Composite conditional likelihood for sparse clustered data

Summary.  Sparse clustered data arise in finely stratified genetic and epidemiologic studies and pose at least two challenges to inference. First, it is difficult to model and interpret the full joint probability of dependent discrete data, which limits the utility of full likelihood methods. Second, standard methods for clustered data, such as pairwise likelihood and the generalized estimating function approach, are unsuitable when the data are sparse owing to the presence of many nuisance parameters. We present a composite conditional likelihood for use with sparse clustered data that provides valid inferences about covariate effects on both the marginal response probabilities and the intracluster pairwise association. Our primary focus is on sparse clustered binary data, in which case the method proposed utilizes doubly discordant quadruplets drawn from each stratum to conduct inference about the intracluster pairwise odds ratios.     

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.     

Estimating the negative binomial dispersion parameter with highly stratified surveys

We investigate several estimators of the negative binomial (NB) dispersion parameter for highly stratified count data for which the statistical model has a separate mean parameter for each stratum. If the number of samples per stratum is small then the model is highly parameterized and the maximum likelihood estimator (MLE) of the NB dispersion parameter can be biased and inefficient. Some of the estimators we investigate include adjustments for the number of mean parameters to reduce bias. We extend other estimators that were developed for the iid case, to reduce bias when there are many mean parameters. We demonstrate using simulations that an adjusted double extended quasi-likelihood estimator we proposed gives much improved estimates compared to the MLE. Adjusted extended quasi-likelihood and adjusted maximum likelihood estimators also give much-improved results. We illustrate the various estimators with stratified random bottom trawl survey data for cod (Gadus morhua) off the south coast of Newfoundland, Canada.     

Simplex Mixed‐Effects Models for Longitudinal Proportional Data

Abstract. Continuous proportional outcomes are collected from many practical studies, where responses are confined within the unit interval (0,1). Utilizing Barndorff‐Nielsen and Jørgensen's simplex distribution, we propose a new type of generalized linear mixed‐effects model for longitudinal proportional data, where the expected value of proportion is directly modelled through a logit function of fixed and random effects. We establish statistical inference along the lines of Breslow and Clayton's penalized quasi‐likelihood (PQL) and restricted maximum likelihood (REML) in the proposed model. We derive the PQL/REML using the high‐order multivariate Laplace approximation, which gives satisfactory estimation of the model parameters. The proposed model and inference are illustrated by simulation studies and a data example. The simulation studies conclude that the fourth order approximate PQL/REML performs satisfactorily. The data example shows that Aitchison's technique of the normal linear mixed model for logit‐transformed proportional outcomes is not robust against outliers.     

Inference in flexible families of distributions with normal kernel

This paper addresses the inference problem for a flexible class of distributions with normal kernel known as skew-bimodal-normal family of distributions. We obtain posterior and predictive distributions assuming different prior specifications. We provide conditions for the existence of the maximum-likelihood estimators (MLE). An EM-type algorithm is built to compute them. As a by product, we obtain important results related to classical and Bayesian inferences for two special subclasses called bimodal-normal and skew-normal (SN) distribution families. We perform a Monte Carlo simulation study to analyse behaviour of the MLE and some Bayesian ones. Considering the frontier data previously studied in the literature, we use the skew-bimodal-normal (SBN) distribution for density estimation. For that data set, we conclude that the SBN model provides as good a fit as the one obtained using the location-scale SN model. Since the former is a more parsimonious model, such a result is shown to be more attractive.     

Corrections for Bias in Maximum Likelihood Parameter Estimates Due to Nuisance Parameters

Abstract

In his Fisher Lecture, Efron (Efron, B. R. A. (1998 Efron, B. R. A. 1998. Fisher in the 21st century (with discussion). Statistical Science, 13: 95–122. [Crossref], [Web of Science ®] , [Google Scholar]). Fisher in the 21st Century (with discussion). Statistical Science 13:95–122) pointed out that maximum likelihood estimates (MLE) can be badly biased in certain situations involving many nuisance parameters. He predicted that with modern computing equipment a computer-modified version of the MLE that was less biased could become the default estimator of choice in applied problems in the 21st century. This article discusses three modifications—Lindsay's conditional likelihood, integrated likelihood, and Bartlett's bias-corrected estimating function. Each is evaluated through a study of the bias and MSE of the estimates in a stratified Weibull model with a moderate number of nuisance parameters. In Lindsay's estimating equation, three different methods for estimation of the nuisance parameters are evaluated—the restricted maximum likelihood estimate (RMLE), a Bayes estimator, and a linear Bayes estimator. In our model, the conditional likelihood with RMLE of the nuisance parameters is equivalent to Bartlett's bias-corrected estimating function. In the simulation we show that Lindsay's conditional likelihood is in general preferred, irrespective of the estimator of the nuisance parameters. Although the integrated likelihood has smaller MSE when the precise nature of the prior distribution of the nuisance parameters is known, this approach may perform poorly in cases where the prior distribution of the nuisance parameters is not known, especially using a non-informative prior. In practice, Lindsay's method using the RMLE of the nuisance parameters is recommended.     

Upper probabilities based only on the likelihood function

In the problem of parametric statistical inference with a finite parameter space, we propose some simple rules for defining posterior upper and lower probabilities directly from the observed likelihood function, without using any prior information. The rules satisfy the likelihood principle and a basic consistency principle ('avoiding sure loss'), they produce vacuous inferences when the likelihood function is constant, and they have other symmetry, monotonicity and continuity properties. One of the rules also satisfies fundamental frequentist principles. The rules can be used to eliminate nuisance parameters, and to interpret the likelihood function and to use it in making decisions. To compare the rules, they are applied to the problem of sampling from a finite population. Our results indicate that there are objective statistical methods which can reconcile three general approaches to statistical inference: likelihood inference, coherent inference and frequentist inference.     

A new algorithm for maximum likelihood estimation in normal scale-mixture generalized autoregressive conditional heteroskedastic models

In this paper, we propose a new generalized autoregressive conditional heteroskedastic (GARCH) model using infinite normal scale-mixtures which can suitably avoid order selection problems in the application of finite normal scale-mixtures. We discuss its theoretical properties and develop a two-stage algorithm for the maximum likelihood estimator to estimate the mixing distribution non-parametric maximum likelihood estimator (NPMLE) as well as GARCH parameters (two-stage MLE). For the estimation of a mixing distribution, we employ a fast computational algorithm proposed by Wang [On fast computation of the non-parametric maximum likelihood estimate of a mixing distribution. J R Stat Soc Ser B. 2007;69:185–198] under the gradient characterization of the non-parametric mixture likelihood. The GARCH parameters are then estimated either using the expectation-mazimization algorithm or general optimization scheme. In addition, we propose a new forecasting algorithm of value-at-risk (VaR) using the two-stage MLE and the NPMLE. Through a simulation study and real data analysis, we compare the performance of the two-stage MLE with the existing ones including quasi-maximum likelihood estimator based on the standard normal density and the finite normal mixture quasi maximum estimated-likelihood estimator (cf. Lee S, Lee T. Inference for Box–Cox transformed threshold GARCH models with nuisance parameters. Scand J Stat. 2012;39:568–589) in terms of the relative efficiency and accuracy of VaR forecasting.     

Likelihood inference for small variance components

The authors explore likelihood‐based methods for making inferences about the components of variance in a general normal mixed linear model. In particular, they use local asymptotic approximations to construct confidence intervals for the components of variance when the components are close to the boundary of the parameter space. In the process, they explore the question of how to profile the restricted likelihood (REML). Also, they show that general REML estimates are less likely to fall on the boundary of the parameter space than maximum‐likelihood estimates and that the likelihood‐ratio test based on the local asymptotic approximation has higher power than the likelihood‐ratio test based on the usual chi‐squared approximation. They examine the finite‐sample properties of the proposed intervals by means of a simulation study.     

Frailty Models for Arbitrarily Censored and Truncated Data

In this paper, we propose a frailty model for statistical inference in the case where we are faced with arbitrarily censored and truncated data. Our results extend those of Alioum and Commenges (1996), who developed a method of fitting a proportional hazards model to data of this kind. We discuss the identifiability of the regression coefficients involved in the model which are the parameters of interest, as well as the identifiability of the baseline cumulative hazard function of the model which plays the role of the infinite dimensional nuisance parameter. We illustrate our method with the use of simulated data as well as with a set of real data on transfusion-related AIDS.     

Relative Risk Regression for Binary Outcomes: Methods and Recommendations

Relative risks are often considered preferable to odds ratios for quantifying the association between a predictor and a binary outcome. Relative risk regression is an alternative to logistic regression where the parameters are relative risks rather than odds ratios. It uses a log link binomial generalised linear model, or log‐binomial model, which requires parameter constraints to prevent probabilities from exceeding 1. This leads to numerical problems with standard approaches for finding the maximum likelihood estimate (MLE), such as Fisher scoring, and has motivated various non‐MLE approaches. In this paper we discuss the roles of the MLE and its main competitors for relative risk regression. It is argued that reliable alternatives to Fisher scoring mean that numerical issues are no longer a motivation for non‐MLE methods. Nonetheless, non‐MLE methods may be worthwhile for other reasons and we evaluate this possibility for alternatives within a class of quasi‐likelihood methods. The MLE obtained using a reliable computational method is recommended, but this approach requires bootstrapping when estimates are on the parameter space boundary. If convenience is paramount, then quasi‐likelihood estimation can be a good alternative, although parameter constraints may be violated. Sensitivity to model misspecification and outliers is also discussed along with recommendations and priorities for future research.     

Using Auxiliary Data for Binomial Parameter Estimation with Nonignorable Nonresponse

Nonignorable nonresponse is a nonresponse mechanism that depends on the values of the variable having nonresponse. When an observed data of a binomial distribution suffer missing values from a nonignorable nonresponse mechanism, the binomial distribution parameters become unidentifiable without any other auxiliary information or assumption. To address the problems of non identifiability, existing methods mostly based on the log-linear regression model. In this article, we focus on the model when the nonresponse is nonignorable and we consider to use the auxiliary data to improve identifiability; furthermore, we derive the maximum likelihood estimator (MLE) for the binomial proportion and its associated variance. We present results for an analysis of real-life data from the SARS study in China. Finally, the simulation study shows that the proposed method gives promising results.     

Statistical inference for the Gompertz distribution based on Type-II progressively hybrid censored data

In this article, the statistical inference for the Gompertz distribution based on Type-II progressively hybrid censored data is discussed. The estimation of the parameters for Gompertz distribution is obtained using maximum likelihood method (MLE) and Bayesian method under three different loss functions. We also proved the existence and uniqueness of the MLE. The one-sample Bayesian prediction intervals are obtained. The work is done for different values of the parameters. We apply the Monto Carlo simulation to compare the proposed methods, also an example is discussed to construct the Prediction intervals.     

A SEMIPARAMETRIC MIXTURE MODEL FOR THE ANALYSIS OF COMPETING RISKS DATA

This paper deals with the regression analysis of failure time data when there are censoring and multiple types of failures. We propose a semiparametric generalization of a parametric mixture model of Larson & Dinse (1985), for which the marginal probabilities of the various failure types are logistic functions of the covariates. Given the type of failure, the conditional distribution of the time to failure follows a proportional hazards model. A marginal like lihood approach to estimating regression parameters is suggested, whereby the baseline hazard functions are eliminated as nuisance parameters. The Monte Carlo method is used to approximate the marginal likelihood; the resulting function is maximized easily using existing software. Some guidelines for choosing the number of Monte Carlo replications are given. Fixing the regression parameters at their estimated values, the full likelihood is maximized via an EM algorithm to estimate the baseline survivor functions. The methods suggested are illustrated using the Stanford heart transplant data.     

Integrated likelihoods in parametric survival models for highly clustered censored data

In studies that involve censored time-to-event data, stratification is frequently encountered due to different reasons, such as stratified sampling or model adjustment due to violation of model assumptions. Often, the main interest is not in the clustering variables, and the cluster-related parameters are treated as nuisance. When inference is about a parameter of interest in presence of many nuisance parameters, standard likelihood methods often perform very poorly and may lead to severe bias. This problem is particularly evident in models for clustered data with cluster-specific nuisance parameters, when the number of clusters is relatively high with respect to the within-cluster size. However, it is still unclear how the presence of censoring would affect this issue. We consider clustered failure time data with independent censoring, and propose frequentist inference based on an integrated likelihood. We then apply the proposed approach to a stratified Weibull model. Simulation studies show that appropriately defined integrated likelihoods provide very accurate inferential results in all circumstances, such as for highly clustered data or heavy censoring, even in extreme settings where standard likelihood procedures lead to strongly misleading results. We show that the proposed method performs generally as well as the frailty model, but it is superior when the frailty distribution is seriously misspecified. An application, which concerns treatments for a frequent disease in late-stage HIV-infected people, illustrates the proposed inferential method in Weibull regression models, and compares different inferential conclusions from alternative methods.     

Bayesian Analysis in Regression Models Using Pseudo-Likelihoods

This article deals with the issue of using a suitable pseudo-likelihood, instead of an integrated likelihood, when performing Bayesian inference about a scalar parameter of interest in the presence of nuisance parameters. The proposed approach has the advantages of avoiding the elicitation on the nuisance parameters and the computation of multidimensional integrals. Moreover, it is particularly useful when it is difficult, or even impractical, to write the full likelihood function.

We focus on Bayesian inference about a scalar regression coefficient in various regression models. First, in the context of non-normal regression-scale models, we give a theroetical result showing that there is no loss of information about the parameter of interest when using a posterior distribution derived from a pseudo-likelihood instead of the correct posterior distribution. Second, we present non trivial applications with high-dimensional, or even infinite-dimensional, nuisance parameters in the context of nonlinear normal heteroscedastic regression models, and of models for binary outcomes and count data, accounting also for possibile overdispersion. In all these situtations, we show that non Bayesian methods for eliminating nuisance parameters can be usefully incorporated into a one-parameter Bayesian analysis.     

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.     

On the integrated maximum likelihood estimators for a closed population capture–recapture model with unequal capture probabilities

Nuisance parameter elimination is a central problem in capture–recapture modelling. In this paper, we consider a closed population capture–recapture model which assumes the capture probabilities varies only with the sampling occasions. In this model, the capture probabilities are regarded as nuisance parameters and the unknown number of individuals is the parameter of interest. In order to eliminate the nuisance parameters, the likelihood function is integrated with respect to a weight function (uniform and Jeffrey's) of the nuisance parameters resulting in an integrated likelihood function depending only on the population size. For these integrated likelihood functions, analytical expressions for the maximum likelihood estimates are obtained and it is proved that they are always finite and unique. Variance estimates of the proposed estimators are obtained via a parametric bootstrap resampling procedure. The proposed methods are illustrated on a real data set and their frequentist properties are assessed by means of a simulation study.     

A nonparametric estimation procedure for the Hawkes process: comparison with maximum likelihood estimation

In earlier work, Kirchner [An estimation procedure for the Hawkes process. Quant Financ. 2017;17(4):571–595], we introduced a nonparametric estimation method for the Hawkes point process. In this paper, we present a simulation study that compares this specific nonparametric method to maximum-likelihood estimation. We find that the standard deviations of both estimation methods decrease as power-laws in the sample size. Moreover, the standard deviations are proportional. For example, for a specific Hawkes model, the standard deviation of the branching coefficient estimate is roughly 20% larger than for MLE – over all sample sizes considered. This factor becomes smaller when the true underlying branching coefficient becomes larger. In terms of runtime, our method clearly outperforms MLE. The present bias of our method can be well explained and controlled. As an incidental finding, we see that also MLE estimates seem to be significantly biased when the underlying Hawkes model is near criticality. This asks for a more rigorous analysis of the Hawkes likelihood and its optimization.     

Maximum likelihood estimation for a nearly random walk model

This paper proposes an effective reparameterization method for the maximum likelihood estimation of a nearly random walk ARIMA (1,1,1) model, an important case where standard method of locating the MLE is not satisfactory. This model is equivalent to the permanent and temporary components model that Fama &French (1988) and others used to capture the slow mean reversion behavior of stock prices. The reparameterization method we prppose for estimating the nearly cancelled AR and MA parameters performs satisfactorily. The exact likelihood function based on the transformed parameters is studied. We argue that the region of interest will get magnified and emphasized in the transformed space, thus making the search for MLE more thorough and effective. Substantiai simuiation evidences are provided to demonstrate the effectiveness of the method. The sample size requirement is critical and is discussed in details. For application, this method is applied to estimate a nearly random walk ARIMA (1,1,1) model for NYSE/AMEX value-weighted market return in daily and longer holding-period horizons.