A Bayesian approach for mixed effects state-space models under skewness and heavy tails.

Human immunodeficiency virus (HIV) dynamics have been the focus of epidemiological and biostatistical research during the past decades to understand the progression of acquired immunodeficiency syndrome (AIDS) in the population. Although there are several approaches for modeling HIV dynamics, one of the most popular is based on Gaussian mixed-effects models because of its simplicity from the implementation and interpretation viewpoints. However, in some situations, Gaussian mixed-effects models cannot (a) capture serial correlation existing in longitudinal data, (b) deal with missing observations properly, and (c) accommodate skewness and heavy tails frequently presented in patients' profiles. For those cases, mixed-effects state-space models (MESSM) become a powerful tool for modeling correlated observations, including HIV dynamics, because of their flexibility in modeling the unobserved states and the observations in a simple way. Consequently, our proposal considers an MESSM where the observations' error distribution is a skew-t. This new approach is more flexible and can accommodate data sets exhibiting skewness and heavy tails. Under the Bayesian paradigm, an efficient Markov chain Monte Carlo algorithm is implemented. To evaluate the properties of the proposed models, we carried out some exciting simulation studies, including missing data in the generated data sets. Finally, we illustrate our approach with an application in the AIDS Clinical Trial Group Study 315 (ACTG-315) clinical trial data set.

Maximum likelihood estimation for stochastic volatility in mean models with heavy-tailed distributions.

In this article, we introduce a likelihood-based estimation method for the stochastic volatility in mean (SVM) model with scale mixtures of normal (SMN) distributions (Abanto-Valle et al., 2012). Our estimation method is based on the fact that the powerful hidden Markov model (HMM) machinery can be applied in order to evaluate an arbitrarily accurate approximation of the likelihood of an SVM model with SMN distributions. The method is based on the proposal of Langrock et al. (2012) and makes explicit the useful link between HMMs and SVM models with SMN distributions. Likelihood-based estimation of the parameters of stochastic volatility models in general, and SVM models with SMN distributions in particular, is usually regarded as challenging as the likelihood is a high-dimensional multiple integral. However, the HMM approximation, which is very easy to implement, makes numerical maximum of the likelihood feasible and leads to simple formulae for forecast distributions, for computing appropriately defined residuals, and for decoding, i.e., estimating the volatility of the process.

Bayesian analysis of stochastic volatility-in-mean model with leverage and asymmetrically heavy-tailed error using generalized hyperbolic skew Student's t-distribution.

A stochastic volatility-in-mean model with correlated errors using the generalized hyperbolic skew Student-t (GHST) distribution provides a robust alternative to the parameter estimation for daily stock returns in the absence of normality. An efficient Markov chain Monte Carlo (MCMC) sampling algorithm is developed for parameter estimation. The deviance information, the Bayesian predictive information and the log-predictive score criterion are used to assess the fit of the proposed model. The proposed method is applied to an analysis of the daily stock return data from the Standard & Poor's 500 index (S&P 500). The empirical results reveal that the stochastic volatility-in-mean model with correlated errors and GH-ST distribution leads to a significant improvement in the goodness-of-fit for the S&P 500 index returns dataset over the usual normal model.

Quantile regression for censored mixed-effects models with applications to HIV studies.

HIV RNA viral load measures are often subjected to some upper and lower detection limits depending on the quantification assays. Hence, the responses are either left or right censored. Linear/nonlinear mixed-effects models, with slight modifications to accommodate censoring, are routinely used to analyze this type of data. Usually, the inference procedures are based on normality (or elliptical distribution) assumptions for the random terms. However, those analyses might not provide robust inference when the distribution assumptions are questionable. In this paper, we discuss a fully Bayesian quantile regression inference using Markov Chain Monte Carlo (MCMC) methods for longitudinal data models with random effects and censored responses. Compared to the conventional mean regression approach, quantile regression can characterize the entire conditional distribution of the outcome variable, and is more robust to outliers and misspecification of the error distribution. Under the assumption that the error term follows an asymmetric Laplace distribution, we develop a hierarchical Bayesian model and obtain the posterior distribution of unknown parameters at the pth level, with the median regression (p = 0.5) as a special case. The proposed procedures are illustrated with two HIV AIDS studies on viral loads that were initially analyzed using the typical normal (censored) mean regression mixed-effects models, as well as a simulation study.

Linear mixed models for skew-normal/independent bivariate responses with an application to periodontal disease.

Bivariate clustered (correlated) data often encountered in epidemiological and clinical research are routinely analyzed under a linear mixed model (LMM) framework with underlying normality assumptions of the random effects and within-subject errors. However, such normality assumptions might be questionable if the data set particularly exhibits skewness and heavy tails. Using a Bayesian paradigm, we use the skew-normal/independent (SNI) distribution as a tool for modeling clustered data with bivariate non-normal responses in an LMM framework. The SNI distribution is an attractive class of asymmetric thick-tailed parametric structure which includes the skew-normal distribution as a special case. We assume that the random effects follow multivariate SNI distributions and the random errors follow SNI distributions which provides substantial robustness over the symmetric normal process in an LMM framework. Specific distributions obtained as special cases, viz. the skew-t, the skew-slash and the skew-contaminated normal distributions are compared, along with the default skew-normal density. The methodology is illustrated through an application to a real data which records the periodontal health status of an interesting population using periodontal pocket depth (PPD) and clinical attachment level (CAL).