Bayesian latent variable models for clustered mixed outcomes

A general framework is proposed for modelling clustered mixed outcomes. A mixture of generalized linear models is used to describe the joint distribution of a set of underlying variables, and an arbitrary function relates the underlying variables to be observed outcomes. The model accommodates multilevel data structures, general covariate effects and distinct link functions and error distributions for each underlying variable. Within the framework proposed, novel models are developed for clustered multiple binary, unordered categorical and joint discrete and continuous outcomes. A Markov chain Monte Carlo sampling algorithm is described for estimating the posterior distributions of the parameters and latent variables. Because of the flexibility of the modelling framework and estimation procedure, extensions to ordered categorical outcomes and more complex data structures are straightforward. The methods are illustrated by using data from a reproductive toxicity study.     

Mixtures of general location model with factor analyzer covariance structure for clustering mixed type data

Cluster analysis is one of the most widely used method in statistical analyses, in which homogeneous subgroups are identified in a heterogeneous population. Due to the existence of the continuous and discrete mixed data in many applications, so far, some ordinary clustering methods such as, hierarchical methods, k-means and model-based methods have been extended for analysis of mixed data. However, in the available model-based clustering methods, by increasing the number of continuous variables, the number of parameters increases and identifying as well as fitting an appropriate model may be difficult. In this paper, to reduce the number of the parameters, for the model-based clustering mixed data of continuous (normal) and nominal data, a set of parsimonious models is introduced. Models in this set are extended, using the general location model approach, for modeling distribution of mixed variables and applying factor analyzer structure for covariance matrices. The ECM algorithm is used for estimating the parameters of these models. In order to show the performance of the proposed models for clustering, results from some simulation studies and analyzing two real data sets are presented.     

A mixture latent variable model for modeling mixed data in heterogeneous populations and its applications

Latent variable models are widely used for jointly modeling of mixed data including nominal, ordinal, count and continuous data. In this paper, we consider a latent variable model for jointly modeling relationships between mixed binary, count and continuous variables with some observed covariates. We assume that, given a latent variable, mixed variables of interest are independent and count and continuous variables have Poisson distribution and normal distribution, respectively. As such data may be extracted from different subpopulations, consideration of an unobserved heterogeneity has to be taken into account. A mixture distribution is considered (for the distribution of the latent variable) which accounts the heterogeneity. The generalized EM algorithm which uses the Newton–Raphson algorithm inside the EM algorithm is used to compute the maximum likelihood estimates of parameters. The standard errors of the maximum likelihood estimates are computed by using the supplemented EM algorithm. Analysis of the primary biliary cirrhosis data is presented as an application of the proposed model.     

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.     

State-space models for multivariate longitudinal data of mixed types

We propose a class of state-space models for multivariate longitudinal data where the components of the response vector may have different distributions. The approach is based on the class of Tweedie exponential dispersion models, which accommodates a wide variety of discrete, continuous and mixed data. The latent process is assumed to be a Markov process, and the observations are conditionally independent given the latent process, over time as well as over the components of the response vector. This provides a fully parametric alternative to the quasilikelihood approach of Liang and Zeger. We estimate the regression parameters for time-varying covariates entering either via the observation model or via the latent process, based on an estimating equation derived from the Kalman smoother. We also consider analysis of residuals from both the observation model and the latent process.     

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.     

A Class of Non-Gaussian State Space Models With Exact Likelihood Inference

The likelihood function of a general nonlinear, non-Gaussian state space model is a high-dimensional integral with no closed-form solution. In this article, I show how to calculate the likelihood function exactly for a large class of non-Gaussian state space models that include stochastic intensity, stochastic volatility, and stochastic duration models among others. The state variables in this class follow a nonnegative stochastic process that is popular in econometrics for modeling volatility and intensities. In addition to calculating the likelihood, I also show how to perform filtering and smoothing to estimate the latent variables in the model. The procedures in this article can be used for either Bayesian or frequentist estimation of the model’s unknown parameters as well as the latent state variables. Supplementary materials for this article are available online.     

Mixture of latent trait analyzers for model-based clustering of categorical data

Model-based clustering methods for continuous data are well established and commonly used in a wide range of applications. However, model-based clustering methods for categorical data are less standard. Latent class analysis is a commonly used method for model-based clustering of binary data and/or categorical data, but due to an assumed local independence structure there may not be a correspondence between the estimated latent classes and groups in the population of interest. The mixture of latent trait analyzers model extends latent class analysis by assuming a model for the categorical response variables that depends on both a categorical latent class and a continuous latent trait variable; the discrete latent class accommodates group structure and the continuous latent trait accommodates dependence within these groups. Fitting the mixture of latent trait analyzers model is potentially difficult because the likelihood function involves an integral that cannot be evaluated analytically. We develop a variational approach for fitting the mixture of latent trait models and this provides an efficient model fitting strategy. The mixture of latent trait analyzers model is demonstrated on the analysis of data from the National Long Term Care Survey (NLTCS) and voting in the U.S. Congress. The model is shown to yield intuitive clustering results and it gives a much better fit than either latent class analysis or latent trait analysis alone.     

Selection of Latent Variables for Multiple Mixed‐outcome Models

Latent variable models have been widely used for modelling the dependence structure of multiple outcomes data. However, the formulation of a latent variable model is often unknown a priori, the misspecification will distort the dependence structure and lead to unreliable model inference. Moreover, multiple outcomes with varying types present enormous analytical challenges. In this paper, we present a class of general latent variable models that can accommodate mixed types of outcomes. We propose a novel selection approach that simultaneously selects latent variables and estimates parameters. We show that the proposed estimator is consistent, asymptotically normal and has the oracle property. The practical utility of the methods is confirmed via simulations as well as an application to the analysis of the World Values Survey, a global research project that explores peoples’ values and beliefs and the social and personal characteristics that might influence them.     

The estimation of gross flows in the presence of measurement error using auxiliary variables

Classification error can lead to substantial biases in the estimation of gross flows from longitudinal data. We propose a method to adjust flow estimates for bias, based on fitting separate multinomial logistic models to the classification error probabilities and the true state transition probabilities using values of auxiliary variables. Our approach has the advantages that it does not require external information on misclassification rates, it permits the identification of factors that are related to misclassification and true transitions and it does not assume independence between classification errors at successive points in time. Constraining the prediction of the stocks to agree with the observed stocks protects against model misspecification. We apply the approach to data on women from the Panel Study of Income Dynamics with three categories of labour force status. The model fitted is shown to have interpretable coefficient estimates and to provide a good fit. Simulation results indicate good performance of the model in predicting the true flows and robustness against departures from the model postulated.     

Latent Variable Modelling: A Survey*

Abstract. Latent variable modelling has gradually become an integral part of mainstream statistics and is currently used for a multitude of applications in different subject areas. Examples of ‘traditional’ latent variable models include latent class models, item–response models, common factor models, structural equation models, mixed or random effects models and covariate measurement error models. Although latent variables have widely different interpretations in different settings, the models have a very similar mathematical structure. This has been the impetus for the formulation of general modelling frameworks which accommodate a wide range of models. Recent developments include multilevel structural equation models with both continuous and discrete latent variables, multiprocess models and nonlinear latent variable models.     

Approximate composite marginal likelihood inference in spatial generalized linear mixed models

Non-Gaussian spatial responses are usually modeled using spatial generalized linear mixed model with spatial random effects. The likelihood function of this model cannot usually be given in a closed form, thus the maximum likelihood approach is very challenging. There are numerical ways to maximize the likelihood function, such as Monte Carlo Expectation Maximization and Quadrature Pairwise Expectation Maximization algorithms. They can be applied but may in such cases be computationally very slow or even prohibitive. Gauss–Hermite quadrature approximation only suitable for low-dimensional latent variables and its accuracy depends on the number of quadrature points. Here, we propose a new approximate pairwise maximum likelihood method to the inference of the spatial generalized linear mixed model. This approximate method is fast and deterministic, using no sampling-based strategies. The performance of the proposed method is illustrated through two simulation examples and practical aspects are investigated through a case study on a rainfall data set.     

Multivariate generalized linear mixed models with random intercepts to analyze cardiovascular risk markers in type-1 diabetic patients

Statistical approaches tailored to analyzing longitudinal data that have multiple outcomes with different distributions are scarce. This paucity is due to the non-availability of multivariate distributions that jointly model outcomes with different distributions other than the multivariate normal. A plethora of research has been done on the specific combination of binary-Gaussian bivariate outcomes but a more general approach that allows other mixtures of distributions for multiple longitudinal outcomes has not been thoroughly demonstrated and examined. Here, we study a multivariate generalized linear mixed models approach that jointly models multiple longitudinal outcomes with different combinations of distributions and incorporates the correlations between the various outcomes through separate yet correlated random intercepts. Every outcome is linked to the set of covariates through a proper link function that allows the incorporation and joint modeling of different distributions. A novel application was demonstrated on a cohort study of Type-1 diabetic patients to jointly model a mix of longitudinal cardiovascular outcomes and to explore for the first time the effect of glycemic control treatment, plasma prekallikrein biomarker, gender and age on cardiovascular risk factors collectively.     

Building and Fitting Non‐Gaussian Latent Variable Models via the Moment‐Generating Function

Abstract. For certain classes of hierarchical models, it is easy to derive an expression for the joint moment‐generating function (MGF) of data, whereas the joint probability density has an intractable form which typically involves an integral. The most important example is the class of linear models with non‐Gaussian latent variables. Parameters in the model can be estimated by approximate maximum likelihood, using a saddlepoint‐type approximation to invert the MGF. We focus on modelling heavy‐tailed latent variables, and suggest a family of mixture distributions that behaves well under the saddlepoint approximation (SPA). It is shown that the well‐known normalization issue renders the ordinary SPA useless in the present context. As a solution we extend the non‐Gaussian leading term SPA to a multivariate setting, and introduce a general rule for choosing the leading term density. The approach is applied to mixed‐effects regression, time‐series models and stochastic networks and it is shown that the modified SPA is very accurate.     

Structural equation models for area health outcomes with model selection

Recent analyses seeking to explain variation in area health outcomes often consider the impact on them of latent measures (i.e. unobserved constructs) of population health risk. The latter are typically obtained by forms of multivariate analysis, with a small set of latent constructs derived from a collection of observed indicators, and a few recent area studies take such constructs to be spatially structured rather than independent over areas. A confirmatory approach is often applicable to the model linking indicators to constructs, based on substantive knowledge of relevant risks for particular diseases or outcomes. In this paper, population constructs relevant to a particular set of health outcomes are derived using an integrated model containing all the manifest variables, namely health outcome variables, as well as indicator variables underlying the latent constructs. A further feature of the approach is the use of variable selection techniques to select significant loadings and factors (especially in terms of effects of constructs on health outcomes), so ensuring parsimonious models are selected. A case study considers suicide mortality and self-harm contrasts in the East of England in relation to three latent constructs: deprivation, fragmentation and urbanicity.     

Bayesian density regression for discrete outcomes

We develop Bayesian models for density regression with emphasis on discrete outcomes. The problem of density regression is approached by considering methods for multivariate density estimation of mixed scale variables, and obtaining conditional densities from the multivariate ones. The approach to multivariate mixed scale outcome density estimation that we describe represents discrete variables, either responses or covariates, as discretised versions of continuous latent variables. We present and compare several models for obtaining these thresholds in the challenging context of count data analysis where the response may be over‐ and/or under‐dispersed in some of the regions of the covariate space. We utilise a nonparametric mixture of multivariate Gaussians to model the directly observed and the latent continuous variables. The paper presents a Markov chain Monte Carlo algorithm for posterior sampling, sufficient conditions for weak consistency, and illustrations on density, mean and quantile regression utilising simulated and real datasets.     

Spatial generalized linear mixed models in small area estimation

In survey sampling, policy decisions regarding the allocation of resources to sub‐groups of a population depend on reliable predictors of their underlying parameters. However, in some sub‐groups, called small areas due to small sample sizes relative to the population, the information needed for reliable estimation is typically not available. Consequently, data on a coarser scale are used to predict the characteristics of small areas. Mixed models are the primary tools in small area estimation (SAE) and also borrow information from alternative sources (e.g., previous surveys and administrative and census data sets). In many circumstances, small area predictors are associated with location. For instance, in the case of chronic disease or cancer, it is important for policy makers to understand spatial patterns of disease in order to determine small areas with high risk of disease and establish prevention strategies. The literature considering SAE with spatial random effects is sparse and mostly in the context of spatial linear mixed models. In this article, small area models are proposed for the class of spatial generalized linear mixed models to obtain small area predictors and corresponding second‐order unbiased mean squared prediction errors via Taylor expansion and a parametric bootstrap approach. The performance of the proposed approach is evaluated through simulation studies and application of the models to a real esophageal cancer data set from Minnesota, U.S.A. The Canadian Journal of Statistics 47: 426–437; 2019 © 2019 Statistical Society of Canada     

Penalized calibration in survey sampling: Design-based estimation assisted by mixed models

Calibration techniques in survey sampling, such as generalized regression estimation (GREG), were formalized in the 1990s to produce efficient estimators of linear combinations of study variables, such as totals or means. They implicitly lie on the assumption of a linear regression model between the variable of interest and some auxiliary variables in order to yield estimates with lower variance if the model is true and remaining approximately design-unbiased even if the model does not hold. We propose a new class of model-assisted estimators obtained by releasing a few calibration constraints and replacing them with a penalty term. This penalization is added to the distance criterion to minimize. By introducing the concept of penalized calibration, combining usual calibration and this ‘relaxed’ calibration, we are able to adjust the weight given to the available auxiliary information. We obtain a more flexible estimation procedure giving better estimates particularly when the auxiliary information is overly abundant or not fully appropriate to be completely used. Such an approach can also be seen as a design-based alternative to the estimation procedures based on the more general class of mixed models, presenting new prospects in some scopes of application such as inference on small domains.     

High dimensional multivariate mixed models for binary questionnaire data

Summary.  Questionnaires that are used to measure the effect of an intervention often consist of different sets of items, each set possibly measuring another concept. Mixed models with set-specific random effects are a flexible tool to model the different sets of items jointly. However, computational problems typically arise as the number of sets increases. This is especially true when the random-effects distribution cannot be integrated out analytically, as with mixed models for binary data. A pairwise modelling strategy, in which all possible bivariate mixed models are fitted and where inference follows from pseudolikelihood theory, has been proposed as a solution. This approach has been applied to assess the effect of physical activity on psychocognitive functioning, the latter measured by a battery of questionnaires.     

Composite Likelihood Estimation for Multivariate Probit Latent Traits Models

Inference in generalized linear mixed models with multivariate random effects is often made cumbersome by the high-dimensional intractable integrals involved in the marginal likelihood. This article presents an inferential methodology based on the marginal composite likelihood approach for the probit latent traits models. This method belonging to the broad class of pseudo-likelihood involves marginal pairs probabilities of the responses which has analytical expression. The different results are illustrated with a simulation study and with an analysis of real data from health related quality of life.