A gradient-based deletion diagnostic measure for generalized linear mixed models

A gradient-statistic-based diagnostic measure is developed in the context of the generalized linear mixed models. Its performance is assessed by some real examples and simulation studies, in terms of ability in detecting influential data structures and of concordance with the most used influence measures.     

On the information-based measure of covariance complexity and its application to the evaluation of multivariate linear models

This paper introduces a new information-theoretic measure of complexity called ICOMP as a decision rule for model selection and evaluation for multivariate linear models. The development of ICOMP is based on the generalization and utilization of the covariance complexity index of van Emden (1971) in estimation of the multivariate linear model. ICOMP is motivated by Akaike's (1973) Information Criterion (AIC), but it is a different procedure than AIC. In linear or nonlinear statistical models ICOMP uses an information-based characterization of: (i) the covariance matrix properties of the parameter estimates of a model starting from their finite sampling distributions, and (ii) the complexity of the inverse-Fisher information matrix (i-FIM) as a new criterion of achievable accuracy of the model As a result, it provides a trade-off between the accuracy of the parameter estimates and the interaction of the residuals of a model via the measure of complexity of their respective covariances. It controls the risks of both insufficient and overparameterized models, and incorporates the assumption of dependence and the independence of the residuals in one criterion function. A model with minimum ICOMP is chosen to be the best model among all possible competing alternative models. ICOMP relieves the researcher of any need to consider the parameter dimension of a model explicitly. A real numerical example is shown in subset selection of variables in multivariate regression analysis to demonstrate the utility and versatility of the new approach.     

Estimation of group means using Bayesian generalized linear mixed models

Generalized linear mixed models (GLMM) are commonly used to model the treatment effect over time while controlling for important clinical covariates. Standard software procedures often provide estimates of the outcome based on the mean of the covariates; however, these estimates will be biased for the true group means in the GLMM. Implementing GLMM in the frequentist framework can lead to issues of convergence. A simulation study demonstrating the use of fully Bayesian GLMM for providing unbiased estimates of group means is shown. These models are very straightforward to implement and can be used for a broad variety of outcomes (eg, binary, categorical, and count data) that arise in clinical trials. We demonstrate the proposed method on a data set from a clinical trial in diabetes.     

A comparison between bootstrap methods and generalized estimating equations for correlated outcomes in generalized linear models

We discuss and evaluate bootstrap algorithms for obtaining confidence intervals for parameters in Generalized Linear Models when the data are correlated. The methods are based on a stratified bootstrap and are suited to correlation occurring within “blocks” of data (e.g., individuals within a family, teeth within a mouth, etc.). Application of the intervals to data from a Dutch follow-up study on preterm infants shows the corroborative usefulness of the intervals, while the intervals are seen to be a powerful diagnostic in studying annual measles data. In a simulation study, we compare the coverage rates of the proposed intervals with existing methods (e.g., via Generalized Estimating Equations). In most cases, the bootstrap intervals are seen to perform better than current methods, and are produced in an automatic fashion, so that the user need not know (or have to guess) the dependence structure within a block.     

Measuring the complexity of generalized linear hierarchical models

Measuring a statistical model's complexity is important for model criticism and comparison. However, it is unclear how to do this for hierarchical models due to uncertainty about how to count the random effects. The authors develop a complexity measure for generalized linear hierarchical models based on linear model theory. They demonstrate the new measure for binomial and Poisson observables modeled using various hierarchical structures, including a longitudinal model and an areal‐data model having both spatial clustering and pure heterogeneity random effects. They compare their new measure to a Bayesian index of model complexity, the effective number p_D of parameters (Spiegelhalter, Best, Carlin & van der Linde 2002); the comparisons are made in the binomial and Poisson cases via simulation and two real data examples. The two measures are usually close, but differ markedly in some instances where p_D is arguably inappropriate. Finally, the authors show how the new measure can be used to approach the difficult task of specifying prior distributions for variance components, and in the process cast further doubt on the commonly‐used vague inverse gamma prior.     

Estimation of group means when adjusting for covariates in generalized linear models

Generalized linear models are commonly used to analyze categorical data such as binary, count, and ordinal outcomes. Adjusting for important prognostic factors or baseline covariates in generalized linear models may improve the estimation efficiency. The model‐based mean for a treatment group produced by most software packages estimates the response at the mean covariate, not the mean response for this treatment group for the studied population. Although this is not an issue for linear models, the model‐based group mean estimates in generalized linear models could be seriously biased for the true group means. We propose a new method to estimate the group mean consistently with the corresponding variance estimation. Simulation showed the proposed method produces an unbiased estimator for the group means and provided the correct coverage probability. The proposed method was applied to analyze hypoglycemia data from clinical trials in diabetes. Copyright © 2014 John Wiley & Sons, Ltd.     

Longitudinal data analysis based on generalized linear partially varying-coefficient models

In this article, we consider a generalized linear partially varying-coefficient model for longitudinal data analysis. A local quasi-likelihood method is proposed to estimate the constant-coefficient and varying-coefficient functions simultaneously based on the local polynomial kernel regression. The corresponding standard error estimates are derived. Large sample properties are investigated. The proposed methodologies are demonstrated by extensive simulation studies and a real example.     

Hidden Markov chains in generalized linear models

We show how the concept of hidden Markov model may be accommodated in a setting involving multiple sequences of observations. The resulting class of models allows for both interrelationships between different sequences and serial dependence within sequences. Missing values in the observation sequences may be handled in a straightforward manner. We also examine a group of methods, based upon the observed Fisher Information matrix, for estimating the covariance matrix of the parameter estimates. We illustrate the methods with both real and simulated data sets.     

Robust quasi-likelihood inference in generalized linear mixed models with outliers

It is well known that in a traditional outlier-free situation, the generalized quasi-likelihood (GQL) approach [B.C. Sutradhar, On exact quasilikelihood inference in generalized linear mixed models, Sankhya: Indian J. Statist. 66 (2004), pp. 261–289] performs very well to obtain the consistent as well as the efficient estimates for the parameters involved in the generalized linear mixed models (GLMMs). In this paper, we first examine the effect of the presence of one or more outliers on the GQL estimation for the parameters in such GLMMs, especially in two important models such as count and binary mixed models. The outliers appear to cause serious biases and hence inconsistency in the estimation. As a remedy, we then propose a robust GQL (RGQL) approach in order to obtain the consistent estimates for the parameters in the GLMMs in the presence of one or more outliers. An extensive simulation study is conducted to examine the consistency performance of the proposed RGQL approach.     

Influence diagnostics in nonlinear reproductive dispersion mixed models

The class of nonlinear reproductive dispersion mixed models (NRDMMs) is an extension of nonlinear reproductive dispersion models and generalized linear mixed models. This paper discusses the influence analysis of the model based on Laplace approximation. The equivalence of case-deletion models and mean-shift outlier models in NRDMMs is investigated, and some diagnostic measures are proposed via the case-deletion method. We also investigate the assessment of local influence of various perturbation schemes. The proposed method is illustrated with an example.     

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     

A note on model selection using information criteria for general linear models estimated using REML

It is common practice to compare the fit of non‐nested models using the Akaike (AIC) or Bayesian (BIC) information criteria. The basis of these criteria is the log‐likelihood evaluated at the maximum likelihood estimates of the unknown parameters. For the general linear model (and the linear mixed model, which is a special case), estimation is usually carried out using residual or restricted maximum likelihood (REML). However, for models with different fixed effects, the residual likelihoods are not comparable and hence information criteria based on the residual likelihood cannot be used. For model selection, it is often suggested that the models are refitted using maximum likelihood to enable the criteria to be used. The first aim of this paper is to highlight that both the AIC and BIC can be used for the general linear model by using the full log‐likelihood evaluated at the REML estimates. The second aim is to provide a derivation of the criteria under REML estimation. This aim is achieved by noting that the full likelihood can be decomposed into a marginal (residual) and conditional likelihood and this decomposition then incorporates aspects of both the fixed effects and variance parameters. Using this decomposition, the appropriate information criteria for model selection of models which differ in their fixed effects specification can be derived. An example is presented to illustrate the results and code is available for analyses using the ASReml‐R package.     

Choice of link and variance function for generalized linear mixed models: a case study with binomial response in proteomics

Abstract

Non-normality is a common phenomenon in data from agricultural and biological research, especially in molecular data (for example; -omics, RNAseq, flow cytometric data, etc.). For over half a century, the leading paradigm called for using analysis of variance (ANOVA) after applying a data transformation. The introduction of generalized linear mixed models (GLMM) provides a new way of analyzing non-normal data. Selecting an apt link function in GLMM can be quite influential, however, and is as critical as selecting an appropriate transformation for ANOVA. In this paper, we assess the performance of different parametric link families available in literature. Then, we propose a new estimation method for selecting an appropriate link function with a suitable variance function in a quasi-likelihood framework. We apply these methods to a proteomics data set, showing that GLMMs provide a very flexible framework for analyzing these kinds of data.     

A consistent simulation-based estimator in generalized linear mixed models

We propose a strongly root-n consistent simulation-based estimator for the generalized linear mixed models. This estimator is constructed based on the first two marginal moments of the response variables, and it allows the random effects to have any parametric distribution (not necessarily normal). Consistency and asymptotic normality for the proposed estimator are derived under fairly general regularity conditions. We also demonstrate that this estimator has a bounded influence function and that it is robust against data outliers. A bias correction technique is proposed to reduce the finite sample bias in the estimation of variance components. The methodology is illustrated through an application to the famed seizure count data and some simulation studies.     

Confidence regions for parameters in linear models with additional information

Using given significant additional information it is possible to improve different confidence regions for the regression parameters in a linear model. Thereby, the given informations may concern the expectation and (or) the variance of the observations, and an improvement is possible in the sense of the decrease of the confidence regions' size. In particular it is possible to improve the so called confidence ellipsoids which are often used to estimate the considered parameters.     

A comparison of mixed and minimax estimators of linear models

In this paper the stochastic properties of two estimators of linear models, mixed and minimax, based on different types of prior information, are compared using quadratic risk as the criterion for superiority. A necessary and sufficient condition for the minimax estimator to be superior to the comparable mixed estimator is derived as well as a simpler necessary but not sufficient condition.     

Bootstrap tests for variance components in generalized linear mixed models

In many applications of generalized linear mixed models to clustered correlated or longitudinal data, often we are interested in testing whether a random effects variance component is zero. The usual asymptotic mixture of chi‐square distributions of the score statistic for testing constrained variance components does not necessarily hold. In this article, the author proposes and explores a parametric bootstrap test that appears to be valid based on its estimated level of significance under the null hypothesis. Results from a simulation study indicate that the bootstrap test has a level much closer to the nominal one while the asymptotic test is conservative, and is more powerful than the usual asymptotic score test based on a mixture of chi‐squares. The proposed bootstrap test is illustrated using two sets of real‐life data obtained from clinical trials. The Canadian Journal of Statistics © 2009 Statistical Society of Canada     

The Bayesian D-optimal design for simple beta regression model in two cases (both known and unknown nuisance parameter)

According to investigated topic in the context of optimal designs, various methods can be used to obtain optimal design, of which Bayesian method is one. In this paper, considering the model and the features of the information matrix, this method (Bayesian optimality criterion) has been used for obtaining optimal designs which due to the variation range of the model parameters, prior distributions such as Uniform, Normal and Exponential have been used and the results analysed.     

Estimation of regression parameters in generalized linear models for cluster correlated data with measurement error

Liang and Zeger (1986) introduced a class of estimating equations that gives consistent estimates of regression parameters and of their asymptotic variances in the class of generalized linear models for cluster correlated data. When the independent variables or covariates in such models are subject to measurement errors, the parameter estimates obtained from these estimating equations are no longer consistent. To correct for the effect of measurement errors, an estimator with smaller asymptotic bias is constructed along the lines of Stefanski (1985), assuming that the measurement error variance is either known or estimable. The asymptotic distribution of the bias-corrected estimator and a consistent estimator of its asymptotic variance are also given. The special case of a binary logistic regression model is studied in detail. For this case, methods based on conditional scores and quasilikelihood are also extended to cluster correlated data. Results of a small simulation study on the performance of the proposed estimators and associated tests of hypotheses are reported.