Latent variable models with ordinal categorical covariates

We propose a general latent variable model for multivariate ordinal categorical variables, in which both the responses and the covariates are ordinal, to assess the effect of the covariates on the responses and to model the covariance structure of the response variables. A?fully Bayesian approach is employed to analyze the model. The Gibbs sampler is used to simulate the joint posterior distribution of the latent variables and the parameters, and the parameter expansion and reparameterization techniques are used to speed up the convergence procedure. The proposed model and method are demonstrated by simulation studies and a real data example.     

有序响应变量的贝叶斯模型选择及其在COPD疾病防治中的应用

慢性阻塞性肺病(COPD)是一种发病率、死亡率都非常高的疾病，且COPD的诊断和严重程度分级依赖于肺功能的检查，但是由于肺功能检查仪器价格昂贵，使得这项检查在很多经济欠发达地区尤其是农村基层医院并没有普及。本文基于有序响应变量模型致力于研究一种便于基层和社区使用的可以初步判别COPD病情的模型，以期提高我国基层和社区的COPD 防治水平。利用贝叶斯变量选择方法和数据增强的潜变量策略得到了易于实施的Gibbs后验抽样算法。数值模拟分析进一步说明了本文提出的有序响应变量贝叶斯模型选择方法的有效性，实例分析得到了易于判别COPD严重程度的稀疏模型。     

A Bayesian conditional model for bivariate mixed ordinal and skew continuous longitudinal responses using quantile regression

In this paper, we develop a conditional model for analyzing mixed bivariate continuous and ordinal longitudinal responses. We propose a quantile regression model with random effects for analyzing continuous responses. For this purpose, an Asymmetric Laplace Distribution (ALD) is allocated for continuous response given random effects. For modeling ordinal responses, a cumulative logit model is used, via specifying a latent variable model, with considering other random effects. Therefore, the intra-association between continuous and ordinal responses is taken into account using their own exclusive random effects. But, the inter-association between two mixed responses is taken into account by adding a continuous response term in the ordinal model. We use a Bayesian approach via Markov chain Monte Carlo method for analyzing the proposed conditional model and to estimate unknown parameters, a Gibbs sampler algorithm is used. Moreover, we illustrate an application of the proposed model using a part of the British Household Panel Survey data set. The results of data analysis show that gender, age, marital status, educational level and the amount of money spent on leisure have significant effects on annual income. Also, the associated parameter is significant in using the best fitting proposed conditional model, thus it should be employed rather than analyzing separate models.     

Latent single-index models for ordinal data

We propose a latent semi-parametric model for ordinal data in which the single-index model is used to evaluate the effects of the latent covariates on the latent response. We develop a Bayesian sampling-based method with free-knot splines to analyze the proposed model. As the index may vary from minus infinity to plus infinity, the traditional spline that is defined on a finite interval cannot be applied directly to approximate the unknown link function. We consider a modified version to address this problem by first transforming the index into the unit interval via a continuously cumulative distribution function and then constructing the spline bases on the unit interval. To obtain a rapidly convergent algorithm, we make use of the partial collapse and parameter expansion and reparameterization techniques, improve the movement step of Bayesian splines with free knots so that all the knots can be relocated each time instead of only one knot, and design a generalized Gibbs step. We check the performance of the proposed model and estimation method by a simulation study and apply them to analyze a real dataset.     

A Bayesian multivariate partially linear single-index probit model for ordinal responses

Combining the multivariate probit models with the multivariate partially linear single-index models, we propose new semiparametric latent variable models for multivariate ordinal response data. Based on the reversible jump Markov chain Monte Carlo technique, we develop a fully Bayesian method with free-knot splines to analyse the proposed models. To address the problem that the ordinary Gibbs sampler usually converges slowly, we make use of the partial-collapse and parameter-expansion techniques in our algorithm. The proposed methodology are demonstrated by simulated and real data examples.     

Univariate and multirater ordinal cumulative link regression with covariate specific cutpoints

The author considers a reparameterized version of the Bayesian ordinal cumulative link regression model as a tool for exploring relationships between covariates and “cutpoint” parameters. The use of this parameterization allows one to fit models using the leapfrog hybrid Monte Carlo method, and to bypass latent variable data augmentation and the slow convergence of the cutpoints which it usually entails. The proposed Gibbs sampler is not model specific and can be easily modified to handle different link functions. The approach is illustrated by considering data from a pediatric radiology study.     

Joint modeling of mixed skewed continuous and ordinal longitudinal responses: a Bayesian approach

In this paper, a joint model for analyzing multivariate mixed ordinal and continuous responses, where continuous outcomes may be skew, is presented. For modeling the discrete ordinal responses, a continuous latent variable approach is considered and for describing continuous responses, a skew-normal mixed effects model is used. A Bayesian approach using Markov Chain Monte Carlo (MCMC) is adopted for parameter estimation. Some simulation studies are performed for illustration of the proposed approach. The results of the simulation studies show that the use of the separate models or the normal distributional assumption for shared random effects and within-subject errors of continuous and ordinal variables, instead of the joint modeling under a skew-normal distribution, leads to biased parameter estimates. The approach is used for analyzing a part of the British Household Panel Survey (BHPS) data set. Annual income and life satisfaction are considered as the continuous and the ordinal longitudinal responses, respectively. The annual income variable is severely skewed, therefore, the use of the normality assumption for the continuous response does not yield acceptable results. The results of data analysis show that gender, marital status, educational levels and the amount of money spent on leisure have a significant effect on annual income, while marital status has the highest impact on life satisfaction.     

Directional Dependence of Genes Using Survival Truncated FGM Type Modification Copulas

Ordinal data, such as student's grades or customer satisfaction surveys, are widely used in daily life. We can fit a probit or logistic regression model to the ordinal data using software such as SAS and get the estimates of regression parameters. However, it is hard to define residuals and detect outliers due to the fact that the estimated probabilities of an observation falling in every category form a vector instead of a scalar. With the help of latent variable and latent residuals, a Bayesian perspective of detecting outliers is explored and several methods were proposed in this article. Several figures are also given.     

Joint modeling of multivariate longitudinal mixed measurements and time to event data using a Bayesian approach

In many longitudinal studies multiple characteristics of each individual, along with time to occurrence of an event of interest, are often collected. In such data set, some of the correlated characteristics may be discrete and some of them may be continuous. In this paper, a joint model for analysing multivariate longitudinal data comprising mixed continuous and ordinal responses and a time to event variable is proposed. We model the association structure between longitudinal mixed data and time to event data using a multivariate zero-mean Gaussian process. For modeling discrete ordinal data we assume a continuous latent variable follows the logistic distribution and for continuous data a Gaussian mixed effects model is used. For the event time variable, an accelerated failure time model is considered under different distributional assumptions. For parameter estimation, a Bayesian approach using Markov Chain Monte Carlo is adopted. The performance of the proposed methods is illustrated using some simulation studies. A real data set is also analyzed, where different model structures are used. Model comparison is performed using a variety of statistical criteria.     

Modeling a mixture of ordinal and continuous repeated measures

We study the correlation structure for a mixture of ordinal and continuous repeated measures using a Bayesian approach. We assume a multivariate probit model for the ordinal variables and a normal linear regression for the continuous variables, where latent normal variables underlying the ordinal data are correlated with continuous variables in the model. Due to the probit model assumption, we are required to sample a covariance matrix with some of the diagonal elements equal to one. The key computational idea is to use parameter-extended data augmentation, which involves applying the Metropolis-Hastings algorithm to get a sample from the posterior distribution of the covariance matrix incorporating the relevant restrictions. The methodology is illustrated through a simulated example and through an application to data from the UCLA Brain Injury Research Center.     

Reparameterizing the generalized linear model to accelerate gibbs sampler convergence

Albert and Chib introduced a complete Bayesian method to analyze data arising from the generalized linear model in which they used the Gibbs sampling algorithm facilitated by latent variables. Recently, Cowles proposed an alternative algorithm to accelerate the convergence of the Albert-Chib algorithm. The novelty in this latter algorithm is achieved by using a Hastings algorithm to generate latent variables and bin boundary parameters jointly instead of individually from their respective full conditionals. In the same spirit, we reparameterize the cumulative-link generalized linear model to accelerate the convergence of Cowles’ algorithm even further. One important advantage of our method is that for the three-bin problem it does not require the Hastings algorithm. In addition, for problems with more than three bins, while the Hastings algorithm is required, we provide a proposal density based on the Dirichlet distribution which is more natural than the truncated normal density used in the competing algorithm. Also, using diagnostic procedures recommended in the literature for the Markov chain Monte Carlo algorithm (both single and multiple runs) we show that our algorithm is substantially better than the one recently obtained. Precisely, our algorithm provides faster convergence and smaller autocorrelations between the iterates. Using the probit link function, extensive results are obtained for the three-bin and the five-bin multinomial ordinal data problems.     

A general class of hierarchical ordinal regression models with applications to correlated roc analysis

The authors discuss a general class of hierarchical ordinal regression models that includes both location and scale parameters, allows link functions to be selected adaptively as finite mixtures of normal cumulative distribution functions, and incorporates flexible correlation structures for the latent scale variables. Exploiting the well‐known correspondence between ordinal regression models and parametric ROC (Receiver Operating Characteristic) curves makes it possible to use a hierarchical ROC (HROC) analysis to study multilevel clustered data in diagnostic imaging studies. The authors present a Bayesian approach to model fitting using Markov chain Monte Carlo methods and discuss HROC applications to the analysis of data from two diagnostic radiology studies involving multiple interpreters.     

A Class of Multidimensional Latent Class IRT Models for Ordinal Polytomous Item Responses

We propose a class of multidimensional Item Response Theory models for polytomously-scored items with ordinal response categories. This class extends an existing class of multidimensional models for dichotomously-scored items in which the latent abilities are represented by a random vector assumed to have a discrete distribution, with support points corresponding to different latent classes in the population. In the proposed approach, we allow for different parameterizations for the conditional distribution of the response variables given the latent traits, which depend on the type of link function and the constraints imposed on the item parameters. Moreover, we suggest a strategy for model selection that is based on a series of steps consisting of selecting specific features, such as the dimension of the model (number of latent traits), the number of latent classes, and the specific parameterization. In order to illustrate the proposed approach, we analyze a dataset from a study on anxiety and depression on a sample of oncological patients.     

Hierarchical marginal models with latent uncertainty

In responding to a rating question, an individual may give answers either according to his/her knowledge/awareness or to his/her level of indecision/uncertainty, typically driven by a response style. As ignoring this dual behavior may lead to misleading results, we define a multivariate model for ordinal rating responses by introducing, for every item and every respondent, a binary latent variable that discriminates aware from uncertain responses. Some independence assumptions among latent and observable variables characterize the uncertain behavior and make the model easier to interpret. Uncertain responses are modeled by specifying probability distributions that can depict different response styles. A marginal parameterization allows a simple and direct interpretation of the parameters in terms of association among aware responses and their dependence on explanatory factors. The effectiveness of the proposed model is attested through an application to real data and supported by a Monte Carlo study.     

A spatial model for the needle losses of pine-trees in the forests of Baden-Württemberg: an application of Bayesian structured additive regression

Summary.  The data that are analysed are from a monitoring survey which was carried out in 1994 in the forests of Baden-Württemberg, a federal state in the south-western region of Germany. The survey is part of a large monitoring scheme that has been carried out since the 1980s at different spatial and temporal resolutions to observe the increase in forest damage. One indicator for tree vitality is tree defoliation, which is mainly caused by intrinsic factors, age and stand conditions, but also by biotic (e.g. insects) and abiotic stresses (e.g. industrial emissions). In the survey, needle loss of pine-trees and many potential covariates are recorded at about 580 grid points of a 4 km × 4 km grid. The aim is to identify a set of predictors for needle loss and to investigate the relationships between the needle loss and the predictors. The response variable needle loss is recorded as a percentage in 5% steps estimated by eye using binoculars and categorized into healthy trees (10% or less), intermediate trees (10–25%) and damaged trees (25% or more). We use a Bayesian cumulative threshold model with non-linear functions of continuous variables and a random effect for spatial heterogeneity. For both the non-linear functions and the spatial random effect we use Bayesian versions of P -splines as priors. Our method is novel in that it deals with several non-standard data requirements: the ordinal response variable (the categorized version of needle loss), non-linear effects of covariates, spatial heterogeneity and prediction with missing covariates. The model is a special case of models with a geoadditive or more generally structured additive predictor. Inference can be based on Markov chain Monte Carlo techniques or mixed model technology.     

ASSESSING FAMILIAL AGGREGATION WITH AN ORDINAL RESPONSE

A latent variable model is considered for the analysis of twin data with an ordinal response. The underlying latent multivariate normally distributed variable is expressed in terms of genetic and environmental effects, and the variance components associated with these effects are estimated. We illustrate this approach with analysis of the NHLBI Twin Study. Model assessment is ascertained by proposing a goodness-of-fit test for ordered categorical data. Extensions of this approach for the investigation of how genetic effects vary over time are discussed.     

A Bayesian approach for misclassified ordinal response data

ABSTRACT

Motivated by a longitudinal oral health study, the Signal-Tandmobiel^® study, a Bayesian approach has been developed to model misclassified ordinal response data. Two regression models have been considered to incorporate misclassification in the categorical response. Specifically, probit and logit models have been developed. The computational difficulties have been avoided by using data augmentation. This idea is exploited to derive efficient Markov chain Monte Carlo methods. Although the method is proposed for ordered categories, it can also be implemented for unordered ones in a simple way. The model performance is shown through a simulation-based example and the analysis of the motivating study.     

Bayesian ROC curve estimation under binormality using an ordinal category likelihood

Receiver operating characteristic (ROC) curve has been widely used in medical diagnosis. Various methods are proposed to estimate ROC curve parameters under the binormal model. In this paper, we propose a Bayesian estimation method from the continuously distributed data which is constituted by the truth-state-runs in the rank-ordered data. By using an ordinal category data likelihood and following the Metropolis–Hastings (M–H) procedure, we compute the posterior distribution of the binormal parameters, as well as the group boundaries parameters. Simulation studies and real data analysis are conducted to evaluate our Bayesian estimation method.     

On the Bayesian estimation and influence diagnostics for the Weibull-Negative-Binomial regression model with cure rate under latent failure causes

The purpose of this paper is to develop a Bayesian approach for the Weibull-Negative-Binomial regression model with cure rate under latent failure causes and presence of randomized activation mechanisms. We assume the number of competing causes of the event of interest follows a Negative Binomial (NB) distribution while the latent lifetimes are assumed to follow a Weibull distribution. Markov chain Monte Carlos (MCMC) methods are used to develop the Bayesian procedure. Model selection to compare the fitted models is discussed. Moreover, we develop case deletion influence diagnostics for the joint posterior distribution based on the ψ-divergence, which has several divergence measures as particular cases. The developed procedures are illustrated with a real data set.     

Point predictors of the latent failure times of censored units in progressively Type-II censored competing risks data from the exponential distributions

In this paper, we discuss the problem of predicting times to the latent failures of units censored in multiple stages in a progressively Type-II censored competing risks model. It is assumed that the lifetime distribution of the latent failure times are independent and exponential-distributed with the different scale parameters. Several classical point predictors such as the maximum likelihood predictor, the best unbiased predictor, the best linear unbiased predictor, the median unbiased predictor and the conditional median predictor are obtained. The Bayesian point predictors are derived under squared error loss criterion. Moreover, the point estimators of the unknown parameters are obtained using the observed data and different point predictors of the latent failure times. Finally, Monte-Carlo simulations are carried out to compare the performances of the different methods of prediction and estimation and one real data is used to illustrate the proposed procedures.