Pseudolikelihood estimation in a class of problems with response-related missing covariates

Many practical situations involve a response variable Y and covariates X , where data on (Y, X ) are incomplete for some portion of a sample of individuals. We consider two general types of pseudolikelihood estimation for problems in which missingness may be response-related. These are typically simpler to implement than ordinary maximum likelihood, which in this context is semiparametric. Asymptotics for the pseudolikelihood methods are presented, and simulations conducted to investigate the methods for an important class of problems involving lifetime data. Our results indicate that for these problems the two methods are effective and comparable with respect to efficiency.     

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.     

A semiparametric maximum likelihood ratio test for the change point in copula models

In the present paper, a semiparametric maximum-likelihood-type test statistic is proposed and proved to have the same limit null distribution as the classical parametric likelihood one. Under some mild conditions, the limiting law of the proposed test statistic, suitably normalized and centralized, is shown to be double exponential, under the null hypothesis of no change in the parameter of copula models. We also discuss the Gaussian-type approximations for the semiparametric likelihood ratio. The asymptotic distribution of the proposed statistic under specified alternatives is shown to be normal, and an approximation to the power function is given. Simulation results are provided to illustrate the finite sample performance of the proposed statistical tests based on the double exponential and Gaussian-type approximations.     

A semiparametric estimation of copula models based on the method of moments

Using the classical estimation method of moments, we propose a new semiparametric estimation procedure for multi-parameter copula models. Consistency and asymptotic normality of the obtained estimators are established. By considering an Archimedean copula model, an extensive simulation study, comparing these estimators with the pseudo maximum likelihood, rho-inversion and tau-inversion ones, is carried out. We show that, with regard to the other methods, the moment based estimation is quick and simple to use with reasonable bias and root mean squared error.     

Pseudo‐likelihood ratio tests for semiparametric multivariate copula model selection

The authors propose pseudo‐likelihood ratio tests for selecting semiparametric multivariate copula models in which the marginal distributions are unspecified, but the copula function is parameterized and can be misspecified. For the comparison of two models, the tests differ depending on whether the two copulas are generalized nonnested or generalized nested. For more than two models, the procedure is built on the reality check test of White (2000). Unlike White (2000), however, the test statistic is automatically standardized for generalized nonnested models (with the benchmark) and ignores generalized nested models asymptotically. The authors illustrate their approach with American insurance claim data.     

Copula‐based semiparametric analysis for time series data with detection limits

The analysis of time series data with detection limits is challenging due to the high‐dimensional integral involved in the likelihood. Existing methods are either computationally demanding or rely on restrictive parametric distributional assumptions. We propose a semiparametric approach, where the temporal dependence is captured by parametric copula, while the marginal distribution is estimated non‐parametrically. Utilizing the properties of copulas, we develop a new copula‐based sequential sampling algorithm, which provides a convenient way to calculate the censored likelihood. Even without full parametric distributional assumptions, the proposed method still allows us to efficiently compute the conditional quantiles of the censored response at a future time point, and thus construct both point and interval predictions. We establish the asymptotic properties of the proposed pseudo maximum likelihood estimator, and demonstrate through simulation and the analysis of a water quality data that the proposed method is more flexible and leads to more accurate predictions than Gaussian‐based methods for non‐normal data. The Canadian Journal of Statistics 47: 438–454; 2019 © 2019 Statistical Society of Canada     

Semiparametric inference for estimating equations with nonignorably missing covariates

We consider statistical inference of unknown parameters in estimating equations (EEs) when some covariates have nonignorably missing values, which is quite common in practice but has rarely been discussed in the literature. When an instrument, a fully observed covariate vector that helps identifying parameters under nonignorable missingness, is available, the conditional distribution of the missing covariates given other covariates can be estimated by the pseudolikelihood method of Zhao and Shao [(2015), ‘Semiparametric pseudo likelihoods in generalised linear models with nonignorable missing data’, Journal of the American Statistical Association, 110, 1577–1590)] and be used to construct unbiased EEs. These modified EEs then constitute a basis for valid inference by empirical likelihood. Our method is applicable to a wide range of EEs used in practice. It is semiparametric since no parametric model for the propensity of missing covariate data is assumed. Asymptotic properties of the proposed estimator and the empirical likelihood ratio test statistic are derived. Some simulation results and a real data analysis are presented for illustration.     

A Class of Pseudolikelihood Ratio Tests for Homogeneity in Exponential Tilt Mixture Models

Mixture models are commonly used in biomedical research to account for possible heterogeneity in population. In this paper, we consider tests for homogeneity between two groups in the exponential tilt mixture models. A novel pairwise pseudolikelihood approach is proposed to eliminate the unknown nuisance function. We show that the corresponding pseudolikelihood ratio test has an asymptotic distribution as a supremum of two squared Gaussian processes under the null hypothesis. To maintain the appeal of simplicity for conventional likelihood ratio tests, we propose two alternative tests, both shown to have a simple asymptotic distribution of under the null. Simulation studies show that the proposed class of pseudolikelihood ratio tests performs well in controlling type I errors and having competitive powers compared with the current tests. The proposed tests are illustrated by an example of partial differential expression detection using microarray data from prostate cancer patients.     

Smooth Tests of Copula Specifications

We present a family of smooth tests for the goodness of fit of semiparametric multivariate copula models. The proposed tests are distribution free and can be easily implemented. They are diagnostic and constructive in the sense that when a null distribution is rejected, the test provides useful pointers to alternative copula distributions. We then propose a method of copula density construction, which can be viewed as a multivariate extension of Efron and Tibshirani. We further generalize our methods to the semiparametric copula-based multivariate dynamic models. We report extensive Monte Carlo simulations and three empirical examples to illustrate the effectiveness and usefulness of our method.     

CONFIDENCE INTERVALS FOR THE DIFFERENCE BETWEEN TWO PARTIAL AUCS

As new diagnostic tests are developed and marketed, it is very important to be able to compare the accuracy of a given two continuous‐scale diagnostic tests. An effective method to evaluate the difference between the diagnostic accuracy of two tests is to compare partial areas under the receiver operating characteristic curves (AUCs). In this paper, we review existing parametric methods. Then, we propose a new semiparametric method and a new nonparametric method to investigate the difference between two partial AUCs. For the difference between two partial AUCs under each method, we derive a normal approximation, define an empirical log‐likelihood ratio, and show that the empirical log‐likelihood ratio follows a scaled chi‐square distribution. We construct five confidence intervals for the difference based on normal approximation, bootstrap, and empirical likelihood methods. Finally, extensive simulation studies are conducted to compare the finite‐sample performances of these intervals, and a real example is used as an application of our recommended intervals. The simulation results indicate that the proposed hybrid bootstrap and empirical likelihood intervals outperform other existing intervals in most cases.     

Semiparametric models of longitudinal and time-to-event data with applications to HIV viral dynamics and CD4 counts

We propose a semiparametric approach based on proportional hazards and copula method to jointly model longitudinal outcomes and the time-to-event. The dependence between the longitudinal outcomes on the covariates is modeled by a copula-based times series, which allows non-Gaussian random effects and overcomes the limitation of the parametric assumptions in existing linear and nonlinear random effects models. A modified partial likelihood method using estimated covariates at failure times is employed to draw statistical inference. The proposed model and method are applied to analyze a set of progression to AIDS data in a study of the association between the human immunodeficiency virus viral dynamics and the time trend in the CD4/CD8 ratio with measurement errors. Simulations are also reported to evaluate the proposed model and method.     

Maximum likelihood analysis of semicompeting risks data with semiparametric regression models

The “semicompeting risks” include a terminal event and a non-terminal event. The terminal event may censor the non-terminal event but not vice versa. Because times to the two events are usually correlated, the non-terminal event is subject to dependent/informative censoring by the terminal event. We seek to conduct marginal regressions and joint association analyses for the two event times under semicompeting risks. The proposed method is based on the modeling setup where the semiparametric transformation models are assumed for marginal regressions, and a copula model is assumed for the joint distribution. We propose a nonparametric maximum likelihood approach for inferences, which provides a martingale representation for the score function and an analytical expression for the information matrix. Direct theoretical developments and computational implementation are allowed for the proposed approach. Simulations and a real data application demonstrate the utility of the proposed methodology.     

Semiparametric methods for response-selective and missing data problems in regression

Suppose that data are generated according to the model f ( y | x ; θ ) g ( x ), where y is a response and x are covariates. We derive and compare semiparametric likelihood and pseudolikelihood methods for estimating θ for situations in which units generated are not fully observed and in which it is impossible or undesirable to model the covariate distribution. The probability that a unit is fully observed may depend on y , and there may be a subset of covariates which is observed only for a subsample of individuals. Our key assumptions are that the probability that a unit has missing data depends only on which of a finite number of strata that ( y , x ) belongs to and that the stratum membership is observed for every unit. Applications include case–control studies in epidemiology, field reliability studies and broad classes of missing data and measurement error problems. Our results make fully efficient estimation of θ feasible, and they generalize and provide insight into a variety of methods that have been proposed for specific problems.     

Bias-corrected maximum semiparametric likelihood estimation under logistic regression models based on case–control data

We consider the corrective approach (Theoretical Statistics, Chapman & Hall, London, 1974, p. 310) and preventive approach (Biometrica 80 (1993) 27) to bias reduction of maximum likelihood estimators under the logistic regression model based on case–control data. The proposed bias-corrected maximum likelihood estimators are based on the semiparametric profile log likelihood function under a two-sample semiparametric model, which is equivalent to the assumed logistic regression model. We show that the prospective and retrospective analyses on the basis of the corrective approach to bias reduction produce identical bias-corrected maximum likelihood estimators of the odds ratio parameter, but this does not hold when using the preventive approach unless the case and control sample sizes are identical. We present some results on simulation and on the analysis of two real data sets.     

Comparing point and interval estimates in the bivariate <Emphasis Type="Italic">t</Emphasis>-copula model with application to financial data

The paper considers joint maximum likelihood (ML) and semiparametric (SP) estimation of copula parameters in a bivariate t-copula. Analytical expressions for the asymptotic covariance matrix involving integrals over special functions are derived, which can be evaluated numerically. These direct evaluations of the Fisher information matrix are compared to Hessian evaluations based on numerical differentiation in a simulation study showing a satisfactory performance of the computationally less demanding Hessian evaluations. Individual asymptotic confidence intervals for the t-copula parameters and the corresponding tail dependence coefficient are derived. For two financial datasets these confidence intervals are calculated using both direct evaluation of the Fisher information and numerical evaluation of the Hessian matrix. These confidence intervals are compared to parametric and nonparametric BCA bootstrap intervals based on ML and SP estimation, respectively, showing a preference for asymptotic confidence intervals based on numerical Hessian evaluations.     

Near universal consistency of the maximum pseudolikelihood estimator for discrete models

Maximum pseudolikelihood (MPL) estimators are useful alternatives to maximum likelihood (ML) estimators when likelihood functions are more difficult to manipulate than their marginal and conditional components. Furthermore, MPL estimators subsume a large number of estimation techniques including ML estimators, maximum composite marginal likelihood estimators, and maximum pairwise likelihood estimators. When considering only the estimation of discrete models (on a possibly countably infinite support), we show that a simple finiteness assumption on an entropy-based measure is sufficient for assessing the consistency of the MPL estimator. As a consequence, we demonstrate that the MPL estimator of any discrete model on a bounded support will be consistent. Our result is valid in parametric, semiparametric, and nonparametric settings.     

Testing generalized linear and semiparametric models against smooth alternatives

We propose goodness-of-fit tests for testing generalized linear models and semiparametric regression models against smooth alternatives. The focus is on models having both continous and factorial covariates. As a smooth extension of a parametric or semiparametric model we use generalized varying-coefficient models as proposed by Hastie and Tibshirani. A likelihood ratio statistic is used for testing. Asymptotic expansions allow us to write the estimates as linear smoothers which in turn guarantees simple and fast bootstrapping of the test statistic. The test is shown to have √ n -power, but in contrast with parametric tests it is powerful against smooth alternatives in general.     

Assessing goodness-of-fit of categorical regression models based on case-control data

Demonstrated equivalence between a categorical regression model based on case‐control data and an I‐sample semiparametric selection bias model leads to a new goodness‐of‐fit test. The proposed test statistic is an extension of an existing Kolmogorov–Smirnov‐type statistic and is the weighted average of the absolute differences between two estimated distribution functions in each response category. The paper establishes an optimal property for the maximum semiparametric likelihood estimator of the parameters in the I‐sample semiparametric selection bias model. It also presents a bootstrap procedure, some simulation results and an analysis of two real datasets.     

Simultaneous tests for homogeneity of two zero-inflated (beta) populations

ABSTRACT

Motivated by an example in marine science, we use Fisher’s method to combine independent likelihood ratio tests (LRTs) and asymptotic independent score tests to assess the equivalence of two zero-inflated Beta populations (mixture distributions with three parameters). For each test, test statistics for the three individual parameters are combined into a single statistic to address the overall difference between the two populations. We also develop non parametric and semiparametric permutation-based tests for simultaneously comparing two or three features of unknown populations. Simulations show that the likelihood-based tests perform well for large sample sizes and that the statistics based on combining LRT statistics outperforms the ones based on combining score test statistics. The permutation-based tests have overall better performance in terms of both power and type I error rate. Our methods are easy to implement and computationally efficient, and can be expanded to more than two populations and to other multiple parameter families. The permutation tests are entirely generic and can be useful in various applications dealing with zero (or other) inflation.     

Semiparametric Regression with Kernel Error Model

Abstract.  We propose and study a class of regression models, in which the mean function is specified parametrically as in the existing regression methods, but the residual distribution is modelled non-parametrically by a kernel estimator, without imposing any assumption on its distribution. This specification is different from the existing semiparametric regression models. The asymptotic properties of such likelihood and the maximum likelihood estimate (MLE) under this semiparametric model are studied. We show that under some regularity conditions, the MLE under this model is consistent (when compared with the possibly pseudo-consistency of the parameter estimation under the existing parametric regression model), is asymptotically normal with rate and efficient. The non-parametric pseudo-likelihood ratio has the Wilks property as the true likelihood ratio does. Simulated examples are presented to evaluate the accuracy of the proposed semiparametric MLE method.