to a parallel group design.