Pseudo Bayesian Estimation of One-way ANOVA Model in Complex Surveys

We devise survey-weighted pseudo posterior distribution estimators under 2-stage informative sampling of both primary clusters and secondary nested units for a one-way ANOVA population generating model as a simple canonical case where population model random effects are defined to be coincident with the primary clusters. We consider estimation on an observed informative sample under both an augmented pseudo likelihood that co-samples random effects, as well as an integrated likelihood that marginalizes out the random effects from the survey-weighted augmented pseudo likelihood. This paper includes a theoretical exposition that enumerates easily verified conditions for which estimation under the augmented pseudo posterior is guaranteed to be consistent at the true generating parameters. We reveal in simulation that both approaches produce asymptotically unbiased estimation of the generating hyperparameters for the random effects when a key condition on the sum of within cluster weighted residuals is met. We present a comparison with frequentist EM and a methods that requires pairwise sampling weights.Comment: 46 pages, 9 figure

Modelling the distribution of health related quality of life of advancedmelanoma patients in a longitudinal multi-centre clinical trial using M-quantile random effects regression

Health-related quality of life assessment is important in the clinical evaluation of patients with metastatic disease that may offer useful information in understanding the clinical effectiveness of a treatment. To assess if a set of explicative variables impacts on the health-related quality of life, regression models are routinely adopted. However, the interest of researchers may be focussed on modelling other parts (e.g. quantiles) of this conditional distribution. In this paper, we present an approach based on quantile and M-quantile regression to achieve this goal. We applied the methodologies to a prospective, randomized, multi-centre clinical trial. In order to take into account the hierarchical nature of the data we extended the M-quantile regression model to a three-level random effects specification and estimated it by maximum likelihood

Binary and Ordinal Random Effects Models Including Variable Selection

A likelihood-based boosting approach for fitting binary and ordinal mixed models is presented. In contrast to common procedures it can be used in high-dimensional settings where a large number of potentially influential explanatory variables is available. Constructed as a componentwise boosting method it is able to perform variable selection with the complexity of the resulting estimator being determined by information criteria. The method is investigated in simulation studies both for cumulative and sequential models and is illustrated by using real data sets

Estimation in Dirichlet random effects models

We develop a new Gibbs sampler for a linear mixed model with a Dirichlet process random effect term, which is easily extended to a generalized linear mixed model with a probit link function. Our Gibbs sampler exploits the properties of the multinomial and Dirichlet distributions, and is shown to be an improvement, in terms of operator norm and efficiency, over other commonly used MCMC algorithms. We also investigate methods for the estimation of the precision parameter of the Dirichlet process, finding that maximum likelihood may not be desirable, but a posterior mode is a reasonable approach. Examples are given to show how these models perform on real data. Our results complement both the theoretical basis of the Dirichlet process nonparametric prior and the computational work that has been done to date.Comment: Published in at http://dx.doi.org/10.1214/09-AOS731 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Nonparametric inference procedure for percentiles of the random effects distribution in meta-analysis

To investigate whether treating cancer patients with erythropoiesis-stimulating agents (ESAs) would increase the mortality risk, Bennett et al. [Journal of the American Medical Association 299 (2008) 914--924] conducted a meta-analysis with the data from 52 phase III trials comparing ESAs with placebo or standard of care. With a standard parametric random effects modeling approach, the study concluded that ESA administration was significantly associated with increased average mortality risk. In this article we present a simple nonparametric inference procedure for the distribution of the random effects. We re-analyzed the ESA mortality data with the new method. Our results about the center of the random effects distribution were markedly different from those reported by Bennett et al. Moreover, our procedure, which estimates the distribution of the random effects, as opposed to just a simple population average, suggests that the ESA may be beneficial to mortality for approximately a quarter of the study populations. This new meta-analysis technique can be implemented with study-level summary statistics. In contrast to existing methods for parametric random effects models, the validity of our proposal does not require the number of studies involved to be large. From the results of an extensive numerical study, we find that the new procedure performs well even with moderate individual study sample sizes.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS280 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

TMB: Automatic Differentiation and Laplace Approximation

TMB is an open source R package that enables quick implementation of complex nonlinear random effect (latent variable) models in a manner similar to the established AD Model Builder package (ADMB, admb-project.org). In addition, it offers easy access to parallel computations. The user defines the joint likelihood for the data and the random effects as a C++ template function, while all the other operations are done in R; e.g., reading in the data. The package evaluates and maximizes the Laplace approximation of the marginal likelihood where the random effects are automatically integrated out. This approximation, and its derivatives, are obtained using automatic differentiation (up to order three) of the joint likelihood. The computations are designed to be fast for problems with many random effects (~10^6) and parameters (~10^3). Computation times using ADMB and TMB are compared on a suite of examples ranging from simple models to large spatial models where the random effects are a Gaussian random field. Speedups ranging from 1.5 to about 100 are obtained with increasing gains for large problems. The package and examples are available at http://tmb-project.org