Restricted likelihood ratio lack-of-fit tests using mixed spline models

Summary.  Penalized regression spline models afford a simple mixed model representation in which variance components control the degree of non-linearity in the smooth function estimates. This motivates the study of lack-of-fit tests based on the restricted maximum likelihood ratio statistic which tests whether variance components are 0 against the alternative of taking on positive values. For this one-sided testing problem a further complication is that the variance component belongs to the boundary of the parameter space under the null hypothesis. Conditions are obtained on the design of the regression spline models under which asymptotic distribution theory applies, and finite sample approximations to the asymptotic distribution are provided. Test statistics are studied for simple as well as multiple-regression models.     

Profile likelihood-based confidence interval for the dispersion parameter in count data

The importance of the dispersion parameter in counts occurring in toxicology, biology, clinical medicine, epidemiology, and other similar studies is well known. A couple of procedures for the construction of confidence intervals (CIs) of the dispersion parameter have been investigated, but little attention has been paid to the accuracy of its CIs. In this paper, we introduce the profile likelihood (PL) approach and the hybrid profile variance (HPV) approach for constructing the CIs of the dispersion parameter for counts based on the negative binomial model. The non-parametric bootstrap (NPB) approach based on the maximum likelihood (ML) estimates of the dispersion parameter is also considered. We then compare our proposed approaches with an asymptotic approach based on the ML and the restricted ML (REML) estimates of the dispersion parameter as well as the parametric bootstrap (PB) approach based on the ML estimates of the dispersion parameter. As assessed by Monte Carlo simulations, the PL approach has the best small-sample performance, followed by the REML, HPV, NPB, and PB approaches. Three examples to biological count data are presented.     

ASYMPTOTIC PROPERTIES OF RESTRICTED MAXIMUM LIKELIHOOD (REML) ESTIMATES FOR HIERARCHICAL MIXED LINEAR MODELS

This paper explores the asymptotic distribution of the restricted maximum likelihood estimator of the variance components in a general mixed model. Restricting attention to hierarchical models, central limit theorems are obtained using elementary arguments with only mild conditions on the covariates in the fixed part of the model and without having to assume that the data are either normally or spherically symmetrically distributed. Further, the REML and maximum likelihood estimators are shown to be asymptotically equivalent in this general framework, and the asymptotic distribution of the weighted least squares estimator (based on the REML estimator) of the fixed effect parameters is derived.     

Maximum Likelihood Estimation for the 4-Parameter Beta Distribution

This paper addresses the problem of obtaining maximum likelihood estimates for the parameters of the Pearson Type I distribution (beta distribution with unknown end points and shape parameters). Since they do not seem to have appeared in the literature, the likelihood equations and the information matrix are derived. The regularity conditions which ensure asymptotic normality and efficiency are examined, and some apparent conflicts in the literature are noted. To ensure regularity, the shape parameters must be greater than two, giving an (assymmetrical) bell-shaped distribution with high contact in the tails. A numerical investigation was carried out to explore the bias and variance of the maximum likelihood estimates and their dependence on sample size. The numerical study indicated that only for large samples (n ≥ 1000) does the bias in the estimates become small and does the Cramér-Rao bound give a good approximation for their variance. The likelihood function has a global maximum which corresponds to parameter estimates that are inadmissable. Useful parameter estimates can be obtained at a local maximum, which is sometimes difficult to locate when the sample size is small.     

ASYMPTOTIC LIKELIHOOD APPROXIMATIONS USING A PARTIAL LAPLACE APPROXIMATION

Elimination of a nuisance variable is often non‐trivial and may involve the evaluation of an intractable integral. One approach to evaluate these integrals is to use the Laplace approximation. This paper concentrates on a new approximation, called the partial Laplace approximation, that is useful when the integrand can be partitioned into two multiplicative disjoint functions. The technique is applied to the linear mixed model and shows that the approximate likelihood obtained can be partitioned to provide a conditional likelihood for the location parameters and a marginal likelihood for the scale parameters equivalent to restricted maximum likelihood (REML). Similarly, the partial Laplace approximation is applied to the t‐distribution to obtain an approximate REML for the scale parameter. A simulation study reveals that, in comparison to maximum likelihood, the scale parameter estimates of the t‐distribution obtained from the approximate REML show reduced bias.     

Empirical Likelihood Local Polynomial Regression Analysis of Clustered Data

Abstract. In this article, a naive empirical likelihood ratio is constructed for a non‐parametric regression model with clustered data, by combining the empirical likelihood method and local polynomial fitting. The maximum empirical likelihood estimates for the regression functions and their derivatives are obtained. The asymptotic distributions for the proposed ratio and estimators are established. A bias‐corrected empirical likelihood approach to inference for the parameters of interest is developed, and the residual‐adjusted empirical log‐likelihood ratio is shown to be asymptotically chi‐squared. These results can be used to construct a class of approximate pointwise confidence intervals and simultaneous bands for the regression functions and their derivatives. Owing to our bias correction for the empirical likelihood ratio, the accuracy of the obtained confidence region is not only improved, but also a data‐driven algorithm can be used for selecting an optimal bandwidth to estimate the regression functions and their derivatives. A simulation study is conducted to compare the empirical likelihood method with the normal approximation‐based method in terms of coverage accuracies and average widths of the confidence intervals/bands. An application of this method is illustrated using a real data set.     

Testing variance components in balanced linear growth curve models

It is well known that the testing of zero variance components is a non-standard problem since the null hypothesis is on the boundary of the parameter space. The usual asymptotic chi-square distribution of the likelihood ratio and score statistics under the null does not necessarily hold because of this null hypothesis. To circumvent this difficulty in balanced linear growth curve models, we introduce an appropriate test statistic and suggest a permutation procedure to approximate its finite-sample distribution. The proposed test alleviates the necessity of any distributional assumptions for the random effects and errors and can easily be applied for testing multiple variance components. Our simulation studies show that the proposed test has Type I error rate close to the nominal level. The power of the proposed test is also compared with the likelihood ratio test in the simulations. An application on data from an orthodontic study is presented and discussed.     

Confidence intervals based on the deviance statistic for the hyperparameters in state space models

The main objective of this work is to evaluate the performance of confidence intervals, built using the deviance statistic, for the hyperparameters of state space models. The first procedure is a marginal approximation to confidence regions, based on the likelihood test, and the second one is based on the signed root deviance profile. Those methods are computationally efficient and are not affected by problems such as intervals with limits outside the parameter space, which can be the case when the focus is on the variances of the errors. The procedures are compared to the usual approaches existing in the literature, which includes the method based on the asymptotic distribution of the maximum likelihood estimator, as well as bootstrap confidence intervals. The comparison is performed via a Monte Carlo study, in order to establish empirically the advantages and disadvantages of each method. The results show that the methods based on the deviance statistic possess a better coverage rate than the asymptotic and bootstrap procedures.     

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.     

Empirical likelihood for the varying‐coefficient single‐index model

In this article the author investigates the application of the empirical‐likelihood‐based inference for the parameters of varying‐coefficient single‐index model (VCSIM). Unlike the usual cases, if there is no bias correction the asymptotic distribution of the empirical likelihood ratio cannot achieve the standard chi‐squared distribution. To this end, a bias‐corrected empirical likelihood method is employed to construct the confidence regions (intervals) of regression parameters, which have two advantages, compared with those based on normal approximation, that is, (1) they do not impose prior constraints on the shape of the regions; (2) they do not require the construction of a pivotal quantity and the regions are range preserving and transformation respecting. A simulation study is undertaken to compare the empirical likelihood with the normal approximation in terms of coverage accuracies and average areas/lengths of confidence regions/intervals. A real data example is given to illustrate the proposed approach. The Canadian Journal of Statistics 38: 434–452; 2010 © 2010 Statistical Society of Canada     

Inference from PseudoLikelihoods with Plug‐In Estimates

Effective implementation of likelihood inference in models for high‐dimensional data often requires a simplified treatment of nuisance parameters, with these having to be replaced by handy estimates. In addition, the likelihood function may have been simplified by means of a partial specification of the model, as is the case when composite likelihood is used. In such circumstances tests and confidence regions for the parameter of interest may be constructed using Wald type and score type statistics, defined so as to account for nuisance parameter estimation or partial specification of the likelihood. In this paper a general analytical expression for the required asymptotic covariance matrices is derived, and suggestions for obtaining Monte Carlo approximations are presented. The same matrices are involved in a rescaling adjustment of the log likelihood ratio type statistic that we propose. This adjustment restores the usual chi‐squared asymptotic distribution, which is generally invalid after the simplifications considered. The practical implication is that, for a wide variety of likelihoods and nuisance parameter estimates, confidence regions for the parameters of interest are readily computable from the rescaled log likelihood ratio type statistic as well as from the Wald type and score type statistics. Two examples, a measurement error model with full likelihood and a spatial correlation model with pairwise likelihood, illustrate and compare the procedures. Wald type and score type statistics may give rise to confidence regions with unsatisfactory shape in small and moderate samples. In addition to having satisfactory shape, regions based on the rescaled log likelihood ratio type statistic show empirical coverage in reasonable agreement with nominal confidence levels.     

Testing for two states in a hidden Markov model

The authors consider hidden Markov models (HMMs) whose latent process has m ≥ 2 states and whose state‐dependent distributions arise from a general one‐parameter family. They propose a test of the hypothesis m = 2. Their procedure is an extension to HMMs of the modified likelihood ratio statistic proposed by Chen, Chen & Kalbfleisch (2004) for testing two states in a finite mixture. The authors determine the asymptotic distribution of their test under the hypothesis m = 2 and investigate its finite‐sample properties in a simulation study. Their test is based on inference for the marginal mixture distribution of the HMM. In order to illustrate the additional difficulties due to the dependence structure of the HMM, they show how to test general regular hypotheses on the marginal mixture of HMMs via a quasi‐modified likelihood ratio. They also discuss two applications.     

Confidence intervals for variance components in unbalanced one-way random effects model using non-normal distributions

In scenarios where the variance of a response variable can be attributed to two sources of variation, a confidence interval for a ratio of variance components gives information about the relative importance of the two sources. For example, if measurements taken from different laboratories are nine times more variable than the measurements taken from within the laboratories, then 90% of the variance in the responses is due to the variability amongst the laboratories and 10% of the variance in the responses is due to the variability within the laboratories. Assuming normally distributed sources of variation, confidence intervals for variance components are readily available. In this paper, however, simulation studies are conducted to evaluate the performance of confidence intervals under non-normal distribution assumptions. Confidence intervals based on the pivotal quantity method, fiducial inference, and the large-sample properties of the restricted maximum likelihood (REML) estimator are considered. Simulation results and an empirical example suggest that the REML-based confidence interval is favored over the other two procedures in unbalanced one-way random effects model.     

Tests and Confidence Intervals for an Extended Variance Component Using the Modified Likelihood Ratio Statistic

Abstract.  The large deviation modified likelihood ratio statistic is studied for testing a variance component equal to a specified value. Formulas are presented in the general balanced case, whereas in the unbalanced case only the one-way random effects model is studied. Simulation studies are presented, showing that the normal approximation to the large deviation modified likelihood ratio statistic gives confidence intervals for variance components with coverage probabilities very close to the nominal confidence coefficient.     

Testing homogeneity in a mixture of von mises distributions with a structural parameter

The modified likelihood ratio statistic can be used to test the homogeneity in a variety of mixture models. Here, the authors propose the use of the modified and the iterative modified likelihood ratio for testing homogeneity against a two‐component von Mises mixture with a structural parameter. They derive the limiting distributions of the test statistics and propose methods to improve the accuracy of the asymptotic approximation in finite samples. Their simulations show that the tests maintain their nominal level and that they have adequate power. Data on movements of turtles are used as an illustration     

Box‐Cox transformations in linear models: Large sample theory and tests of normality

The authors provide a rigorous large sample theory for linear models whose response variable has been subjected to the Box‐Cox transformation. They provide a continuous asymptotic approximation to the distribution of estimators of natural parameters of the model. They show, in particular, that the maximum likelihood estimator of the ratio of slope to residual standard deviation is consistent and relatively stable. The authors further show the importance for inference of normality of the errors and give tests for normality based on the estimated residuals. For non‐normal errors, they give adjustments to the log‐likelihood and to asymptotic standard errors.     

Interval estimation for log-linear models with one variable subject to non-ignorable non-response

Summary.  Log-linear models for multiway contingency tables where one variable is subject to non-ignorable non-response will often yield boundary solutions, with the probability of non-respondents being classified in some cells of the table estimated as 0. The paper considers the effect of this non-standard behaviour on two methods of interval estimation based on the distribution of the maximum likelihood estimator. The first method relies on the estimator being approximately normally distributed with variance equal to the inverse of the information matrix. It is shown that the information matrix is singular for boundary solutions, but intervals can be calculated after a simple transformation. For the second method, based on the bootstrap, asymptotic results suggest that the coverage properties may be poor for boundary solutions. Both methods are compared with profile likelihood intervals in a simulation study based on data from the British General Election Panel Study. The results of this study indicate that all three methods perform poorly for a parameter of the non-response model, whereas they all perform well for a parameter of the margin model, irrespective of whether or not there is a boundary solution.     

Asymptotic theory of the likelihood ratio test for the identification of a mixture

The problems that arise when using the likelihood ratio test for the identification of a mixture distribution are well known: non-identifiability of the parameters and null hypothesis corresponding to a boundary point of the parameter space. In their approach to the problem of testing homogeneity against a mixture with two components, Ghosh and Sen took into account these specific problems. Under general assumptions, they obtained the asymptotic distribution of the likelihood ratio test statistic. However, their result requires a separation condition which is not completely satisfactory. We show that it is possible to remove this condition with assumptions which involve the second derivatives of the density only.     

An improved test of equality of mean directions for the Langevin‐von Mises‐Fisher distribution

A multi‐sample test for equality of mean directions is developed for populations having Langevin‐von Mises‐Fisher distributions with a common unknown concentration. The proposed test statistic is a monotone transformation of the likelihood ratio. The high‐concentration asymptotic null distribution of the test statistic is derived. In contrast to previously suggested high‐concentration tests, the high‐concentration asymptotic approximation to the null distribution of the proposed test statistic is also valid for large sample sizes with any fixed nonzero concentration parameter. Simulations of size and power show that the proposed test outperforms competing tests. An example with three‐dimensional data from an anthropological study illustrates the practical application of the testing procedure.