The use of variance components for the assessment of outcome measures in rheumatology

There is current interest in the development of new or improved outcome measures for rheumatological diseases. In the early stages of development, attention is usually directed to how well the measure distinguishes between patients and whether different observers attach similar values of the measure to the same patient. An approach, based on variance components, to the assessment of outcome measures is presented. The need to assess different aspects of variation associated with a measure is stressed. The terms ‘observer reliability’ and ‘agreement’ are frequently used in the evaluation of measurement instruments, and are often used interchangeably. In this paper, we use the terms to refer to different concepts assessing different aspects of variation. They are likely to correspond well in heterogeneous populations, but not in homogeneous populations where reliability will generally be low but agreement may well be high. Results from a real patient exercise, designed to study a set of tools for assessing myositis outcomes, are used to illustrate the approach that examines both reliability and agreement, and the need to evaluate both is demonstrated. A new measure of agreement, based on the ratio of standard deviations, is presented and inference procedures are discussed. To facilitate the interpretation of the combination of measures of reliability and agreement, a classification system is proposed that provides a summary of the performance of the tools. The approach is demonstrated for discrete ordinal and continuous outcomes.     

Assessing inter- and intra-agreement for dependent binary data: a Bayesian hierarchical correlation approach

Agreement measures are designed to assess consistency between different instruments rating measurements of interest. When the individual responses are correlated with multilevel structure of nestings and clusters, traditional approaches are not readily available to estimate the inter- and intra-agreement for such complex multilevel settings. Our research stems from conformity evaluation between optometric devices with measurements on both eyes, equality tests of agreement in high myopic status between monozygous twins and dizygous twins, and assessment of reliability for different pathologists in dysplasia. In this paper, we focus on applying a Bayesian hierarchical correlation model incorporating adjustment for explanatory variables and nesting correlation structures to assess the inter- and intra-agreement through correlations of random effects for various sources. This Bayesian generalized linear mixed-effects model (GLMM) is further compared with the approximate intra-class correlation coefficients and kappa measures by the traditional Cohen’s kappa statistic and the generalized estimating equations (GEE) approach. The results of comparison studies reveal that the Bayesian GLMM provides a reliable and stable procedure in estimating inter- and intra-agreement simultaneously after adjusting for covariates and correlation structures, in marked contrast to Cohen’s kappa and the GEE approach.     

Posterior analysis of the compound Rayleigh distribution under balanced loss functions for censored data

This paper develops Bayesian analysis in the context of progressively Type II censored data from the compound Rayleigh distribution. The maximum likelihood and Bayes estimates along with associated posterior risks are derived for reliability performances under balanced loss functions by assuming continuous priors for parameters of the distribution. A practical example is used to illustrate the estimation methods. A simulation study has been carried out to compare the performance of estimates. The study indicates that Bayesian estimation should be preferred over maximum likelihood estimation. In Bayesian estimation, the balance general entropy loss function can be effectively employed for optimal decision-making.     

Assessing safety at the end of clinical trials using system organ classes: A case and comparative study

Recent approaches to the statistical analysis of adverse event (AE) data in clinical trials have proposed the use of groupings of related AEs, such as by system organ class (SOC). These methods have opened up the possibility of scanning large numbers of AEs while controlling for multiple comparisons, making the comparative performance of the different methods in terms of AE detection and error rates of interest to investigators. We apply two Bayesian models and two procedures for controlling the false discovery rate (FDR), which use groupings of AEs, to real clinical trial safety data. We find that while the Bayesian models are appropriate for the full data set, the error controlling methods only give similar results to the Bayesian methods when low incidence AEs are removed. A simulation study is used to compare the relative performances of the methods. We investigate the differences between the methods over full trial data sets, and over data sets with low incidence AEs and SOCs removed. We find that while the removal of low incidence AEs increases the power of the error controlling procedures, the estimated power of the Bayesian methods remains relatively constant over all data sizes. Automatic removal of low-incidence AEs however does have an effect on the error rates of all the methods, and a clinically guided approach to their removal is needed. Overall we found that the Bayesian approaches are particularly useful for scanning the large amounts of AE data gathered.     

Forecasting Performance of an Open Economy DSGE Model

This paper analyzes the forecasting performance of an open economy dynamic stochastic general equilibrium (DSGE) model, estimated with Bayesian methods, for the Euro area during 1994Q1–2002Q4. We compare the DSGE model and a few variants of this model to various reduced-form forecasting models such as vector autoregressions (VARs) and vector error correction models (VECM), estimated both by maximum likelihood and two different Bayesian approaches, and traditional benchmark models, e.g., the random walk. The accuracy of point forecasts, interval forecasts and the predictive distribution as a whole are assessed in an out-of-sample rolling event evaluation using several univariate and multivariate measures. The results show that the open economy DSGE model compares well with more empirical models and thus that the tension between rigor and fit in older generations of DSGE models is no longer present. We also critically examine the role of Bayesian model probabilities and other frequently used low-dimensional summaries, e.g., the log determinant statistic, as measures of overall forecasting performance.     

Forecasting Performance of an Open Economy DSGE Model

This paper analyzes the forecasting performance of an open economy dynamic stochastic general equilibrium (DSGE) model, estimated with Bayesian methods, for the Euro area during 1994Q1-2002Q4. We compare the DSGE model and a few variants of this model to various reduced-form forecasting models such as vector autoregressions (VARs) and vector error correction models (VECM), estimated both by maximum likelihood and two different Bayesian approaches, and traditional benchmark models, e.g., the random walk. The accuracy of point forecasts, interval forecasts and the predictive distribution as a whole are assessed in an out-of-sample rolling event evaluation using several univariate and multivariate measures. The results show that the open economy DSGE model compares well with more empirical models and thus that the tension between rigor and fit in older generations of DSGE models is no longer present. We also critically examine the role of Bayesian model probabilities and other frequently used low-dimensional summaries, e.g., the log determinant statistic, as measures of overall forecasting performance.     

Bayesian reliability when system and subsystem failure data are obtained in the same time period

Previously, Bayesian anomaly was reported for estimating reliability when subsystem failure data and system failure data were obtained from the same time period. As a result, a practical method for mitigating Bayesian anomaly was developed. In the first part of this paper, however, we show that the Bayesian anomaly can be avoided as long as the same failure information is incorporated in the model. In the second part of this paper, we consider a problem of estimating the Bayesian reliability when the failure count data on subsystems and systems are obtained from the same time period. We show that Bayesian anomaly does not exist when using the multinomial distribution with the Dirichlet prior distribution. A numerical example is given to compare the proposed method with the previous methods.     

Failure probability estimation under additional subsystem information with application to semiconductor burn-in

In the classical approach to qualitative reliability demonstration, system failure probabilities are estimated based on a binomial sample drawn from the running production. In this paper, we show how to take account of additional available sampling information for some or even all subsystems of a current system under test with serial reliability structure. In that connection, we present two approaches, a frequentist and a Bayesian one, for assessing an upper bound for the failure probability of serial systems under binomial subsystem data. In the frequentist approach, we introduce (i) a new way of deriving the probability distribution for the number of system failures, which might be randomly assembled from the failed subsystems and (ii) a more accurate estimator for the Clopper–Pearson upper bound using a beta mixture distribution. In the Bayesian approach, however, we infer the posterior distribution for the system failure probability on the basis of the system/subsystem testing results and a prior distribution for the subsystem failure probabilities. We propose three different prior distributions and compare their performances in the context of high reliability testing. Finally, we apply the proposed methods to reduce the efforts of semiconductor burn-in studies by considering synergies such as comparable chip layers, among different chip technologies.     

An adaptive empirical Bayesian thresholding procedure for analysing microarray experiments with replication

Summary.  A typical microarray experiment attempts to ascertain which genes display differential expression in different samples. We model the data by using a two-component mixture model and develop an empirical Bayesian thresholding procedure, which was originally introduced for thresholding wavelet coefficients, as an alternative to the existing methods for determining differential expression across thousands of genes. The method is built on sound theoretical properties and has easy computer implementation in the R statistical package. Furthermore, we consider improvements to the standard empirical Bayesian procedure when replication is present, to increase the robustness and reliability of the method. We provide an introduction to microarrays for those who are unfamilar with the field and the proposed procedure is demonstrated with applications to two-channel complementary DNA microarray experiments.     

A bayesian alternative to the sign test in the presence of ties

Bayesian alternatives to the sign test are proposed which incorporate the number of ties observed. These alternatives arise from different strategies in dealing with the number of ties. One strategy is incorporating the true proportion of ties into the hypotheses of interest. The Bayesian methods are compared to each other and to the typical sign test in a simulation study. Also, the new methods are compared to another version of the sign test proposed by Coakley and Heise (1996). This new version of the sign test was shown to perform especially well in situations where the probability of observing a tie is very high. Although one of the Bayesian methods appears to perform best overall in the simulation study, its performance is not dominating and the easy to use typical sign test generally performs very well.     

Diagnostics of prior-data agreement in applied Bayesian analysis

This article focused on the definition and the study of a binary Bayesian criterion which measures a statistical agreement between a subjective prior and data information. The setting of this work is concrete Bayesian studies. It is an alternative and a complementary tool to the method recently proposed by Evans and Moshonov, [M. Evans and H. Moshonov, Checking for Prior-data conflict, Bayesian Anal. 1 (2006), pp. 893–914]. Both methods try to help the work of the Bayesian analyst, from preliminary to the posterior computation. Our criterion is defined as a ratio of Kullback–Leibler divergences; two of its main features are to make easy the check of a hierarchical prior and be used as a default calibration tool to obtain flat but proper priors in applications. Discrete and continuous distributions exemplify the approach and an industrial case study in reliability, involving the Weibull distribution, is highlighted.     

Bayesian Interval Estimation for the Difference in TPRs and FPRs of Two Diagnostic Tests with Unverified Negatives

We derive Bayesian interval estimators for the differences in the true positive rates and false positive rates of two dichotomous diagnostic tests applied to the members of two distinct populations. The populations have varying disease prevalences with unverified negatives. We compare the performance of the Bayesian credible interval to the Wald interval using Monte Carlo simulation for a spectrum of different TPRs, FPRs, and sample sizes. For the case of a low TPR and low FPR, we found that a Bayesian credible interval with relatively noninformative priors performed well. We obtain similar interval comparison results for the cases of a high TPR and high FPR, a high TPR and low FPR, and of a high TPR and mixed FPR after incorporating mildly informative priors.     

Optimal sequential Bayesian analysis for degradation tests

Degradation tests are especially difficult to conduct for items with high reliability. Test costs, caused mainly by prolonged item duration and item destruction costs, establish the necessity of sequential degradation test designs. We propose a methodology that sequentially selects the optimal observation times to measure the degradation, using a convenient rule that maximizes the inference precision and minimizes test costs. In particular our objective is to estimate a quantile of the time to failure distribution, where the degradation process is modelled as a linear model using Bayesian inference. The proposed sequential analysis is based on an index that measures the expected discrepancy between the estimated quantile and its corresponding prediction, using Monte Carlo methods. The procedure was successfully implemented for simulated and real data.     

A comparison of estimators for regression models with change points

We consider two problems concerning locating change points in a linear regression model. One involves jump discontinuities (change-point) in a regression model and the other involves regression lines connected at unknown points. We compare four methods for estimating single or multiple change points in a regression model, when both the error variance and regression coefficients change simultaneously at the unknown point(s): Bayesian, Julious, grid search, and the segmented methods. The proposed methods are evaluated via a simulation study and compared via some standard measures of estimation bias and precision. Finally, the methods are illustrated and compared using three real data sets. The simulation and empirical results overall favor both the segmented and Bayesian methods of estimation, which simultaneously estimate the change point and the other model parameters, though only the Bayesian method is able to handle both continuous and dis-continuous change point problems successfully. If it is known that regression lines are continuous then the segmented method ranked first among methods.     

Reliability estimation in multicomponent stress–strength model for Topp-Leone distribution

In this paper, we consider the estimation reliability in multicomponent stress-strength (MSS) model when both the stress and strengths are drawn from Topp-Leone (TL) distribution. The maximum likelihood (ML) and Bayesian methods are used in the estimation procedure. Bayesian estimates are obtained by using Lindley’s approximation and Gibbs sampling methods, since they cannot be obtained in explicit form in the context of TL. The asymptotic confidence intervals are constructed based on the ML estimators. The Bayesian credible intervals are also constructed using Gibbs sampling. The reliability estimates are compared via an extensive Monte-Carlo simulation study. Finally, a real data set is analysed for illustrative purposes.     

面板数据的可加分位回归模型研究与应用

本文在贝叶斯分析的框架下讨论了面板数据的可加模型分位回归建模方法。首先通过低秩薄板惩罚样条展开和个体效应虚拟变量的引进将非参数模型转换为参数模型,然后在假定随机误差项服从非对称Laplace分布的基础上建立了贝叶斯分层分位回归模型。通过对非对称Laplace分布的分解,论文给出了所有待估参数的条件后验分布,并构造了待估参数的 Gibbs抽样估计算法。计算机模拟仿真结果显示,新提出的方法相比于传统的可加模型均值回归方法在估计稳健性上明显占优。最后以消费支出面板数据为例研究了我国农村居民收入结构对消费支出的影响,发现对于农村居民来说,无论是高、中、低消费群体,工资性收入与经营净收入的增加对其消费支出的正向刺激作用更为明显。进一步,相比于高消费农村居民人群,低消费农村居民人群随着收入的增加消费支出上升速度较为缓慢。     

A new multivariate imputation method based on Bayesian networks

Dealing with incomplete data is a pervasive problem in statistical surveys. Bayesian networks have been recently used in missing data imputation. In this research, we propose a new methodology for the multivariate imputation of missing data using discrete Bayesian networks and conditional Gaussian Bayesian networks. Results from imputing missing values in coronary artery disease data set and milk composition data set as well as a simulation study from cancer-neapolitan network are presented to demonstrate and compare the performance of three Bayesian network-based imputation methods with those of multivariate imputation by chained equations (MICE) and the classical hot-deck imputation method. To assess the effect of the structure learning algorithm on the performance of the Bayesian network-based methods, two methods called Peter-Clark algorithm and greedy search-and-score have been applied. Bayesian network-based methods are: first, the method introduced by Di Zio et al. [Bayesian networks for imputation, J. R. Stat. Soc. Ser. A 167 (2004), 309–322] in which, each missing item of a variable is imputed using the information given in the parents of that variable; second, the method of Di Zio et al. [Multivariate techniques for imputation based on Bayesian networks, Neural Netw. World 15 (2005), 303–310] which uses the information in the Markov blanket set of the variable to be imputed and finally, our new proposed method which applies the whole available knowledge of all variables of interest, consisting the Markov blanket and so the parent set, to impute a missing item. Results indicate the high quality of our new proposed method especially in the presence of high missingness percentages and more connected networks. Also the new method have shown to be more efficient than the MICE method for small sample sizes with high missing rates.     

Estimators for the Finite Mixture of Rayleigh Model Based on Progressively Censored Data

In this article, based on progressively Type-II censored samples from a heterogeneous population that can be represented by a finite mixture of two-component Rayleigh lifetime model, the problem of estimating the parameters and some lifetime parameters (reliability and hazard functions) are considered. Both Bayesian and maximum likelihood estimators are of interest. A class of natural conjugate prior densities is considered in the Bayesian setting. The Bayes estimators are obtained using both the symmetric (squared error) loss function, and the asymmetric (LINEX and General Entropy) loss functions. It has been seen that the estimators obtained can be easily evaluated for this type of censoring by using suitable numerical methods. Finally, the performance of the estimates have been compared on the basis of their simulated maximum square error via a Monte Carlo simulation study.     

Estimation of reliability of multicomponent stress–strength for a Kumaraswamy distribution

This article deals with the Bayesian and non Bayesian estimation of multicomponent stress–strength reliability by assuming the Kumaraswamy distribution. Both stress and strength are assumed to have a Kumaraswamy distribution with common and known shape parameter. The reliability of such a system is obtained by the methods of maximum likelihood and Bayesian approach and the results are compared using Markov Chain Monte Carlo (MCMC) technique for both small and large samples. Finally, two data sets are analyzed for illustrative purposes.     

Estimation of generalized exponential distribution based on an adaptive progressively type-II censored sample

In this paper, based on an adaptive Type-II progressively censored sample from the generalized exponential distribution, the maximum likelihood and Bayesian estimators are derived for the unknown parameters as well as the reliability and hazard functions. Also, the approximate confidence intervals of the unknown parameters, and the reliability and hazard functions are calculated. Markov chain Monte Carlo method is applied to carry out a Bayesian estimation procedure and in turn calculate the credible intervals. Moreover, results from simulation studies assessing the performance of our proposed method are included. Finally, an illustrative example using real data set is presented for illustrating all the inferential procedures developed here.