Bayes factor consistency for unbalanced ANOVA models

In practical situations, most experimental designs often yield unbalanced data which have different numbers of observations per unit because of cost constraints, missing data, etc. In this paper, we consider the Bayesian approach to hypothesis testing or model selection under the one-way unbalanced fixed-effects analysis-of-variance (ANOVA) model. We adopt Zellner's g-prior with the beta-prime distribution for g, which results in an explicit closed-form expression of the Bayes factor without integral representation. Furthermore, we investigate the model selection consistency of the Bayes factor under three different asymptotic scenarios: either the number of units goes to infinity, the number of observations per unit goes to infinity, or both go to infinity. The results presented extend some existing ones of the Bayes factor for the balanced ANOVA models in the literature.     

Corrected empirical Bayes confidence intervals in nested error regression models

In the small area estimation, the empirical best linear unbiased predictor (EBLUP) or the empirical Bayes estimator (EB) in the linear mixed model is recognized to be useful because it gives a stable and reliable estimate for a mean of a small area. In practical situations where EBLUP is applied to real data, it is important to evaluate how much EBLUP is reliable. One method for the purpose is to construct a confidence interval based on EBLUP. In this paper, we obtain an asymptotically corrected empirical Bayes confidence interval in a nested error regression model with unbalanced sample sizes and unknown components of variance. The coverage probability is shown to satisfy the confidence level in the second-order asymptotics. It is numerically revealed that the corrected confidence interval is superior to the conventional confidence interval based on the sample mean in terms of the coverage probability and the expected width of the interval. Finally, it is applied to the posted land price data in Tokyo and the neighboring prefecture.     

Bayes estimates in multivariate semiparametric linear models

Bayes estimates are derived in multivariate linear models with unknown distribution. The prior distribution is defined using a Dirichlet prior for the unknown error distribution and a normal-Wishart distribution for the parameters. The posterior distribution is determined and explicit expressions are given in the special cases of location-scale and two-sample models. The calculation of self-informative limits of Bayes estimates yields standard estimates.     

Sensitivity of the fractional Bayes factor to prior distributions

The authors derive a measure of the sensitivity of the fractional Bayes factor, an index which is used to compare models when the priors for their respective parameters are improper, or when there is concern about robustness of the prior specification. They prove that in a large class of problems, this measure is a decreasing function of the fraction of the sample used to update the prior distribution before the models are compared.     

An F-type small sample simultaneous test for nested linear regression models

A small sample simultaneous testing method is proposed for nested linear regression model. The methodology is based on the generalized likelihood ratio test which is the large sample simultaneous testing method for general nested models. The proposed test is also used for model identification.     

Minimum-volume confidence sets for normal linear regression models

In this article, we establish the minimum-volume confidence sets for normal linear regression models, extending the results in Zhang [Minimum volume confidence sets for parameters of normal distributions. Adv Stat Anal. 2017;101:309–320] on building the minimum-volume confidence sets for parameters of normal distributions. Compared with classical confidence sets, the proposed optimal confidence set is proved to have the smallest volume, for whatever confidence level, sample size and sample data.     

A test for variance-covarianch parameters in normal linear models

This paper derives a test statistic for the variance-covariance parameters which is a quadratic function of their MINQUE (Minimum Norm Quadratic Unbiased Estimation) estimates. The test is a Wald-type test, and its development closely parallels the theory used to derive a similar test for the coefficients in linear models. In fact, the derivation proceeds by first setting up the estimation problem in a derived linear model in which the dispersion parameters are the coefficients. The test statistic is shown to be the sum of the squares of independent standardized x² variables.     

Improved robust Bayes estimators of the error variance in linear models

We consider the problem of estimating the error variance in a general linear model when the error distribution is assumed to be spherically symmetric, but not necessary Gaussian. In particular we study the case of a scale mixture of Gaussians including the particularly important case of the multivariate-t distribution. Under Stein's loss, we construct a class of estimators that improve on the usual best unbiased (and best equivariant) estimator. Our class has the interesting double robustness property of being simultaneously generalized Bayes (for the same generalized prior) and minimax over the entire class of scale mixture of Gaussian distributions.     

Robustness measures for Bayes linear analyses

We consider the role of global robustness measures in Bayes linear analysis. We suggest two such measures, one for expectation comparisons and one for variance comparisons. Geometric interpretations of the measures are presented. The approach is illustrated by considering the robustness of certain multiplicative models to assumptions of independence, with particular application to a problem arising in an asset management model for water resources.     

Bayesian adaptive lasso with variational Bayes for variable selection in high-dimensional generalized linear mixed models

This article describes a full Bayesian treatment for simultaneous fixed-effect selection and parameter estimation in high-dimensional generalized linear mixed models. The approach consists of using a Bayesian adaptive Lasso penalty for signal-level adaptive shrinkage and a fast Variational Bayes scheme for estimating the posterior mode of the coefficients. The proposed approach offers several advantages over the existing methods, for example, the adaptive shrinkage parameters are automatically incorporated, no Laplace approximation step is required to integrate out the random effects. The performance of our approach is illustrated on several simulated and real data examples. The algorithm is implemented in the R package glmmvb and is made available online.     

A test of separate hypotheses for comparing linear mixed models with non nested fixed effects

As researchers increasingly rely on linear mixed models to characterize longitudinal data, there is a need for improved techniques for selecting among this class of models which requires specification of both fixed and random effects via a mean model and variance-covariance structure. The process is further complicated when fixed and/or random effects are non nested between models. This paper explores the development of a hypothesis test to compare non nested linear mixed models based on extensions of the work begun by Sir David Cox. We assess the robustness of this approach for comparing models containing correlated measures of body fat for predicting longitudinal cardiometabolic risk.     

Consistent Bayesian information criterion based on a mixture prior for possibly high-dimensional multivariate linear regression models

In the problem of selecting variables in a multivariate linear regression model, we derive new Bayesian information criteria based on a prior mixing a smooth distribution and a delta distribution. Each of them can be interpreted as a fusion of the Akaike information criterion (AIC) and the Bayesian information criterion (BIC). Inheriting their asymptotic properties, our information criteria are consistent in variable selection in both the large-sample and the high-dimensional asymptotic frameworks. In numerical simulations, variable selection methods based on our information criteria choose the true set of variables with high probability in most cases.     

Generalization of the order-restricted information criterion for multivariate normal linear models

The generalized order-restricted information criterion (goric) is a model selection criterion which can, up to now, solely be applied to the analysis of variance models and, so far, only evaluate restrictions of the form Rθ≤0$R\theta \le 0$, where θ$\theta$ is a vector of k group means and R   a _cm×k$c_m\times k$ matrix. In this paper, we generalize the goric in two ways: (i) such that it can be applied to t  -variate normal linear models and (ii) such that it can evaluate a more general form of order restrictions: Rθ≤r$R\theta \le r$, where θ$\theta$ is a vector of length tk, r a vector of length c_m, and R   a _cm×tk$c_m\times \mathit{tk}$ matrix of full rank (when r≠0$r\ne 0$). At the end, we illustrate that the goric is easy to implement in a multivariate regression model.     

Choosing the link function and accounting for link uncertainty in generalized linear models using Bayes factors

One important component of model selection using generalized linear models (GLM) is the choice of a link function. We propose using approximate Bayes factors to assess the improvement in fit over a GLM with canonical link when a parametric link family is used. The approximate Bayes factors are calculated using the Laplace approximations given in [32], together with a reference set of prior distributions. This methodology can be used to differentiate between different parametric link families, as well as allowing one to jointly select the link family and the independent variables. This involves comparing nonnested models and so standard significance tests cannot be used. The approach also accounts explicitly for uncertainty about the link function. The methods are illustrated using parametric link families studied in [12] for two data sets involving binomial responses. The first author was supported by Sonderforschungsbereich 386 Statistische Analyse Diskreter Strukturen, and the second author by NIH Grant 1R01CA094212-01 and ONR Grant N00014-01-10745.     

Bayes linear analysis for graphical models: The geometric approach to local computation and interpretive graphics

This paper concerns the geometric treatment of graphical models using Bayes linear methods. We introduce Bayes linear separation as a second order generalised conditional independence relation, and Bayes linear graphical models are constructed using this property. A system of interpretive and diagnostic shadings are given, which summarise the analysis over the associated moral graph. Principles of local computation are outlined for the graphical models, and an algorithm for implementing such computation over the junction tree is described. The approach is illustrated with two examples. The first concerns sales forecasting using a multivariate dynamic linear model. The second concerns inference for the error variance matrices of the model for sales, and illustrates the generality of our geometric approach by treating the matrices directly as random objects. The examples are implemented using a freely available set of object-oriented programming tools for Bayes linear local computation and graphical diagnostic display.     

Pseudo-empirical Bayes estimation of small area means under a nested error linear regression model with functional measurement errors

Small area estimation is studied under a nested error linear regression model with area level covariate subject to measurement error. Ghosh and Sinha (2007) obtained a pseudo-Bayes (PB) predictor of a small area mean and a corresponding pseudo-empirical Bayes (PEB) predictor, using the sample means of the observed covariate values to estimate the true covariate values. In this paper, we first derive an efficient PB predictor by using all the available data to estimate true covariate values. We then obtain a corresponding PEB predictor and show that it is asymptotically “optimal”. In addition, we employ a jackknife method to estimate the mean squared prediction error (MSPE) of the PEB predictor. Finally, we report the results of a simulation study on the performance of our PEB predictor and associated jackknife MSPE estimator. Our results show that the proposed PEB predictor can lead to significant gain in efficiency over the previously proposed PEB predictor. Area level models are also studied.     

Designing fractional two-level experiments with nested error structures

A common feature of experiments with a random blocking factor and splitplot experiments is their nested error structure. This paper proposes a general strategy to handle fractional two-level experiments with such error structures. The strategy aims to create error strata with sufficient numbers of contrasts to separate active effects from inactive effects. The strategy also details the construction of treatment generators, given the constraints of a predetermined error structure. The key elements of the strategy are illustrated with a chemical experiment that has 16 factors and 32 runs blocked according to working days, and a cheese-making experiment that has 11 factors and 128 runs, divided over milk supplies as whole plots, curds productions as subplots and sets of identically treated cheeses as sub-subplots.     

Spherical radial approximation for nested mixed effects models

We consider a likelihood approximation in generalized linear mixed-effects models (GLMM) with multilevel nested random effects. Likelihood evaluation in such models is difficult, hindered by the need for high dimensional integration, where the dimension is proportional to the number of units per level and the number of random effects per unit. Various integration approaches have been proposed, including the penalized quasi-likelihood method, Laplace approximation, quadrature approximation, simulation, and MCMC algorithms. We propose a new quadrature approximation method, which is based on the spherical radial integration approach of Monahan and Genz (J Am Stat Assoc 92:664–674 1997), and at the same time takes advantage of the hierarchical structure of the integration. Our new hierarchical spherical radial method has a time complexity that is linear in the number of units per level and the number of random effects per unit, in contrast to the exponential complexity of the adaptive Gaussian quadrature method of Pinheiro and Chao (J Comput Graph Stat 15:58–81 2006) for the same problem. Using a spline approximation, the generalized additive mixed models (GAMM) are GLMMs with two levels of nested random effects. We apply our method to estimation of GAMMs. We compare it with competing methods through simulations and apply our method to analyze virologic and immunologic responses in an AIDS clinical trial. An R package is written and available at http://?users.?wpi.?edu/?~jgagnon/?software.?html.