Harmonic mean approach to uunbalanced random effects models under heteroscedasticity

In this paper we consider unbalanced random effects models under heteroscedastic variances. By using' the harmonic mean approach, it is shown that the problems are analogous to those from balanced random effects models under horaoscedastic variances. Thus, by using the harmonic mean approach, statistical inferences about variance components are derived by using procedures from balanced models under homoscedastic variances. Laguerre polynomial expansion is used to approximate the sampling distributions of relevant statistics.     

Nonproper variance balanced designs and optimality

This communication deals with the construction and optimality of non-proper (unequal block sized) variance balanced (VB) designs obtainable under linear homoscedastic normal model. Several methods of construction of non-proper VB designs have been given. Some constructed designs are universally optimal non-proper variance balanced designs.     

A note on fiducial generalized pivots for in one-way heteroscedastic ANOVA with random effects

The paper deals with generalized confidence intervals for the between-group variance in one-way heteroscedastic (unbalanced) ANOVA with random effects. The approach used mimics the standard one applied in mixed linear models with two variance components, where interval estimators are based on a minimal sufficient statistic derived after an initial reduction by the principle of invariance. A minimal sufficient statistic under heteroscedasticity is found to resemble its homoscedastic counterpart and further analogies between heteroscedastic and homoscedastic cases lead us to two classes of fiducial generalized pivots for the between-group variance. The procedures suggested formerly by Wimmer and Witkovský [Between group variance component interval estimation for the unbalanced heteroscedastic one-way random effects model, J. Stat. Comput. Simul. 73 (2003), pp. 333–346] and Li [Comparison of confidence intervals on between group variance in unbalanced heteroscedastic one-way random models, Comm. Statist. Simulation Comput. 36 (2007), pp. 381–390] are found to belong to these two classes. We comment briefly on some of their properties that were not mentioned in the original papers. In addition, properties of another particular generalized pivot are considered.     

Short confidence intervals for variance components

Four approximate methods are proposed to construct confidence intervals for the estimation of variance components in unbalanced mixed models. The first three methods are modifications of the Wald, arithmetic and harmonic mean procedures, see Harville and Fenech (1985), while the fourth is an adaptive approach, combining the arithmetic and harmonic mean procedures. The performances of the proposed methods were assessed by a Monte Carlo simulation study. It was found that the intervals based on Wald's method maintained the nominal confidence levels across all designs and values of the parameters under study. On the other hand, the arithmetic (harmonic) mean method performed well for small (large) values of the variance component, relative to the error variance component. The adaptive procedure performed rather well except for extremely unbalanced designs. Further, compared with equal tails intervals, the intervals which use special tables, e.g., Table 678 of Tate and Klett (1959), provided adequate coverage while having much shorter lengths and are thus recommended for use in practice.     

Prediction in a class of mixed models with two variance components

A best unbiased predictor (BUP) of an arbitrary linear combination of fixed and random effects in mixed linear models is available when the true values of the variance ratios are known. When the true values are unknown, a two-stage predictor, obtained from the BUP by replacing the true values by estimated values, can be used. In this article, exact mean squared errors of two-stage predictors are obtained for a class of mixed models with two variance components that includes the balanced one-way random model and other analysis-of-variance models with proportional frequencies and one balanced random factor.     

Balanced and partially balanced incomplete block designs with autocorrelation errors

The paper aims to find variance balanced and variance partially balanced incomplete block designs when observations within blocks are autocorrelated and we call them BIBAC and PBIBAC designs. Orthogonal arrays of type I and type II when used as BIBAC designs have smaller average variance of elementary contrasts of treatment effects compared to the corresponding Balanced Incomplete Block (BIB) designs with homoscedastic, uncorrelated errors. The relative efficiency of BIB designs compared to BIBAC designs depends on the block size k and the autocorrelation ρ and is independent of the number of treatments. Further this relative efficiency increases with increasing k. Partially balanced incomplete block designs with autocorrelated errors are introduced using partially balanced incomplete block designs and orthogonal arrays of type I and type II.     

Modification of GEE1 and linear mixed-effects models for heteroscedastic longitudinal Gaussian data

A characterization of GLMs is given. Modification of the Gaussian GEE1, modified GEE1, was applied to heteroscedastic longitudinal data, to which linear mixed-effects models are usually applied. The modified GEE1 models scale multivariate data to homoscedastic data maintaining the correlation structure and apply usual GEE1 to homoscedastic data, which needs no-diagnostics for diagonal variances. Relationships among multivariate linear regression methods, ordinary/generalized LS, naïve/modified GEE1, and linear mixed-effects models were discussed. An application showed modified GEE1 gave most efficient parameter estimation. Correct specification of the main diagonals of heteroscedastic data variance appears to be more important for efficient mean parameter estimation.     

A new class of unbiased estimators of the variance of the systematic sample mean

We propose a class of estimators of the variance of the systematic sample mean, which is unbiased under the assumption that the population follows a superpopulation model that satisfies some mild conditions. The approach is based on the separate estimation of the portion of the variance due to the systematic component of the model and that due to the stochastic component. In particular, we deal with two estimators belonging to the proposed class that are based on moving averages and local polynomials to estimate the systematic component of the model. The latter estimators are unbiased under the assumption that the population follows a linear trend and the errors are homoscedastic and uncorrelated. Through a simulation study we show that these estimators generally outperform, in terms of bias and mean square error, the usual estimator based on the first differences also when the superpopulation model departs significantly from linearity and the errors are heteroscedastic.     

Predicting random effects with an expanded finite population mixed model

Prediction of random effects is an important problem with expanding applications. In the simplest context, the problem corresponds to prediction of the latent value (the mean) of a realized cluster selected via two-stage sampling. Recently, Stanek and Singer [Predicting random effects from finite population clustered samples with response error. J. Amer. Statist. Assoc. 99, 119–130] developed best linear unbiased predictors (BLUP) under a finite population mixed model that outperform BLUPs from mixed models and superpopulation models. Their setup, however, does not allow for unequally sized clusters. To overcome this drawback, we consider an expanded finite population mixed model based on a larger set of random variables that span a higher dimensional space than those typically applied to such problems. We show that BLUPs for linear combinations of the realized cluster means derived under such a model have considerably smaller mean squared error (MSE) than those obtained from mixed models, superpopulation models, and finite population mixed models. We motivate our general approach by an example developed for two-stage cluster sampling and show that it faithfully captures the stochastic aspects of sampling in the problem. We also consider simulation studies to illustrate the increased accuracy of the BLUP obtained under the expanded finite population mixed model.     

On unweighted sums of squares in unbalanced analysis of variance

The well-known method of unweighted sums of squares (USSs) is examined using, as an example, a random two-way classification model with interaction. In particular, a better motivation is given to the association between the harmonic mean of the cell frequencies and the USSs. Furthermore, a procedure is developed for determining the adequacy of the USSs as approximate balanced analysis of variance (ANOVA) sums of squares. This procedure is easy to apply and provides a better insight into the effects of design and model’s variance components on such an approximation. The proposed methodology can be extended to higher-order models and other types of sums of squares.     

Estimation of variance components in the mixed effects models: A comparison between analysis of variance and spectral decomposition

The mixed effects models with two variance components are often used to analyze longitudinal data. For these models, we compare two approaches to estimating the variance components, the analysis of variance approach and the spectral decomposition approach. We establish a necessary and sufficient condition for the two approaches to yield identical estimates, and some sufficient conditions for the superiority of one approach over the other, under the mean squared error criterion. Applications of the methods to circular models and longitudinal data are discussed. Furthermore, simulation results indicate that better estimates of variance components do not necessarily imply higher power of the tests or shorter confidence intervals.     

Some algebra and geometry for hierarchical models, applied to diagnostics

Recent advances in computing make it practical to use complex hierarchical models. However, the complexity makes it difficult to see how features of the data determine the fitted model. This paper describes an approach to diagnostics for hierarchical models, specifically linear hierarchical models with additive normal or t -errors. The key is to express hierarchical models in the form of ordinary linear models by adding artificial `cases' to the data set corresponding to the higher levels of the hierarchy. The error term of this linear model is not homoscedastic, but its covariance structure is much simpler than that usually used in variance component or random effects models. The re-expression has several advantages. First, it is extremely general, covering dynamic linear models, random effect and mixed effect models, and pairwise difference models, among others. Second, it makes more explicit the geometry of hierarchical models, by analogy with the geometry of linear models. Third, the analogy with linear models provides a rich source of ideas for diagnostics for all the parts of hierarchical models. This paper gives diagnostics to examine candidate added variables, transformations, collinearity, case influence and residuals.     

Variance components estimation for the balanced random effects model under mixed prior distributions

For the balanced random effects models, when the variance components are correlated either naturally or through common prior structures, by assuming a mixed prior distribution for the variance components, we propose some new Bayesian estimators. To contrast and compare the new estimators with the minimum variance unbiased (MVUE) and restricted maximum likelihood estimators (RMLE), some simulation studies are also carried out. It turns out that the proposed estimators have smaller mean squared errors than the MVUE and RMLE.     

Multiphase experiments with at least one later laboratory phase. II. Nonorthogonal designs

Principles and laws that apply to nonorthogonal multiphase experiments are developed and illustrated using examples that are nonorthogonal but structure‐balanced, not structure, but first‐order, balanced or unbalanced, thus exposing the differences between the different design types. The design of such experiments using standard designs, a catalogue of designs and computer searches is exemplified. Factor–allocation diagrams are employed to depict the allocations in the examples, and used in producing the anatomies of designs or, when possible, the related skeleton‐analysis‐of‐variance tables, to assess the properties of designs. The formulation of mixed models based on them is also described. Tools used for structure‐balanced experiments are also shown to be applicable to those experiments that are not.     

Analysis of overdispersed paired count data

This article is about the statistical analysis of overdispersed paired count data for comparing two treatments. The data consist of the number of events obtained in a stratum during the fixed observation period. Three types of model are discussed: the Poisson, a mixed, and a semiparametric model. Overdispersion is represented in the last two models but not in the Poisson model. Of particular interests are to examine whether there is any loss of efficiency in using the estimate of the treatment effect obtained under other two models if the mixed model is true, and also whether overdispersion leads to a larger variance of the estimate than that expected from the Poisson model. It is shown that all three models provide the same estimate of the treatment effect (i.e., there is no loss of efficiency) and that the variance of the estimate of the treatment effect obtained under the Poisson model is the same as that based on the mixed model. However, the semiparametric model provides the variance of the estimate larger than those obtained under the other two models.     

On Measuring Uncertainty of Benchmarked Predictors with Application to Disease Risk Estimate

Empirical Bayes (EB) estimates in general linear mixed models are useful for the small area estimation in the sense of increasing precision of estimation of small area means. However, one potential difficulty of EB is that the overall estimate for a larger geographical area based on a (weighted) sum of EB estimates is not necessarily identical to the corresponding direct estimate such as the overall sample mean. Another difficulty is that EB estimates yield over‐shrinking, which results in the sampling variance smaller than the posterior variance. One way to fix these problems is the benchmarking approach based on the constrained empirical Bayes (CEB) estimators, which satisfy the constraints that the aggregated mean and variance are identical to the requested values of mean and variance. In this paper, we treat the general mixed models, derive asymptotic approximations of the mean squared error (MSE) of CEB and provide second‐order unbiased estimators of MSE based on the parametric bootstrap method. These results are applied to natural exponential families with quadratic variance functions. As a specific example, the Poisson‐gamma model is dealt with, and it is illustrated that the CEB estimates and their MSE estimates work well through real mortality data.     

Improved estimation of variance components in balanced hierarchical mixed models

The problem of simultaneous estimation of variance components is considered for a balanced hierarchical mixed model under a sum of squared error loss. A new class of estimators is suggested which dominate the usual sensible estimators. These estimators shrink towards the geometric mean of the component mean squares that appear in the ANOVA table. Numerical results are tabled to exhibit the improvement in risk under a simple model.     

Simulation-based Bayesian inferences for two-variance components linear models

We present a Bayesian analysis of variance component models via simulation. In particular, we study the 2-component hierarchical design model under balanced and unbalanced experiments. Also, we consider 2-factor additive random effect models and mixed models in a cross-classified design. We assess the sensitivity of inference to the choice of prior by a sampling/resampling technique. Finally, attention is given to non-normal error distributions such as the heavy-tailed t distribution.     

Mixture model on the variance for the differential analysis of gene expression data

Summary.  In microarray experiments, accurate estimation of the gene variance is a key step in the identification of differentially expressed genes. Variance models go from the too stringent homoscedastic assumption to the overparameterized model assuming a specific variance for each gene. Between these two extremes there is some room for intermediate models. We propose a method that identifies clusters of genes with equal variance. We use a mixture model on the gene variance distribution. A test statistic for ranking and detecting differentially expressed genes is proposed. The method is illustrated with publicly available complementary deoxyribonucleic acid microarray experiments, an unpublished data set and further simulation studies.