Fitting via alternative random-effect models

When there are two alternative random-effect models leading to the same marginal model, inferences from one model can be used for the other model. We illustrate how a likelihood method for fitting models with independent random effects can be applied to seemingly very different models with correlated random effects. We also discuss some merits of using these alternative models.     

Marginal zero-inflated regression models for count data

Data sets with excess zeroes are frequently analyzed in many disciplines. A common framework used to analyze such data is the zero-inflated (ZI) regression model. It mixes a degenerate distribution with point mass at zero with a non-degenerate distribution. The estimates from ZI models quantify the effects of covariates on the means of latent random variables, which are often not the quantities of primary interest. Recently, marginal zero-inflated Poisson (MZIP; Long et al. [A marginalized zero-inflated Poisson regression model with overall exposure effects. Stat. Med. 33 (2014), pp. 5151–5165]) and negative binomial (MZINB; Preisser et al., 2016) models have been introduced that model the mean response directly. These models yield covariate effects that have simple interpretations that are, for many applications, more appealing than those available from ZI regression. This paper outlines a general framework for marginal zero-inflated models where the latent distribution is a member of the exponential dispersion family, focusing on common distributions for count data. In particular, our discussion includes the marginal zero-inflated binomial (MZIB) model, which has not been discussed previously. The details of maximum likelihood estimation via the EM algorithm are presented and the properties of the estimators as well as Wald and likelihood ratio-based inference are examined via simulation. Two examples presented illustrate the advantages of MZIP, MZINB, and MZIB models for practical data analysis.     

A doubly restricted exponential dispersion model

In this paper, we propose and develop a doubly restricted exponential dispersion model, i.e. a varying dispersion generalized linear model with two sets of restrictions, a set of linear restrictions for the mean response, and at the same time, for another set of linear restrictions for the dispersion of the distribution. This model would be useful to consider several situations where it is necessary to control/analyze drug-doses, active effects in factorial experiments, mean-variance relationships, among other situations. A penalized likelihood function is proposed and developed in order to achieve the restricted parameters and to develop the inferential results. Several special cases from the literature are commented on. A simply restricted varying dispersion beta regression model is exemplified by means of real and simulated data. Satisfactory and promising results are found.     

Nonnull asymptotic distributions of the LR,Wald, score and gradient statistics in generalized linear models with dispersion covariates

The class of generalized linear models with dispersion covariates, which allows us to jointly model the mean and dispersion parameters, is a natural extension to the classical generalized linear models. In this paper, we derive the asymptotic expansions under a sequence of Pitman alternatives (up to order n ^?1/2) for the nonnull distribution functions of the likelihood ratio, Wald, Rao score and gradient statistics in this class of models. The asymptotic distributions of these statistics are obtained for testing a subset of regression parameters and for testing a subset of dispersion parameters. Based on these nonnull asymptotic expansions, the power of all four tests, which are equivalent to first order, are compared. Furthermore, we consider Monte Carlo simulations in order to compare the finite-sample performance of these tests in this class of models. We present two empirical applications to two real data sets for illustrative purposes.     

Generalized linear models for the analysis of quality-improvement experiments

Generalized linear models provide a useful tool for analyzing data from quality-improvement experiments. We discuss why analysis must be done for all the data, not just for summarizing quantities, and show by examples how residuals can be used for model checking. A restricted-maximum-likelihood-type adjustment for the dispersion analysis is developed.     

Residual-based specification of the random-effects distribution for cluster data

We propose a method for specifying the distribution of random effects included in a model for cluster data. The class of models we consider includes mixed models and frailty models whose random effects and explanatory variables are constant within clusters. The method is based on cluster residuals obtained by assuming that the random effects are equal between clusters. We exhibit an asymptotic relationship between the cluster residuals and variations of the random effects as the number of observations increases and the variance of the random effects decreases. The asymptotic relationship is used to specify the random-effects distribution. The method is applied to a frailty model and a model used to describe the spread of plant diseases.     

LEVERAGE ADJUSTMENTS FOR DISPERSION MODELLING IN GENERALIZED NONLINEAR MODELS

For normal linear models, it is generally accepted that residual maximum likelihood estimation is appropriate when covariance components require estimation. This paper considers generalized linear models in which both the mean and the dispersion are allowed to depend on unknown parameters and on covariates. For these models there is no closed form equivalent to residual maximum likelihood except in very special cases. Using a modified profile likelihood for the dispersion parameters, an adjusted score vector and adjusted information matrix are found under an asymptotic development that holds as the leverages in the mean model become small. Subsequently, the expectation of the fitted deviances is obtained directly to show that the adjusted score vector is unbiased at least to O(1/n) . Exact results are obtained in the single‐sample case. The results reduce to residual maximum likelihood estimation in the normal linear case.     

Robust variance estimators for fixed-effect estimates with hierarchical-likelihood

In longitudinal studies, robust sandwich variance estimators are often used, and are especially useful when model assumptions are in doubt. However, the usual sandwich estimator does not allow for models with crossed random effects. The hierarchical likelihood extends the idea of the sandwich estimator to models not currently covered. By simulation studies, we show that the new sandwich estimator is robust against heteroscedastic errors and against misspecification of overdispersion in the y | v component.     

Linear Transformations of Linear Mixed-Effects Models

A number of articles have discussed the way lower order polynomial and interaction terms should be handled in linear regression models. Only if all lower order terms are included in the model will the regression model be invariant with respect to coding transformations of the variables. If lower order terms are omitted, the regression model will not be well formulated. In this paper, we extend this work to examine the implications of the ordering of variables in the linear mixed-effects model. We demonstrate how linear transformations of the variables affect the model and tests of significance of fixed effects in the model. We show how the transformations modify the random effects in the model, as well as their covariance matrix and the value of the restricted log-likelihood. We suggest a variable selection strategy for the linear mixed-effects model.     

A dynamic model for double‐bounded time series with chaotic‐driven conditional averages

In this work, we introduce a class of dynamic models for time series taking values on the unit interval. The proposed model follows a generalized linear model approach where the random component, conditioned on the past information, follows a beta distribution, while the conditional mean specification may include covariates and also an extra additive term given by the iteration of a map that can present chaotic behavior. The resulting model is very flexible and its systematic component can accommodate short‐ and long‐range dependence, periodic behavior, laminar phases, etc. We derive easily verifiable conditions for the stationarity of the proposed model, as well as conditions for the law of large numbers and a Birkhoff‐type theorem to hold. A Monte Carlo simulation study is performed to assess the finite sample behavior of the partial maximum likelihood approach for parameter estimation in the proposed model. Finally, an application to the proportion of stored hydroelectrical energy in Southern Brazil is presented.     

Identification of the variance components in the general two-variance linear model

Bayesian analyses frequently employ two-stage hierarchical models involving two-variance parameters: one controlling measurement error and the other controlling the degree of smoothing implied by the model's higher level. These analyses can be hampered by poorly identified variances which may lead to difficulty in computing and in choosing reference priors for these parameters. In this paper, we introduce the class of two-variance hierarchical linear models and characterize the aspects of these models that lead to well-identified or poorly identified variances. These ideas are illustrated with a spatial analysis of a periodontal data set and examined in some generality for specific two-variance models including the conditionally autoregressive (CAR) and one-way random effect models. We also connect this theory with other constrained regression methods and suggest a diagnostic that can be used to search for missing spatially varying fixed effects in the CAR model.     

Mixture of linear mixed models using multivariate t distribution

Linear mixed models are widely used when multiple correlated measurements are made on each unit of interest. In many applications, the units may form several distinct clusters, and such heterogeneity can be more appropriately modelled by a finite mixture linear mixed model. The classical estimation approach, in which both the random effects and the error parts are assumed to follow normal distribution, is sensitive to outliers, and failure to accommodate outliers may greatly jeopardize the model estimation and inference. We propose a new mixture linear mixed model using multivariate t distribution. For each mixture component, we assume the response and the random effects jointly follow a multivariate t distribution, to conveniently robustify the estimation procedure. An efficient expectation conditional maximization algorithm is developed for conducting maximum likelihood estimation. The degrees of freedom parameters of the t distributions are chosen data adaptively, for achieving flexible trade-off between estimation robustness and efficiency. Simulation studies and an application on analysing lung growth longitudinal data showcase the efficacy of the proposed approach.     

Estimating the variance for heterogeneity in arm‐based network meta‐analysis

Network meta‐analysis can be implemented by using arm‐based or contrast‐based models. Here we focus on arm‐based models and fit them using generalized linear mixed model procedures. Full maximum likelihood (ML) estimation leads to biased trial‐by‐treatment interaction variance estimates for heterogeneity. Thus, our objective is to investigate alternative approaches to variance estimation that reduce bias compared with full ML. Specifically, we use penalized quasi‐likelihood/pseudo‐likelihood and hierarchical (h) likelihood approaches. In addition, we consider a novel model modification that yields estimators akin to the residual maximum likelihood estimator for linear mixed models. The proposed methods are compared by simulation, and 2 real datasets are used for illustration. Simulations show that penalized quasi‐likelihood/pseudo‐likelihood and h‐likelihood reduce bias and yield satisfactory coverage rates. Sum‐to‐zero restriction and baseline contrasts for random trial‐by‐treatment interaction effects, as well as a residual ML‐like adjustment, also reduce bias compared with an unconstrained model when ML is used, but coverage rates are not quite as good. Penalized quasi‐likelihood/pseudo‐likelihood and h‐likelihood are therefore recommended.     

Prediction in linear mixed models

Following estimation of effects from a linear mixed model, it is often useful to form predicted values for certain factor/variate combinations. The process has been well defined for linear models, but the introduction of random effects into the model means that a decision has to be made about the inclusion or exclusion of random model terms from the predictions. This paper discusses the interpretation of predictions formed including or excluding random terms. Four datasets are used to illustrate circumstances where different prediction strategies may be appropriate: in an orthogonal design, an unbalanced nested structure, a model with cubic smoothing spline terms and for kriging after spatial analysis. The examples also show the need for different weighting schemes that recognize nesting and aliasing during prediction, and the necessity of being able to detect inestimable predictions.     

Multilevel Mixed Linear Models for Survival Data

For the analysis of correlated survival data mixed linear models are useful alternatives to frailty models. By their use the survival times can be directly modelled, so that the interpretation of the fixed and random effects is straightforward. However, because of intractable integration involved with the use of marginal likelihood the class of models in use has been severely restricted. Such a difficulty can be avoided by using hierarchical-likelihood, which provides a statistically efficient and fast fitting algorithm for multilevel models. The proposed method is illustrated using the chronic granulomatous disease data. A simulation study is carried out to evaluate the performance.     

Generalized additive models for location, scale and shape

Summary.  A general class of statistical models for a univariate response variable is presented which we call the generalized additive model for location, scale and shape (GAMLSS). The model assumes independent observations of the response variable y given the parameters, the explanatory variables and the values of the random effects. The distribution for the response variable in the GAMLSS can be selected from a very general family of distributions including highly skew or kurtotic continuous and discrete distributions. The systematic part of the model is expanded to allow modelling not only of the mean (or location) but also of the other parameters of the distribution of y , as parametric and/or additive nonparametric (smooth) functions of explanatory variables and/or random-effects terms. Maximum (penalized) likelihood estimation is used to fit the (non)parametric models. A Newton–Raphson or Fisher scoring algorithm is used to maximize the (penalized) likelihood. The additive terms in the model are fitted by using a backfitting algorithm. Censored data are easily incorporated into the framework. Five data sets from different fields of application are analysed to emphasize the generality of the GAMLSS class of models.     

Count data and treatment heterogeneity in 2×2 crossover trials

Count data are routinely assumed to have a Poisson distribution, especially when there are no straightforward diagnostic procedures for checking this assumption. We reanalyse two data sets from crossover trials of treatments for angina pectoris , in which the outcomes are counts of anginal attacks. Standard analyses focus on treatment effects, averaged over subjects; we are also interested in the dispersion of these effects (treatment heterogeneity). We set up a log-Poisson model with random coefficients to estimate the distribution of the treatment effects and show that the analysis is very sensitive to the distributional assumption; the population variance of the treatment effects is confounded with the (variance) function that relates the conditional variance of the outcomes, given the subject's rate of attacks, to the conditional mean. Diagnostic model checks based on resampling from the fitted distribution indicate that the default choice of the Poisson distribution for the analysed data sets is poorly supported. We propose to augment the data sets with observations of the counts, made possibly outside the clinical setting, so that the conditional distribution of the counts could be established.     

The Use of Working Variables in the Bayesian Modeling of Mean and Dispersion Parameters in Generalized Nonlinear Models with Random Effects

This article is aimed at reviewing a novel Bayesian approach to handle inference and estimation in the class of generalized nonlinear models. These models include some of the main techniques of statistical methodology, namely generalized linear models and parametric nonlinear regression. In addition, this proposal extends to methods for the systematic treatment of variation that is not explicitly predicted within the model, through the inclusion of random effects, and takes into account the modeling of dispersion parameters in the class of two-parameter exponential family. The methodology is based on the implementation of a two-stage algorithm that induces a hybrid approach based on numerical methods for approximating the likelihood to a normal density using a Taylor linearization around the values of current parameters in an MCMC routine.     

SIMULATED MAXIMUM LIKELIHOOD APPLIED TO NON-GAUSSIAN AND NONLINEAR MIXED EFFECTS AND STATE–SPACE MODELS

The paper presents an overview of maximum likelihood estimation using simulated likelihood, including the use of antithetic variables and evaluation of the simulation error of the resulting estimates. It gives a general purpose implementation of simulated maximum likelihood and uses it to re‐visit four models that have previously appeared in the published literature: a state–space model for count data; a nested random effects model for binomial data; a nonlinear growth model with crossed random effects; and a crossed random effects model for binary salamander‐mating data. In the case of the last three examples, this appears to be the first time that maximum likelihood fits of these models have been presented.     

Generalized linear models with random effects in the two-parameter exponential family

In this paper, we develop a new class of double generalized linear models, introducing a random-effect component in the link function describing the linear predictor related to the precision parameter. This is a useful procedure to take into account extra variability and also to make the model more robust. The Bayesian paradigm is adopted to make inference in this class of models. Samples of the joint posterior distribution are drawn using standard Monte Carlo Markov Chain procedures. Finally, we illustrate this algorithm by considering simulated and real data sets.