Modified profile likelihood estimation for the Weibull regression models in survival analysis

In this study, adjustment of profile likelihood function of parameter of interest in presence of many nuisance parameters is investigated for survival regression models. Our objective is to extend the Barndorff–Nielsen’s technique to Weibull regression models for estimation of shape parameter in presence of many nuisance and regression parameters. We conducted Monte-Carlo simulation studies and a real data analysis, all of which demonstrate and suggest that the modified profile likelihood estimators outperform the profile likelihood estimators in terms of three comparison criterion: mean squared errors, bias and standard errors.     

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.     

Hierarchical likelihood approach for the Weibull frailty model

In this article, the proportional hazard model with Weibull frailty, which is outside the range of the exponential family, is used for analysing the right-censored longitudinal survival data. Complex multidimensional integrals are avoided by using hierarchical likelihood to estimate the regression parameters and to predict the realizations of random effects. The adjusted profile hierarchical likelihood is adopted to estimate the parameters in frailty distribution, during which the first- and second-order methods are used. The simulation studies indicate that the regression-parameter estimates in the Weibull frailty model are accurate, which is similar to the gamma frailty and lognormal frailty models. Two published data sets are used for illustration.     

Statistical Inference in Partially Linear Varying-Coefficient Models with Missing Responses at Random

This article considers statistical inference for partially linear varying-coefficient models when the responses are missing at random. We propose a profile least-squares estimator for the parametric component with complete-case data and show that the resulting estimator is asymptotically normal. To avoid to estimate the asymptotic covariance in establishing confidence region of the parametric component with the normal-approximation method, we define an empirical likelihood based statistic and show that its limiting distribution is chi-squared distribution. Then, the confidence regions of the parametric component with asymptotically correct coverage probabilities can be constructed by the result. To check the validity of the linear constraints on the parametric component, we construct a modified generalized likelihood ratio test statistic and demonstrate that it follows asymptotically chi-squared distribution under the null hypothesis. Then, we extend the generalized likelihood ratio technique to the context of missing data. Finally, some simulations are conducted to illustrate the proposed methods.     

Modified quasi-profile likelihoods from estimating functions

We discuss higher-order adjustments for a quasi-profile likelihood for a scalar parameter of interest, in order to alleviate some of the problems inherent to the presence of nuisance parameters, such as bias and inconsistency. Indeed, quasi-profile score functions for the parameter of interest have bias of order O(1)$\mathrm{O}(1)$, and such bias can lead to poor inference on the parameter of interest. The higher-order adjustments are obtained so that the adjusted quasi-profile score estimating function is unbiased and its variance is the negative expected derivative matrix of the adjusted profile estimating equation. The modified quasi-profile likelihood is then obtained as the integral of the adjusted profile estimating function. We discuss two methods for the computation of the modified quasi-profile likelihoods: a bootstrap simulation method and a first-order asymptotic expression, which can be simplified under an orthogonality assumption. Examples in the context of generalized linear models and of robust inference are provided, showing that the use of a modified quasi-profile likelihood ratio statistic may lead to coverage probabilities more accurate than those pertaining to first-order Wald-type confidence intervals.     

Statistical Inference and Applications of Mixture of Varying Coefficient Models

In this paper, we consider a new mixture of varying coefficient models, in which each mixture component follows a varying coefficient model and the mixing proportions and dispersion parameters are also allowed to be unknown smooth functions. We systematically study the identifiability, estimation and inference for the new mixture model. The proposed new mixture model is rather general, encompassing many mixture models as its special cases such as mixtures of linear regression models, mixtures of generalized linear models, mixtures of partially linear models and mixtures of generalized additive models, some of which are new mixture models by themselves and have not been investigated before. The new mixture of varying coefficient model is shown to be identifiable under mild conditions. We develop a local likelihood procedure and a modified expectation–maximization algorithm for the estimation of the unknown non‐parametric functions. Asymptotic normality is established for the proposed estimator. A generalized likelihood ratio test is further developed for testing whether some of the unknown functions are constants. We derive the asymptotic distribution of the proposed generalized likelihood ratio test statistics and prove that the Wilks phenomenon holds. The proposed methodology is illustrated by Monte Carlo simulations and an analysis of a CO₂‐GDP data set.     

Maximum likelihood estimators for ARMA and ARFIMA models: a Monte Carlo study

We analyze by simulation the properties of two time domain and two frequency domain estimators for low-order autoregressive fractionally integrated moving-average Gaussian models, ARFIMA (p,d,q). The estimators considered are the exact maximum likelihood for demeaned data (EML) the associated modified profile likelihood (MPL) and the Whittle estimator with (WLT) and without tapered data (WL). Length of the series is 100. The estimators are compared in terms of pile-up effect, mean square error, bias, and empirical confidence level. The tapered version of the Whittle likelihood turns out to be a reliable estimator for ARMA and ARFIMA models. Its small losses in performance in case of ‘well-behaved’ models are compensated sufficiently in more ‘difficult’ models. The modified profile likelihood is an alternative to the WLT but is computationally more demanding. It is either equivalent to the EML or more favorable than the EML. For fractionally integrated models, particularly, it dominates clearly the EML. The WL has serious deficiencies for large ranges of parameters, and so cannot be recommended in general. The EML, on the other hand, should only be used with care for fractionally integrated models due to its potential large negative bias of the fractional integration parameter. In general, one should proceed with caution for ARMA(1,1) models with almost canceling roots, and, in particular, in case of the EML and the MPL for inference in the vicinity of a moving-average root of +1.     

Robust Inference in Conditionally Linear Nonlinear Regression Models

Abstract.  We consider robust methods of likelihood and frequentist inference for the nonlinear parameter, say α , in conditionally linear nonlinear regression models. We derive closed-form expressions for robust conditional, marginal, profile and modified profile likelihood functions for α under elliptically contoured data distributions. Next, we develop robust exact-F confidence intervals for α and consider robust Fieller intervals for ratios of regression parameters in linear models. Several well-known examples are considered and Monte Carlo simulation results are presented.     

Modified Profile Likelihood for Fixed-Effects Panel Data Models

We show how modified profile likelihood methods, developed in the statistical literature, may be effectively applied to estimate the structural parameters of econometric models for panel data, with a remarkable reduction of bias with respect to ordinary likelihood methods. Initially, the implementation of these methods is illustrated for general models for panel data including individual-specific fixed effects and then, in more detail, for the truncated linear regression model and dynamic regression models for binary data formulated along with different specifications. Simulation studies show the good behavior of the inference based on the modified profile likelihood, even when compared to an ideal, although infeasible, procedure (in which the fixed effects are known) and also to alternative estimators existing in the econometric literature. The proposed estimation methods are implemented in an R package that we make available to the reader.     

Generalised quasi‐likelihood inference in a semi‐parametric binary dynamic mixed logit model

There exists a recent study where dynamic mixed‐effects regression models for count data have been extended to a semi‐parametric context. However, when one deals with other discrete data such as binary responses, the results based on count data models are not directly applicable. In this paper, we therefore begin with existing binary dynamic mixed models and generalise them to the semi‐parametric context. For inference, we use a new semi‐parametric conditional quasi‐likelihood (SCQL) approach for the estimation of the non‐parametric function involved in the semi‐parametric model, and a semi‐parametric generalised quasi‐likelihood (SGQL) approach for the estimation of the main regression, dynamic dependence and random effects variance parameters. A semi‐parametric maximum likelihood (SML) approach is also used as a comparison to the SGQL approach. The properties of the estimators are examined both asymptotically and empirically. More specifically, the consistency of the estimators is established and finite sample performances of the estimators are examined through an intensive simulation study.     

Profile likelihood in directed graphical models from BUGS output

We present a method for using posterior samples produced by the computer program BUGS (Bayesian inference Using Gibbs Sampling) to obtain approximate profile likelihood functions of parameters or functions of parameters in directed graphical models with incomplete data. The method can also be used to approximate integrated likelihood functions. It is easily implemented and it performs a good approximation. The profile likelihood represents an aspect of the parameter uncertainty which does not depend on the specification of prior distributions, and it can be used as a worthwhile supplement to BUGS that enable us to do both Bayesian and likelihood based analyses in directed graphical models.     

Bias Reduction of Likelihood Estimators in Semiparametric Frailty Models

Abstract. Frailty models with a non‐parametric baseline hazard are widely used for the analysis of survival data. However, their maximum likelihood estimators can be substantially biased in finite samples, because the number of nuisance parameters associated with the baseline hazard increases with the sample size. The penalized partial likelihood based on a first‐order Laplace approximation still has non‐negligible bias. However, the second‐order Laplace approximation to a modified marginal likelihood for a bias reduction is infeasible because of the presence of too many complicated terms. In this article, we find adequate modifications of these likelihood‐based methods by using the hierarchical likelihood.     

Closed‐form likelihoods for stochastic differential equation growth models

The authors derive closed‐form expressions for the full, profile, conditional and modified profile likelihood functions for a class of random growth parameter models they develop as well as Garcia's additive model. These expressions facilitate the determination of parameter estimates for both types of models. The profile, conditional and modified profile likelihood functions are maximized over few parameters to yield a complete set of parameter estimates. In the development of their random growth parameter models the authors specify the drift and diffusion coefficients of the growth parameter process in a natural way which gives interpretive meaning to these coefficients while yielding highly tractable models. They fit several of their random growth parameter models and Garcia's additive model to stock market data, and discuss the results. The Canadian Journal of Statistics 38: 474–487; 2010 © 2010 Statistical Society of Canada     

Conditional inference in linear versus nonlinear models for binary time series

The modelling of discrete such as binary time series, unlike the continuous time series, is not easy. This is due to the fact that there is no unique way to model the correlation structure of the repeated binary data. Some models may also provide a complicated correlation structure with narrow ranges for the correlations. In this paper, we consider a nonlinear dynamic binary time series model that provides a correlation structure which is easy to interpret and the correlations under this model satisfy the full?1 to 1 range. For the estimation of the parameters of this nonlinear model, we use a conditional generalized quasilikelihood (CGQL) approach which provides the same estimates as those of the well-known maximum likelihood approach. Furthermore, we consider a competitive linear dynamic binary time series model and examine the performance of the CGQL approach through a simulation study in estimating the parameters of this linear model. The model mis-specification effects on estimation as well as forecasting are also examined through simulations.     

Profile likelihood approaches for semiparametric copula and frailty models for clustered survival data

ABSTRACT

In clustered survival data, the dependence among individual survival times within a cluster has usually been described using copula models and frailty models. In this paper we propose a profile likelihood approach for semiparametric copula models with different cluster sizes. We also propose a likelihood ratio method based on profile likelihood for testing the absence of association parameter (i.e. test of independence) under the copula models, leading to the boundary problem of the parameter space. For this purpose, we show via simulation study that the proposed likelihood ratio method using an asymptotic chi-square mixture distribution performs well as sample size increases. We compare the behaviors of the two models using the profile likelihood approach under a semiparametric setting. The proposed method is demonstrated using two well-known data sets.     

Restricted maximum likelihood estimation of joint mean‐covariance models

The class of joint mean‐covariance models uses the modified Cholesky decomposition of the within subject covariance matrix in order to arrive to an unconstrained, statistically meaningful reparameterisation. The new parameterisation of the covariance matrix has two sets of parameters that separately describe the variances and correlations. Thus, with the mean or regression parameters, these models have three sets of distinct parameters. In order to alleviate the problem of inefficient estimation and downward bias in the variance estimates, inherent in the maximum likelihood estimation procedure, the usual REML estimation procedure adjusts for the degrees of freedom lost due to the estimation of the mean parameters. Because of the parameterisation of the joint mean covariance models, it is possible to adapt the usual REML procedure in order to estimate the variance (correlation) parameters by taking into account the degrees of freedom lost by the estimation of both the mean and correlation (variance) parameters. To this end, here we propose adjustments to the estimation procedures based on the modified and adjusted profile likelihoods. The methods are illustrated by an application to a real data set and simulation studies. The Canadian Journal of Statistics 40: 225–242; 2012 © 2012 Statistical Society of Canada     

Modified likelihood ratio statistics for inflated beta regressions

The class of inflated beta regression models generalizes that of beta regressions [S.L.P. Ferrari and F. Cribari-Neto, Beta regression for modelling rates and proportions, J. Appl. Stat. 31 (2004), pp. 799–815] by incorporating a discrete component that allows practitioners to model data on rates and proportions with observations that equal an interval limit. For instance, one can model responses that assume values in (0, 1]. The likelihood ratio test tends to be quite oversized (liberal, anticonservative) in inflated beta regressions estimated with a small number of observations. Indeed, our numerical results show that its null rejection rate can be almost twice the nominal level. It is thus important to develop alternative testing strategies. This paper develops small-sample adjustments to the likelihood ratio and signed likelihood ratio test statistics in inflated beta regression models. The adjustments do not require orthogonality between the parameters of interest and the nuisance parameters and are fairly simple since they only require first- and second-order log-likelihood cumulants. Simulation results show that the modified likelihood ratio tests deliver much accurate inference in small samples. An empirical application is presented and discussed.     

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.     

Bias Corrected Maximum Likelihood Estimator Under the Generalized Linear Model for a Binary Variable

Under the generalized linear models for a binary variable, an approximate bias of the maximum likelihood estimator of the coefficient, that is a special case of linear parameter in Cordeiro and McCullagh (1991), is derived without a calculation of the third-order derivative of the log likelihood function. Using the obtained approximate bias of the maximum likelihood estimator, a bias-corrected maximum likelihood estimator is defined. Through a simulation study, we show that the bias-corrected maximum likelihood estimator and its variance estimator have a better performance than the maximum likelihood estimator and its variance estimator.     

Corrected likelihood-ratio tests in logistic regression using small-sample data

Likelihood-ratio tests (LRTs) are often used for inferences on one or more logistic regression coefficients. Conventionally, for given parameters of interest, the nuisance parameters of the likelihood function are replaced by their maximum likelihood estimates. The new function created is called the profile likelihood function, and is used for inference from LRT. In small samples, LRT based on the profile likelihood does not follow χ² distribution. Several corrections have been proposed to improve LRT when used with small-sample data. Additionally, complete or quasi-complete separation is a common geometric feature for small-sample binary data. In this article, for small-sample binary data, we have derived explicitly the correction factors of LRT for models with and without separation, and proposed an algorithm to construct confidence intervals. We have investigated the performances of different LRT corrections, and the corresponding confidence intervals through simulations. Based on the simulation results, we propose an empirical rule of thumb on the use of these methods. Our simulation findings are also supported by real-world data.