Bayesian analysis of multivariate t linear mixed models with missing responses at random

The multivariate t linear mixed model (MtLMM) has been recently proposed as a robust tool for analysing multivariate longitudinal data with atypical observations. Missing outcomes frequently occur in longitudinal research even in well controlled situations. As a powerful alternative to the traditional expectation maximization based algorithm employing single imputation, we consider a Bayesian analysis of the MtLMM to account for the uncertainties of model parameters and missing outcomes through multiple imputation. An inverse Bayes formulas sampler coupled with Metropolis-within-Gibbs scheme is used to effectively draw the posterior distributions of latent data and model parameters. The techniques for multiple imputation of missing values, estimation of random effects, prediction of future responses, and diagnostics of potential outliers are investigated as well. The proposed methodology is illustrated through a simulation study and an application to AIDS/HIV data.     

A note on transformed likelihood approach in linear dynamic panel models

The transformed likelihood approach to estimation of fixed effects dynamic panel data models is shown to present very good inferential properties but it is not directly implemented in the most diffused statistical software. The present paper aims at showing how a simple model reformulation can be adopted to describe the problem in terms of classical linear mixed models. The transformed likelihood approach is based on the first differences data transformation, the following results derive from a convenient reformulation in terms of deviations from the first observations. Given the invariance to data transformation, the likelihood functions defined in the two cases coincide. Resulting in a classical random effect linear model form, the proposed approach significantly improves the number of available estimation procedures and provides a straightforward interpretation for the parameters. Moreover, the proposed model specification allows to consider all the estimation improvements typical of the random effects model literature. Simulation studies are conducted in order to study the robustness of the estimation method to mean stationarity violation.     

A Bayesian random effects model for analyzing mixed negative binomial and continuous longitudinal responses

ABSTRACT

A general Bayesian random effects model for analyzing longitudinal mixed correlated continuous and negative binomial responses with and without missing data is presented. This Bayesian model, given some random effects, uses a normal distribution for the continuous response and a negative binomial distribution for the count response. A Markov Chain Monte Carlo sampling algorithm is described for estimating the posterior distribution of the parameters. This Bayesian model is illustrated by a simulation study. For sensitivity analysis to investigate the change of parameter estimates with respect to the perturbation from missing at random to not missing at random assumption, the use of posterior curvature is proposed. The model is applied to a medical data, obtained from an observational study on women, where the correlated responses are the negative binomial response of joint damage and continuous response of body mass index. The simultaneous effects of some covariates on both responses are also investigated.     

Comparison of Additive and Multiplicative Bayesian Models for Longitudinal Count Data with Overdispersion Parameters: A Simulation Study

In applied statistical data analysis, overdispersion is a common feature. It can be addressed using both multiplicative and additive random effects. A multiplicative model for count data incorporates a gamma random effect as a multiplicative factor into the mean, whereas an additive model assumes a normally distributed random effect, entered into the linear predictor. Using Bayesian principles, these ideas are applied to longitudinal count data, based on the so-called combined model. The performance of the additive and multiplicative approaches is compared using a simulation study.     

Inference in generalized additive mixed modelsby using smoothing splines

Generalized additive mixed models are proposed for overdispersed and correlated data, which arise frequently in studies involving clustered, hierarchical and spatial designs. This class of models allows flexible functional dependence of an outcome variable on covariates by using nonparametric regression, while accounting for correlation between observations by using random effects. We estimate nonparametric functions by using smoothing splines and jointly estimate smoothing parameters and variance components by using marginal quasi-likelihood. Because numerical integration is often required by maximizing the objective functions, double penalized quasi-likelihood is proposed to make approximate inference. Frequentist and Bayesian inferences are compared. A key feature of the method proposed is that it allows us to make systematic inference on all model components within a unified parametric mixed model framework and can be easily implemented by fitting a working generalized linear mixed model by using existing statistical software. A bias correction procedure is also proposed to improve the performance of double penalized quasi-likelihood for sparse data. We illustrate the method with an application to infectious disease data and we evaluate its performance through simulation.     

Additive mixed models with approximate Dirichlet process mixtures: the EM approach

We consider additive mixed models for longitudinal data with a nonlinear time trend. As random effects distribution an approximate Dirichlet process mixture is proposed that is based on the truncated version of the stick breaking presentation of the Dirichlet process and provides a Gaussian mixture with a data driven choice of the number of mixture components. The main advantage of the specification is its ability to identify clusters of subjects with a similar random effects structure. For the estimation of the trend curve the mixed model representation of penalized splines is used. An Expectation-Maximization algorithm is given that solves the estimation problem and that exhibits advantages over Markov chain Monte Carlo approaches, which are typically used when modeling with Dirichlet processes. The method is evaluated in a simulation study and applied to theophylline data and to body mass index profiles of children.     

A general joint model for longitudinal measurements and competing risks survival data with heterogeneous random effects

This article studies a general joint model for longitudinal measurements and competing risks survival data. The model consists of a linear mixed effects sub-model for the longitudinal outcome, a proportional cause-specific hazards frailty sub-model for the competing risks survival data, and a regression sub-model for the variance–covariance matrix of the multivariate latent random effects based on a modified Cholesky decomposition. The model provides a useful approach to adjust for non-ignorable missing data due to dropout for the longitudinal outcome, enables analysis of the survival outcome with informative censoring and intermittently measured time-dependent covariates, as well as joint analysis of the longitudinal and survival outcomes. Unlike previously studied joint models, our model allows for heterogeneous random covariance matrices. It also offers a framework to assess the homogeneous covariance assumption of existing joint models. A Bayesian MCMC procedure is developed for parameter estimation and inference. Its performances and frequentist properties are investigated using simulations. A real data example is used to illustrate the usefulness of the approach.     

Random Effects Modeling and the Zero-Inflated Poisson Distribution

Overdispersion due to a large proportion of zero observations in data sets is a common occurrence in many applications of many fields of research; we consider such scenarios in count panel (longitudinal) data. A well-known and widely implemented technique for handling such data is that of random effects modeling, which addresses the serial correlation inherent in panel data, as well as overdispersion. To deal with the excess zeros, a zero-inflated Poisson distribution has come to be canonical, which relaxes the equal mean-variance specification of a traditional Poisson model and allows for the larger variance characteristic of overdispersed data. A natural proposal then to approach count panel data with overdispersion due to excess zeros is to combine these two methodologies, deriving a likelihood from the resulting conditional probability. In performing simulation studies, we find that this approach in fact poses problems of identifiability. In this article, we construct and explain in full detail why a model obtained from the marriage of two classical and well-established techniques is unidentifiable and provide results of simulation studies demonstrating this effect. A discussion on alternative methodologies to resolve the problem is provided in the conclusion.     

Bayesian Analysis of Nonlinear Reproductive Dispersion Mixed Models for Longitudinal Data with Nonignorable Missing Covariates

This article proposes a Bayesian approach, which can simultaneously obtain the Bayesian estimates of unknown parameters and random effects, to analyze nonlinear reproductive dispersion mixed models (NRDMMs) for longitudinal data with nonignorable missing covariates and responses. The logistic regression model is employed to model the missing data mechanisms for missing covariates and responses. A hybrid sampling procedure combining the Gibber sampler and the Metropolis-Hastings algorithm is presented to draw observations from the conditional distributions. Because missing data mechanism is not testable, we develop the logarithm of the pseudo-marginal likelihood, deviance information criterion, the Bayes factor, and the pseudo-Bayes factor to compare several competing missing data mechanism models in the current considered NRDMMs with nonignorable missing covaraites and responses. Three simulation studies and a real example taken from the paediatric AIDS clinical trial group ACTG are used to illustrate the proposed methodologies. Empirical results show that our proposed methods are effective in selecting missing data mechanism models.     

Reversible jump MCMC to identify dropout mechanism in longitudinal data

Existence of missing values is an inseparable part of longitudinal studies in epidemiology, medical and clinical studies. Usually researchers, for simplicity, ignore the missingness mechanism while, ignoring a not at random mechanism may lead to misleading results. In this paper, we use a Bayesian paradigm for fitting selection model of Heckman, which allows the non-ignorable missingness for longitudinal data. Also, we use reversible-jump Markov chain Monte Carlo to allow the model to choose between non-ignorable and ignorable structures for missingness mechanism, and show how the selection can be incorporated. Some simulation studies are performed for illustration of the proposed approach. The approach is also used for analyzing two real data sets.     

Bayesian Longitudinal Data Analysis with Mixed Models and Thick-tailed Distributions using MCMC

Linear mixed effects models are frequently used to analyse longitudinal data, due to their flexibility in modelling the covariance structure between and within observations. Further, it is easy to deal with unbalanced data, either with respect to the number of observations per subject or per time period, and with varying time intervals between observations. In most applications of mixed models to biological sciences, a normal distribution is assumed both for the random effects and for the residuals. This, however, makes inferences vulnerable to the presence of outliers. Here, linear mixed models employing thick-tailed distributions for robust inferences in longitudinal data analysis are described. Specific distributions discussed include the Student-t, the slash and the contaminated normal. A Bayesian framework is adopted, and the Gibbs sampler and the Metropolis-Hastings algorithms are used to carry out the posterior analyses. An example with data on orthodontic distance growth in children is discussed to illustrate the methodology. Analyses based on either the Student-t distribution or on the usual Gaussian assumption are contrasted. The thick-tailed distributions provide an appealing robust alternative to the Gaussian process for modelling distributions of the random effects and of residuals in linear mixed models, and the MCMC implementation allows the computations to be performed in a flexible manner.     

Prediction of transplant-free survival in idiopathic pulmonary fibrosis patients using joint models for event times and mixed multivariate longitudinal data

We implement a joint model for mixed multivariate longitudinal measurements, applied to the prediction of time until lung transplant or death in idiopathic pulmonary fibrosis. Specifically, we formulate a unified Bayesian joint model for the mixed longitudinal responses and time-to-event outcomes. For the longitudinal model of continuous and binary responses, we investigate multivariate generalized linear mixed models using shared random effects. Longitudinal and time-to-event data are assumed to be independent conditional on available covariates and shared parameters. A Markov chain Monte Carlo algorithm, implemented in OpenBUGS, is used for parameter estimation. To illustrate practical considerations in choosing a final model, we fit 37 different candidate models using all possible combinations of random effects and employ a deviance information criterion to select a best-fitting model. We demonstrate the prediction of future event probabilities within a fixed time interval for patients utilizing baseline data, post-baseline longitudinal responses, and the time-to-event outcome. The performance of our joint model is also evaluated in simulation studies.     

Factor Multivariate Stochastic Volatility via Wishart Processes

This paper proposes a high dimensional factor multivariate stochastic volatility (MSV) model in which factor covariance matrices are driven by Wishart random processes. The framework allows for unrestricted specification of intertemporal sensitivities, which can capture the persistence in volatilities, kurtosis in returns, and correlation breakdowns and contagion effects in volatilities. The factor structure allows addressing high dimensional setups used in portfolio analysis and risk management, as well as modeling conditional means and conditional variances within the model framework. Owing to the complexity of the model, we perform inference using Markov chain Monte Carlo simulation from the posterior distribution. A simulation study is carried out to demonstrate the efficiency of the estimation algorithm. We illustrate our model on a data set that includes 88 individual equity returns and the two Fama–French size and value factors. With this application, we demonstrate the ability of the model to address high dimensional applications suitable for asset allocation, risk management, and asset pricing.     

A flexible approach for multivariate mixed-effects models with non-ignorable missing values

We propose a flexible model approach for the distribution of random effects when both response variables and covariates have non-ignorable missing values in a longitudinal study. A Bayesian approach is developed with a choice of nonparametric prior for the distribution of random effects. We apply the proposed method to a real data example from a national long-term survey by Statistics Canada. We also design simulation studies to further check the performance of the proposed approach. The result of simulation studies indicates that the proposed approach outperforms the conventional approach with normality assumption when the heterogeneity in random effects distribution is salient.     

Factor Multivariate Stochastic Volatility via Wishart Processes

This paper proposes a high dimensional factor multivariate stochastic volatility (MSV) model in which factor covariance matrices are driven by Wishart random processes. The framework allows for unrestricted specification of intertemporal sensitivities, which can capture the persistence in volatilities, kurtosis in returns, and correlation breakdowns and contagion effects in volatilities. The factor structure allows addressing high dimensional setups used in portfolio analysis and risk management, as well as modeling conditional means and conditional variances within the model framework. Owing to the complexity of the model, we perform inference using Markov chain Monte Carlo simulation from the posterior distribution. A simulation study is carried out to demonstrate the efficiency of the estimation algorithm. We illustrate our model on a data set that includes 88 individual equity returns and the two Fama-French size and value factors. With this application, we demonstrate the ability of the model to address high dimensional applications suitable for asset allocation, risk management, and asset pricing.     

Empirical Bayes estimates for correlated hierarchical data with overdispersion

An extension of the generalized linear mixed model was constructed to simultaneously accommodate overdispersion and hierarchies present in longitudinal or clustered data. This so‐called combined model includes conjugate random effects at observation level for overdispersion and normal random effects at subject level to handle correlation, respectively. A variety of data types can be handled in this way, using different members of the exponential family. Both maximum likelihood and Bayesian estimation for covariate effects and variance components were proposed. The focus of this paper is the development of an estimation procedure for the two sets of random effects. These are necessary when making predictions for future responses or their associated probabilities. Such (empirical) Bayes estimates will also be helpful in model diagnosis, both when checking the fit of the model as well as when investigating outlying observations. The proposed procedure is applied to three datasets of different outcome types. Copyright © 2014 John Wiley & Sons, Ltd.     

Bayesian variable selection in a finite mixture of linear mixed-effects models

Mixture of linear mixed-effects models has received considerable attention in longitudinal studies, including medical research, social science and economics. The inferential question of interest is often the identification of critical factors that affect the responses. We consider a Bayesian approach to select the important fixed and random effects in the finite mixture of linear mixed-effects models. To accomplish our goal, latent variables are introduced to facilitate the identification of influential fixed and random components and to classify the membership of observations in the longitudinal data. A spike-and-slab prior for the regression coefficients is adopted to sidestep the potential complications of highly collinear covariates and to handle large p and small n issues in the variable selection problems. Here we employ Markov chain Monte Carlo (MCMC) sampling techniques for posterior inferences and explore the performance of the proposed method in simulation studies, followed by an actual psychiatric data analysis concerning depressive disorder.     

Bayesian analysis of skew-normal independent linear mixed models with heterogeneity in the random-effects population

We present a new class of models to fit longitudinal data, obtained with a suitable modification of the classical linear mixed-effects model. For each sample unit, the joint distribution of the random effect and the random error is a finite mixture of scale mixtures of multivariate skew-normal distributions. This extension allows us to model the data in a more flexible way, taking into account skewness, multimodality and discrepant observations at the same time. The scale mixtures of skew-normal form an attractive class of asymmetric heavy-tailed distributions that includes the skew-normal, skew-Student-t, skew-slash and the skew-contaminated normal distributions as special cases, being a flexible alternative to the use of the corresponding symmetric distributions in this type of models. A simple efficient MCMC Gibbs-type algorithm for posterior Bayesian inference is employed. In order to illustrate the usefulness of the proposed methodology, two artificial and two real data sets are analyzed.     

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.