The posterior distribution of the fixed and random effects in a mixed-effects linear model

The subject of this paper is Bayesian inference about the fixed and random effects of a mixed-effects linear statistical model with two variance components. It is assumed that a priori the fixed effects have a noninformative distribution and that the reciprocals of the variance components are distributed independently (of each other and of the fixed effects) as gamma random variables. It is shown that techniques similar to those employed in a ridge analysis of a response surface can be used to construct a one-dimensional curve that contains all of the stationary points of the posterior density of the random effects. The “ridge analysis” (of the posterior density) can be useful (from a computational standpoint) in finding the number and the locations of the stationary points and can be very informative about various features of the posterior density. Depending on what is revealed by the ridge analysis, a multivariate normal or multivariate-t distribution that is centered at a posterior mode may provide a satisfactory approximation to the posterior distribution of the random effects (which is of the poly-t form).     

a bayesian analysis of the multivariate mixed-linear model

The Bayesian analysis of the multivariate mixed linear model is considered. The exact posterior distribution for the fixed effects matrix and the error covariance matrix are obtained. The exact posterior means and variances of the Bayesian estimators for the covariance matrices of random effects are also derived. These posterior moments are computed without constrained optimization and numerical integration. The calculations are feasible for arbitrary models. Reasonable approximations for the posterior distributions for the covariance matrices associated with the random effects are obtained also. Results are illustrated with a numerical example.     

Conditional and unconditional tests with historical controls

Score statistics utilizing historical control data have been proposed to test for increasing trend in tumour occurrence rates in laboratory carcinogenicity studies. Novel invariance arguments are used to confirm, under slightly weaker conditions, previously established asymptotic distributions (mixtures of normal distributions) of tests unconditional on the tumor response rate in the concurrent control group. Conditioning on the control response rate, an ancillary statistic, leads to a new conditional limit theorem in which the test statistic converges to an unknown random variable. Because of this, a subasymptotic approximation to the conditional limiting distribution is also considered. The adequacy of these large-sample approximations in finite samples is evaluated using computer simulation. Bootstrap methods for use in finite samples are also proposed. The application of the conditional and unconditional tests is illustrated using bioassay data taken from the literature. The results presented in this paper are used to formulate recommendations for the use of tests for trend with historical controls in practice.     

A bayesian analysis of the mixed linear model

The mixed model is defined. The exact posterior distribution for the fixed effect vector is obtained. The exact posterior distribution for the error variance is obtained. The exact posterior mean and variance of a Bayesian estimator for the variances of random effects is also derived. All computations are non-iterative and avoid numerical integrations.     

Generalized Laplacian approximations in Bayesian inference

This paper presents a new Laplacian approximation to the posterior density of η = g(θ). It has a simpler analytical form than that described by Leonard et al. (1989). The approximation derived by Leonard et al. requires a conditional information matrix R_η to be positive definite for every fixed η. However, in many cases, not all R_η are positive definite. In such cases, the computations of their approximations fail, since the approximation cannot be normalized. However, the new approximation may be modified so that the corresponding conditional information matrix can be made positive definite for every fixed η. In addition, a Bayesian procedure for contingency-table model checking is provided. An example of cross-classification between the educational level of a wife and fertility-planning status of couples is used for explanation. Various Laplacian approximations are computed and compared in this example and in an example of public school expenditures in the context of Bayesian analysis of the multiparameter Fisher-Behrens problem.     

Approximating the distribution of a renewal process using generalized poisson distributions

The exact distribution of a renewal counting process is not easy to compute and is rarely of closed form. In this article, we approximate the distribution of a renewal process using families of generalized Poisson distributions. We first compute approximations to the first several moments of the renewal process. In some cases, a closed form approximation is obtained. It is found that each family considered has its own strengths and weaknesses. Some new families of generalized Poisson distributions are recommended. Theorems are obtained determining when these variance to mean ratios are less than (or exceed) one without having to find the mean and variance. Some numerical comparisons are also made.     

Modified Normal-based Approximation to the Percentiles of Linear Combination of Independent Random Variables with Applications

A modified normal-based approximation for calculating the percentiles of a linear combination of independent random variables is proposed. This approximation is applicable in situations where expectations and percentiles of the individual random variables can be readily obtained. The merits of the approximation are evaluated for the chi-square and beta distributions using Monte Carlo simulation. An approximation to the percentiles of the ratio of two independent random variables is also given. Solutions based on the approximations are given for some classical problems such as interval estimation of the normal coefficient of variation, survival probability, the difference between or the ratio of two binomial proportions, and for some other problems. Furthermore, approximation to the percentiles of a doubly noncentral F distribution is also given. For all the problems considered, the approximation provides simple satisfactory solutions. Two examples are given to show applications of the approximation.     

Saddlepoint approximations to tail expectations under non-Gaussian base distributions: option pricing applications

The saddlepoint approximation formulas provide versatile tools for analytic approximation of the tail expectation of a random variable by approximating the complex Laplace integral of the tail expectation expressed in terms of the cumulant generating function of the random variable. We generalize the saddlepoint approximation formulas for calculating tail expectations from the usual Gaussian base distribution to an arbitrary base distribution. Specific discussion is presented on the criteria of choosing the base distribution that fits better the underlying distribution. Numerical performance and comparison of accuracy are made among different saddlepoint approximation formulas. Improved accuracy of the saddlepoint approximations to tail expectations is revealed when proper base distributions are chosen. We also demonstrate enhanced accuracy of the generalized saddlepoint approximation formulas under non-Gaussian base distributions in pricing European options on continuous integrated variance under the Heston stochastic volatility model.     

Confidence intervals following Box-Cox transformation

What is the interpretation of a confidence interval following estimation of a Box-Cox transformation parameter λ? Several authors have argued that confidence intervals for linear model parameters ψ can be constructed as if λ. were known in advance, rather than estimated, provided the estimand is interpreted conditionally given $\hat \lambda$. If the estimand is defined as $\psi \left( {\hat \lambda } \right)$, a function of the estimated transformation, can the nominal confidence level be regarded as a conditional coverage probability given $\hat \lambda$, where the interval is random and the estimand is fixed? Or should it be regarded as an unconditional probability, where both the interval and the estimand are random? This article investigates these questions via large-n approximations, small- σ approximations, and simulations. It is shown that, when model assumptions are satisfied and n is large, the nominal confidence level closely approximates the conditional coverage probability. When n is small, this conditional approximation is still good for regression models with small error variance. The conditional approximation can be poor for regression models with moderate error variance and single-factor ANOVA models with small to moderate error variance. In these situations the nominal confidence level still provides a good approximation for the unconditional coverage probability. This suggests that, while the estimand may be interpreted conditionally, the confidence level should sometimes be interpreted unconditionally.     

Estimating the parameters of mixed linear models with modal estimators

This paper presents a procedure to estimate the variance components and fixed effects of mixed linear models. The mode of the joint posterior distribution of all the parameters is obtained by an iterative technique.

The proposed method is illustrated with one-way and two-fold nested random models. Two numerical examples demonstrate the iterative solution.     

Bayesian estimates in a one-way ANOVA random effects model

Bayesian estimators of variance components are developed, based on posterior mean and posterior mode, respectively, in a one-way ANOVA random effects model with independent prior distributions. The formulas for the proposed estimators are simple. The estimators give sensible results for 'badly-behaved' datasets, where the standard unbiased estimates are negative. They are markedly robust as compared to the existing estimators such as the maximum likelihood estimators and the maximum posterior density estimators.     

Analysis of Linear Models with One Factor Having Both Fixed and Random Levels

ABSTRACT

A general theory for a case where a factor has both fixed and random effect levels is developed under one-way treatment structure model. Estimation procedures for the fixed effects and variance components are consider for the model. The testing of fixed effects is considered when the variance–covariance matrix is known and unknown. Confidence intervals for estimable functions and prediction intervals for predictable functions are constructed. The computational procedures are illustrated using data from an on-farm trial.     

Markov chain Monte Carlo with the Integrated Nested Laplace Approximation

The Integrated Nested Laplace Approximation (INLA) has established itself as a widely used method for approximate inference on Bayesian hierarchical models which can be represented as a latent Gaussian model (LGM). INLA is based on producing an accurate approximation to the posterior marginal distributions of the parameters in the model and some other quantities of interest by using repeated approximations to intermediate distributions and integrals that appear in the computation of the posterior marginals. INLA focuses on models whose latent effects are a Gaussian Markov random field. For this reason, we have explored alternative ways of expanding the number of possible models that can be fitted using the INLA methodology. In this paper, we present a novel approach that combines INLA and Markov chain Monte Carlo (MCMC). The aim is to consider a wider range of models that can be fitted with INLA only when some of the parameters of the model have been fixed. We show how new values of these parameters can be drawn from their posterior by using conditional models fitted with INLA and standard MCMC algorithms, such as Metropolis–Hastings. Hence, this will extend the use of INLA to fit models that can be expressed as a conditional LGM. Also, this new approach can be used to build simpler MCMC samplers for complex models as it allows sampling only on a limited number of parameters in the model. We will demonstrate how our approach can extend the class of models that could benefit from INLA, and how the R-INLA package will ease its implementation. We will go through simple examples of this new approach before we discuss more advanced applications with datasets taken from the relevant literature. In particular, INLA within MCMC will be used to fit models with Laplace priors in a Bayesian Lasso model, imputation of missing covariates in linear models, fitting spatial econometrics models with complex nonlinear terms in the linear predictor and classification of data with mixture models. Furthermore, in some of the examples we could exploit INLA within MCMC to make joint inference on an ensemble of model parameters.     

A Comparative Study of Approaches for Predicting Prostate Cancer from Longitudinal Data

Disease prediction based on longitudinal data can be done using various modeling approaches. Alternative approaches are compared using data from a longitudinal study to predict the onset of disease. The data are modeled using linear mixed-effects models. Posterior probabilities of group membership are computed starting with the first observation and sequentially adding observations until the subject is classified as developing the disease or until the last measurement is used. Individuals are classified by computing posterior probabilities using the marginal distributions of the mixed-effects models, the conditional distributions (conditional on the group-specific random effects), and the distributions of the random effects.     

Approximate Small-Sample Tests of Fixed Effects in Nonlinear Mixed Models

Nonlinear mixed effect models have been studied extensively over several decades, particularly in pharmacokinetic and pharmacodynamic applications. Here, we focus on investigating the performance of commonly applied tests of linear hypotheses about the fixed effect parameters under different approximations to the likelihood function and to the estimated covariance matrix of the estimators. Included are the first-order approximation (FIRO), first-order conditional approximation (FOCE), and Gaussian quadrature approximation (AGQ) estimation methods. There is no straightforward way to mimic the approximations and adjustments taken in linear mixed models, such as the Kackar–Harville–Jeske–Kenward–Roger approach. By simulations, we illustrate the accuracy of p-values for the tests considered here. The observed results indicate that FOCE and AGQ estimation methods outperform FIRO. The test with an adjustment coefficient that takes into consideration the number of sampling units and the number of fixed effect parameters (Gallant-type) seems to perform closest to desirable even for small-sample sizes.     

Approximate estimation in nonlinear panel data models

This paper is concerned with the estimation of a general class of nonlinear panel data models in which the conditional distribution of the dependent variable and the distribution of the heterogeneity factors are arbitrary. In general, exact analytical results for this problem do not exist. Here, Laplace and small-sigma appriximations for the marginal likelihood are presented. The computation of the MLE from both approximations is straightforward. It is shown that the accuracy of the Laplace approximation depends on both the sample size and the variance of the individual effects, whereas the accuracy of the small-sigma approximation is 0(1) with respect to the sample size. The results are applied to count, duration and probit panel data models. The accuracy of the approximations is evaluated through a Monte Carlo simulation experiment. The approximations are also applied in an analysis of youth unemployment in Australia.     

A generalization of the logistic linear'model

Consider the logistic linear model, with some explanatory variables overlooked. Those explanatory variables may be quantitative or qualitative. In either case, the resulting true response variable is not a binomial or a beta-binomial but a sum of binomials. Hence, standard computer packages for logistic regression can be inappropriate even if an overdispersion factor is incorporated. Therefore, a discrete exponential family assumption is considered to broaden the class of sampling models. Likelihood and Bayesian analyses are discussed. Bayesian computation techniques such as Laplacian approximations and Markov chain simulations are used to compute posterior densities and moments. Approximate conditional distributions are derived and are shown to be accurate. The Markov chain simulations are performed effectively to calculate posterior moments by using the approximate conditional distributions. The methodology is applied to Keeler's hardness of winter wheat data for checking binomial assumptions and to Matsumura's Accounting exams data for detailed likelihood and Bayesian analyses.     

Using a correlated probit model approximation to estimate the variance for binary matched pairs

A correlated probit model approximation for conditional probabilities (Mendell and Elston 1974) is used to estimate the variance for binary matched pairs data by maximum likelihood. Using asymptotic data, the bias of the estimates is shown to be small for a wide range of intra-class correlations and incidences. This approximation is also compared with other recently published, or implemented, improved approximations. For the small sample examples presented, it shows a substantial advantage over other approximations. The method is extended to allow covariates for each observation, and fitting by iteratively reweighted least squares.     

The distribution of a linear predictor after model selection: conditional finite-sample distributions and asymptotic approximations

This paper studies the distribution of a linear predictor that is constructed after a data-driven model selection step in a linear regression model. The finite-sample cumulative distribution function (cdf) of the linear predictor is derived and a detailed analysis of the effects of the model selection step is given. Moreover, a simple approximation to the (complicated) finite-sample cdf is proposed. This approximation facilitates the study of the large-sample limit behavior of the linear predictor and its cdf, in the fixed-parameter case and under local alternatives. The focus of this paper is on the conditional distribution of a linear predictor, conditional on the event that a fixed (possibly incorrect) model has been selected. The unconditional distribution of a linear predictor is studied in the companion paper Leeb (The distribution of a linear predictor after model selection: unconditional finite-sample distributions and asymptotic approximations, Technical Report, Department of Statistics, University of Vienna, 2002).     

On linear statistical models of commutative quadratic type

By defining a special class of vector decompositions we consider linear statistical models of commutative quadratic type, which especially cover balanced complete and incomplete ANOVA models with fixed, random and mixed effects. Under the assumption of normal distribution we are concerned with distributions of general quadratic forms, with point and confidence region estimation as well as with hypothesis testing for fixed effects (including multiple comparisons) and variance components.