Joint mean–covariance model in generalized partially linear varying coefficient models for longitudinal data

In longitudinal data analysis, efficient estimation of regression coefficients requires a correct specification of certain covariance structure, and efficient estimation of covariance matrix requires a correct specification of mean regression model. In this article, we propose a general semiparametric model for the mean and the covariance simultaneously using the modified Cholesky decomposition. A regression spline-based approach within the framework of generalized estimating equations is proposed to estimate the parameters in the mean and the covariance. Under regularity conditions, asymptotic properties of the resulting estimators are established. Extensive simulation is conducted to investigate the performance of the proposed estimator and in the end a real data set is analysed using the proposed approach.     

A cautionary note on generalized linear models for covariance of unbalanced longitudinal data

Missing data in longitudinal studies can create enormous challenges in data analysis when coupled with the positive-definiteness constraint on a covariance matrix. For complete balanced data, the Cholesky decomposition of a covariance matrix makes it possible to remove the positive-definiteness constraint and use a generalized linear model setup to jointly model the mean and covariance using covariates (Pourahmadi, 2000). However, this approach may not be directly applicable when the longitudinal data are unbalanced, as coherent regression models for the dependence across all times and subjects may not exist. Within the existing generalized linear model framework, we show how to overcome this and other challenges by embedding the covariance matrix of the observed data for each subject in a larger covariance matrix and employing the familiar EM algorithm to compute the maximum likelihood estimates of the parameters and their standard errors. We illustrate and assess the methodology using real data sets and simulations.     

Bayesian inference in joint modelling of location and scale parameters of the t distribution for longitudinal data

This paper presents a fully Bayesian approach to multivariate t regression models whose mean vector and scale covariance matrix are modelled jointly for analyzing longitudinal data. The scale covariance structure is factorized in terms of unconstrained autoregressive and scale innovation parameters through a modified Cholesky decomposition. A computationally flexible data augmentation sampler coupled with the Metropolis-within-Gibbs scheme is developed for computing the posterior distributions of parameters. The Bayesian predictive inference for the future response vector is also investigated. The proposed methodologies are illustrated through a real example from a sleep dose–response study.     

Adaptive robust estimation in joint mean–covariance regression model for bivariate longitudinal data

The estimation of the covariance matrix is important in the analysis of bivariate longitudinal data. A good estimator for the covariance matrix can improve the efficiency of the estimators of the mean regression coefficients. Furthermore, the covariance estimation itself is also of interest, but it is a challenging job to model the covariance matrix of bivariate longitudinal data due to the complex structure and positive definite constraint. In addition, most of existing approaches are based on the maximum likelihood, which is very sensitive to outliers or heavy-tail error distributions. In this article, an adaptive robust estimation method is proposed for bivariate longitudinal data. Unlike the existing likelihood-based methods, the proposed method can adapt to different error distributions. Specifically, at first, we utilize the modified Cholesky block decomposition to parameterize the covariance matrices. Secondly, we apply the bounded Huber's score function to develop a set of robust generalized estimating equations to estimate the parameters both in the mean and the covariance models simultaneously. A data-driven approach is presented to select the parameter c in the Huber's score function, which can ensure that the proposed method is robust and efficient. A simulation study and a real data analysis are conducted to illustrate the robustness and efficiency of the proposed approach.     

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.     

Restricted maximum likelihood estimation of joint mean‐covariance models

The class of joint mean‐covariance models uses the modified Cholesky decomposition of the within subject covariance matrix in order to arrive to an unconstrained, statistically meaningful reparameterisation. The new parameterisation of the covariance matrix has two sets of parameters that separately describe the variances and correlations. Thus, with the mean or regression parameters, these models have three sets of distinct parameters. In order to alleviate the problem of inefficient estimation and downward bias in the variance estimates, inherent in the maximum likelihood estimation procedure, the usual REML estimation procedure adjusts for the degrees of freedom lost due to the estimation of the mean parameters. Because of the parameterisation of the joint mean covariance models, it is possible to adapt the usual REML procedure in order to estimate the variance (correlation) parameters by taking into account the degrees of freedom lost by the estimation of both the mean and correlation (variance) parameters. To this end, here we propose adjustments to the estimation procedures based on the modified and adjusted profile likelihoods. The methods are illustrated by an application to a real data set and simulation studies. The Canadian Journal of Statistics 40: 225–242; 2012 © 2012 Statistical Society of Canada     

Bayesian parsimonious covariance estimation for hierarchical linear mixed models

We consider a non-centered parameterization of the standard random-effects model, which is based on the Cholesky decomposition of the variance-covariance matrix. The regression type structure of the non-centered parameterization allows us to use Bayesian variable selection methods for covariance selection. We search for a parsimonious variance-covariance matrix by identifying the non-zero elements of the Cholesky factors. With this method we are able to learn from the data for each effect whether it is random or not, and whether covariances among random effects are zero. An application in marketing shows a substantial reduction of the number of free elements in the variance-covariance matrix.     

Joint Mean-Covariance Models with Applications to Longitudinal Data in Partially Linear Model

Semiparametric regression models and estimating covariance functions are very useful in longitudinal study. Unfortunately, challenges arise in estimating the covariance function of longitudinal data collected at irregular time points. In this article, for mean term, a partially linear model is introduced and for covariance structure, a modified Cholesky decomposition approach is proposed to heed the positive-definiteness constraint. We estimate the regression function by using the local linear technique and propose quasi-likelihood estimating equations for both the mean and covariance structures. Moreover, asymptotic normality of the resulting estimators is established. Finally, simulation study and real data analysis are used to illustrate the proposed approach.     

A robust approach to joint modeling of mean and scale covariance for longitudinal data

In this paper, we propose a multivariate t$t$ regression model with its mean and scale covariance modeled jointly for the analysis of longitudinal data. A modified Cholesky decomposition is adopted to factorize the dependence structure in terms of unconstrained autoregressive and scale innovation parameters. We present three distinct representations of the log-likelihood function of the model and study the associated properties. A computationally efficient Fisher scoring algorithm is developed for carrying out maximum likelihood estimation. The technique for the prediction of future responses in this context is also investigated. The implementation of the proposed methodology is illustrated through two real-life examples and extensive simulation studies.     

Bayesian analysis of vector-autoregressive models with noninformative priors

In this paper, we investigate the properties of Bayes estimators of vector autoregression (VAR) coefficients and the covariance matrix under two commonly employed loss functions. We point out that the posterior mean of the variances of the VAR errors under the Jeffreys prior is likely to have an over-estimation bias. Our Bayesian computation results indicate that estimates using the constant prior on the VAR regression coefficients and the reference prior of Yang and Berger (Ann. Statist. 22 (1994) 1195) on the covariance matrix dominate the constant-Jeffreys prior estimates commonly used in applications of VAR models in macroeconomics. We also estimate a VAR model of consumption growth using both constant-reference and constant-Jeffreys priors.     

Selection of Multivariate Stochastic Volatility Models via Bayesian Stochastic Search

We propose a Bayesian stochastic search approach to selecting restrictions on multivariate regression models where the errors exhibit deterministic or stochastic conditional volatilities. We develop a Markov chain Monte Carlo (MCMC) algorithm that generates posterior restrictions on the regression coefficients and Cholesky decompositions of the covariance matrix of the errors. Numerical simulations with artificially generated data show that the proposed method is effective in selecting the data-generating model restrictions and improving the forecasting performance of the model. Applying the method to daily foreign exchange rate data, we conduct stochastic search on a VAR model with stochastic conditional volatilities.     

A multivariate volatility vine copula model

This article proposes a dynamic framework for modeling and forecasting of realized covariance matrices using vine copulas to allow for more flexible dependencies between assets. Our model automatically guarantees positive definiteness of the forecast through the use of a Cholesky decomposition of the realized covariance matrix. We explicitly account for long-memory behavior by using fractionally integrated autoregressive moving average (ARFIMA) and heterogeneous autoregressive (HAR) models for the individual elements of the decomposition. Furthermore, our model incorporates non-Gaussian innovations and GARCH effects, accounting for volatility clustering and unconditional kurtosis. The dependence structure between assets is studied using vine copula constructions, which allow for nonlinearity and asymmetry without suffering from an inflexible tail behavior or symmetry restrictions as in conventional multivariate models. Further, the copulas have a direct impact on the point forecasts of the realized covariances matrices, due to being computed as a nonlinear transformation of the forecasts for the Cholesky matrix. Beside studying in-sample properties, we assess the usefulness of our method in a one-day-ahead forecasting framework, comparing recent types of models for the realized covariance matrix based on a model confidence set approach. Additionally, we find that in Value-at-Risk (VaR) forecasting, vine models require less capital requirements due to smoother and more accurate forecasts.     

Bayesian modelling of the mean and covariance matrix in normal nonlinear models

An important problem in statistics is the study of longitudinal data taking into account the effect of other explanatory variables such as treatments and time. In this paper, a new Bayesian approach for analysing longitudinal data is proposed. This innovative approach takes into account the possibility of having nonlinear regression structures on the mean and linear regression structures on the variance–covariance matrix of normal observations, and it is based on the modelling strategy suggested by Pourahmadi [M. Pourahmadi, Joint mean-covariance models with applications to longitudinal data: Unconstrained parameterizations, Biometrika, 87 (1999), pp. 667–690.]. We initially extend the classical methodology to accommodate the fitting of nonlinear mean models then we propose our Bayesian approach based on a generalization of the Metropolis–Hastings algorithm of Cepeda [E.C. Cepeda, Variability modeling in generalized linear models, Unpublished Ph.D. Thesis, Mathematics Institute, Universidade Federal do Rio de Janeiro, 2001]. Finally, we illustrate the proposed methodology by analysing one example, the cattle data set, that is used to study cattle growth.     

Model‐based clustering of longitudinal data

A new family of mixture models for the model‐based clustering of longitudinal data is introduced. The covariance structures of eight members of this new family of models are given and the associated maximum likelihood estimates for the parameters are derived via expectation–maximization (EM) algorithms. The Bayesian information criterion is used for model selection and a convergence criterion based on the Aitken acceleration is used to determine the convergence of these EM algorithms. This new family of models is applied to yeast sporulation time course data, where the models give good clustering performance. Further constraints are then imposed on the decomposition to allow a deeper investigation of the correlation structure of the yeast data. These constraints greatly extend this new family of models, with the addition of many parsimonious models. The Canadian Journal of Statistics 38:153–168; 2010 © 2010 Statistical Society of Canada     

Bayesian estimation of the efficient frontier

In this paper, we consider the estimation of the three determining parameters of the efficient frontier, the expected return, and the variance of the global minimum variance portfolio and the slope parameter, from a Bayesian perspective. Their posterior distribution is derived by assigning the diffuse and the conjugate priors to the mean vector and the covariance matrix of the asset returns and is presented in terms of a stochastic representation. Furthermore, Bayesian estimates together with the standard uncertainties for all three parameters are provided, and their asymptotic distributions are established. All obtained findings are applied to real data, consisting of the returns on assets included into the S&P 500. The empirical properties of the efficient frontier are then examined in detail.     

Parsimonious Estimation of the Covariance Matrix in Multinomial Probit Models

This article presents a Bayesian analysis of a multinomial probit model by building on previous work that specified priors on identified parameters. The main contribution of our article is to propose a prior on the covariance matrix of the latent utilities that permits elements of the inverse of the covariance matrix to be identically zero. This allows a parsimonious representation of the covariance matrix when such parsimony exists. The methodology is applied to both simulated and real data, and its ability to obtain more efficient estimators of the covariance matrix and regression coefficients is assessed using simulated data.     

A Bayesian nonparametric Markovian model for non-stationary time series

Stationary time series models built from parametric distributions are, in general, limited in scope due to the assumptions imposed on the residual distribution and autoregression relationship. We present a modeling approach for univariate time series data, which makes no assumptions of stationarity, and can accommodate complex dynamics and capture non-standard distributions. The model for the transition density arises from the conditional distribution implied by a Bayesian nonparametric mixture of bivariate normals. This results in a flexible autoregressive form for the conditional transition density, defining a time-homogeneous, non-stationary Markovian model for real-valued data indexed in discrete time. To obtain a computationally tractable algorithm for posterior inference, we utilize a square-root-free Cholesky decomposition of the mixture kernel covariance matrix. Results from simulated data suggest that the model is able to recover challenging transition densities and non-linear dynamic relationships. We also illustrate the model on time intervals between eruptions of the Old Faithful geyser. Extensions to accommodate higher order structure and to develop a state-space model are also discussed.     

Covariance Matrix Estimation via Network Structure

In this article, we employ a regression formulation to estimate the high-dimensional covariance matrix for a given network structure. Using prior information contained in the network relationships, we model the covariance as a polynomial function of the symmetric adjacency matrix. Accordingly, the problem of estimating a high-dimensional covariance matrix is converted to one of estimating low dimensional coefficients of the polynomial regression function, which we can accomplish using ordinary least squares or maximum likelihood. The resulting covariance matrix estimator based on the maximum likelihood approach is guaranteed to be positive definite even in finite samples. Under mild conditions, we obtain the theoretical properties of the resulting estimators. A Bayesian information criterion is also developed to select the order of the polynomial function. Simulation studies and empirical examples illustrate the usefulness of the proposed methods.     

Estimation of covariance matrix via the sparse Cholesky factor with lasso

In this paper, we discuss a parsimonious approach to estimation of high-dimensional covariance matrices via the modified Cholesky decomposition with lasso. Two different methods are proposed. They are the equi-angular and equi-sparse methods. We use simulation to compare the performance of the proposed methods with others available in the literature, including the sample covariance matrix, the banding method, and the L₁-penalized normal loglikelihood method. We then apply the proposed methods to a portfolio selection problem using 80 series of daily stock returns. To facilitate the use of lasso in high-dimensional time series analysis, we develop the dynamic weighted lasso (DWL) algorithm that extends the LARS-lasso algorithm. In particular, the proposed algorithm can efficiently update the lasso solution as new data become available. It can also add or remove explanatory variables. The entire solution path of the L₁-penalized normal loglikelihood method is also constructed.     

Spatial sampling design for parameter estimation of the covariance function

We study the spatial optimal sampling design for covariance parameter estimation. The spatial process is modeled as a Gaussian random field and maximum likelihood (ML) is used to estimate the covariance parameters. We use the log determinant of the inverse Fisher information matrix as the design criterion and run simulations to investigate the relationship between the inverse Fisher information matrix and the covariance matrix of the ML estimates. A simulated annealing algorithm is developed to search for an optimal design among all possible designs on a fine grid. Since the design criterion depends on the unknown parameters, we define relative efficiency of a design and consider minimax and Bayesian criteria to find designs that are robust for a range of parameter values. Simulation results are presented for the Matérn class of covariance functions.