Orthogonalized Residuals for Estimation of Marginally Specified Association Parameters in Multivariate Binary Data

Abstract. This paper focuses on marginal regression models for correlated binary responses when estimation of the association structure is of primary interest. A new estimating function approach based on orthogonalized residuals is proposed. A special case of the proposed procedure allows a new representation of the alternating logistic regressions method through marginal residuals. The connections between second‐order generalized estimating equations, alternating logistic regressions, pseudo‐likelihood and other methods are explored. Efficiency comparisons are presented, with emphasis on variable cluster size and on the role of higher‐order assumptions. The new method is illustrated with an analysis of data on impaired pulmonary function.     

Generalized fiducial inference for generalized exponential distribution

This article mainly considers interval estimation of the scale and shape parameters of the generalized exponential (GE) distribution. We adopt the generalized fiducial method to construct a kind of new confidence intervals for the parameters of interest and compare them with the frequentist and Bayesian methods. In addition, we give the comparison of the point estimation based on the frequentist, generalized fiducial and Bayesian methods. Simulation results show that a new procedure based on generalized fiducial inference is more applicable than the non-fiducial methods for the point and interval estimation of the GE distribution. Finally, two lifetime data sets are used to illustrate the application of our new procedure.     

Inference for the Birnbaum–Saunders Lifetime Regression Model with Applications

The Birnbaum–Saunders distribution is a positively skewed distribution that is frequently used for analyzing lifetime data. Regression analysis is widely used in this context when some covariates are involved in the life-test. In this article, we discuss the maximum likelihood estimation of the model parameters and associated inference. We discuss the likelihood-ratio tests for some hypotheses of interest as well as some interval estimation methods. A Monte Carlo simulation study is then carried out to examine the performance of the proposed estimators and the interval estimation methods. Finally, some numerical data analyses are done for illustrating all the inferential methods developed here.     

Likelihood-free inference via classification

Increasingly complex generative models are being used across disciplines as they allow for realistic characterization of data, but a common difficulty with them is the prohibitively large computational cost to evaluate the likelihood function and thus to perform likelihood-based statistical inference. A likelihood-free inference framework has emerged where the parameters are identified by finding values that yield simulated data resembling the observed data. While widely applicable, a major difficulty in this framework is how to measure the discrepancy between the simulated and observed data. Transforming the original problem into a problem of classifying the data into simulated versus observed, we find that classification accuracy can be used to assess the discrepancy. The complete arsenal of classification methods becomes thereby available for inference of intractable generative models. We validate our approach using theory and simulations for both point estimation and Bayesian inference, and demonstrate its use on real data by inferring an individual-based epidemiological model for bacterial infections in child care centers.     

M-quantile models with application to poverty mapping

Over the last decade there has been growing demand for estimates of population characteristics at small area level. Unfortunately, cost constraints in the design of sample surveys lead to small sample sizes within these areas and as a result direct estimation, using only the survey data, is inappropriate since it yields estimates with unacceptable levels of precision. Small area models are designed to tackle the small sample size problem. The most popular class of models for small area estimation is random effects models that include random area effects to account for between area variations. However, such models also depend on strong distributional assumptions, require a formal specification of the random part of the model and do not easily allow for outlier robust inference. An alternative approach to small area estimation that is based on the use of M-quantile models was recently proposed by Chambers and Tzavidis (Biometrika 93(2):255–268, 2006) and Tzavidis and Chambers (Robust prediction of small area means and distributions. Working paper, 2007). Unlike traditional random effects models, M-quantile models do not depend on strong distributional assumption and automatically provide outlier robust inference. In this paper we illustrate for the first time how M-quantile models can be practically employed for deriving small area estimates of poverty and inequality. The methodology we propose improves the traditional poverty mapping methods in the following ways: (a) it enables the estimation of the distribution function of the study variable within the small area of interest both under an M-quantile and a random effects model, (b) it provides analytical, instead of empirical, estimation of the mean squared error of the M-quantile small area mean estimates and (c) it employs a robust to outliers estimation method. The methodology is applied to data from the 2002 Living Standards Measurement Survey (LSMS) in Albania for estimating (a) district level estimates of the incidence of poverty in Albania, (b) district level inequality measures and (c) the distribution function of household per-capita consumption expenditure in each district. Small area estimates of poverty and inequality show that the poorest Albanian districts are in the mountainous regions (north and north east) with the wealthiest districts, which are also linked with high levels of inequality, in the coastal (south west) and southern part of country. We discuss the practical advantages of our methodology and note the consistency of our results with results from previous studies. We further demonstrate the usefulness of the M-quantile estimation framework through design-based simulations based on two realistic survey data sets containing small area information and show that the M-quantile approach may be preferable when the aim is to estimate the small area distribution function.     

Analysis of two-phase sampling data with semiparametric additive hazards models

Under the case-cohort design introduced by Prentice (Biometrica 73:1–11, 1986), the covariate histories are ascertained only for the subjects who experience the event of interest (i.e., the cases) during the follow-up period and for a relatively small random sample from the original cohort (i.e., the subcohort). The case-cohort design has been widely used in clinical and epidemiological studies to assess the effects of covariates on failure times. Most statistical methods developed for the case-cohort design use the proportional hazards model, and few methods allow for time-varying regression coefficients. In addition, most methods disregard data from subjects outside of the subcohort, which can result in inefficient inference. Addressing these issues, this paper proposes an estimation procedure for the semiparametric additive hazards model with case-cohort/two-phase sampling data, allowing the covariates of interest to be missing for cases as well as for non-cases. A more flexible form of the additive model is considered that allows the effects of some covariates to be time varying while specifying the effects of others to be constant. An augmented inverse probability weighted estimation procedure is proposed. The proposed method allows utilizing the auxiliary information that correlates with the phase-two covariates to improve efficiency. The asymptotic properties of the proposed estimators are established. An extensive simulation study shows that the augmented inverse probability weighted estimation is more efficient than the widely adopted inverse probability weighted complete-case estimation method. The method is applied to analyze data from a preventive HIV vaccine efficacy trial.     

Regression-based,regression-free and model-free approaches for robust online scale estimation

This paper compares the methods for variability extraction from a univariate time series in real time. The online scale estimation is achieved by applying a robust scale functional to a moving time window. Scale estimators based on the residuals of a preceding regression step are compared with regression-free and model-free techniques in a simulation study and in an application to a real time series. In the presence of level shifts or strong non-linear trends in the signal level, the model-free scale estimators perform especially well. However, the investigated regression-free and regression-based methods have higher breakdown points, they are applicable to data containing temporal correlations, and they are much more efficient.     

An approximation of logarithmic functions in the regression setting

We consider a method of moments approach for dealing with censoring at zero for data expressed in levels when researchers would like to take logarithms. A Box–Cox transformation is employed. We explore this approach in the context of linear regression where both dependent and independent variables are censored. We contrast this method to two others, (1) dropping records of data containing censored values and (2) assuming normality for censored observations and the residuals in the model. Across the methods considered, where researchers are interested primarily in the slope parameter, estimation bias is consistently reduced using the method of moments approach.     

A new method for interval estimation of the mean of the Gamma distribution

The two parameter Gamma distribution is widely used for modeling lifetime distributions in reliability theory. There is much literature on the inference on the individual parameters of the Gamma distribution, namely the shape parameter k and the scale parameter θ when the other parameter is known. However, usually the reliability professionals have a major interest in making statistical inference about the mean lifetime μ, which equals the product θk for the Gamma distribution. The problem of inference on the mean μ when both parameters θ and k are unknown has been less attended in the literature for the Gamma distribution. In this paper we review the existing methods for interval estimation of μ. A comparative study in this paper indicates that the existing methods are either too approximate and yield less reliable confidence intervals or are computationally quite complicated and need advanced computing facilities. We propose a new simple method for interval estimation of the Gamma mean and compare its performance with the existing methods. The comparative study showed that the newly proposed computationally simple optimum power normal approximation method works best even for small sample sizes.     

A class of semiparametric cure models with current status data

Current status data occur in many biomedical studies where we only know whether the event of interest occurs before or after a particular time point. In practice, some subjects may never experience the event of interest, i.e., a certain fraction of the population is cured or is not susceptible to the event of interest. We consider a class of semiparametric transformation cure models for current status data with a survival fraction. This class includes both the proportional hazards and the proportional odds cure models as two special cases. We develop efficient likelihood-based estimation and inference procedures. We show that the maximum likelihood estimators for the regression coefficients are consistent, asymptotically normal, and asymptotically efficient. Simulation studies demonstrate that the proposed methods perform well in finite samples. For illustration, we provide an application of the models to a study on the calcification of the hydrogel intraocular lenses.

     

Nearest Neighbor Adjusted Best Linear Unbiased Prediction

Statistical inference for linear models has classically focused on either estimation or hypothesis testing of linear combinations of fixed effects or of variance components for random effects. A third form of inference—prediction of linear combinations of fixed and random effects—has important advantages over conventional estimators in many applications. None of these approaches will result in accurate inference if the data contain strong, unaccounted for local gradients, such as spatial trends in field-plot data. Nearest neighbor methods to adjust for such trends have been widely discussed in recent literature. So far, however, these methods have been developed exclusively for classical estimation and hypothesis testing. In this article a method of obtaining nearest neighbor adjusted (NNA) predictors, along the lines of “best linear unbiased prediction,” or BLUP, is developed. A simulation study comparing “NNABLUP” to conventional NNA methods and to non-NNA alternatives suggests considerable potential for improved efficiency.     

Monte Carlo Methods for Bayesian Inference on the Linear Hazard Rate Distribution

The Bayesian estimation and prediction problems for the linear hazard rate distribution under general progressively Type-II censored samples are considered in this article. The conventional Bayesian framework as well as the Markov Chain Monte Carlo (MCMC) method to generate the Bayesian conditional probabilities of interest are discussed. Sensitivity of the prior for the model is also examined. The flood data on Fox River, Wisconsin, from 1918 to 1950, are used to illustrate all the methods of inference discussed in this article.     

Performance of asymmetric links and correction methods for imbalanced data in binary regression

In binary regression, imbalanced data result from the presence of values equal to zero (or one) in a proportion that is significantly greater than the corresponding real values of one (or zero). In this work, we evaluate two methods developed to deal with imbalanced data and compare them to the use of asymmetric links. The results based on simulation study show, that correction methods do not adequately correct bias in the estimation of regression coefficients and that the models with power links and reverse power considered produce better results for certain types of imbalanced data. Additionally, we present an application for imbalanced data, identifying the best model among the various ones proposed. The parameters are estimated using a Bayesian approach, considering the Hamiltonian Monte-Carlo method, utilizing the No-U-Turn Sampler algorithm and the comparisons of models were developed using different criteria for model comparison, predictive evaluation and quantile residuals.     

Improved simultaneous intervals for linear combinations of parameters from generalized linear models

When employing generalized linear models, interest often focuses on estimation of odds ratios or relative risks. Additionally, researchers often make overall conclusions, requiring accurate estimation of a set of these quantities. Consequently, simultaneous estimation is warranted. Current simultaneous estimation methods only perform well in this setting when there are a very small number of comparisons and/or the sample size is relatively large. Additionally, the estimated quantities can have significant bias especially at small sample sizes. The proposed bounds: (1) perform well for a small or large number of comparisons, (2) exhibit improved performance over current methods for small to moderate sample sizes, (3) provide bias adjustment not reliant on asymptotics, and (4) avoid the infinite parameter estimates that can occur with maximum-likelihood estimators. Simulations demonstrate that the proposed bounds achieve the desired level of confidence at smaller sample sizes than previous methods.     

Models for surveillance data under reporting delay: applications to US veteran first-time suicide attempters

Surveillance data provide a vital source of information for assessing the spread of a health problem or disease of interest and for planning for future health-care needs. However, the use of surveillance data requires proper adjustments of the reported caseload due to underreporting caused by reporting delays within a limited observation period. Although methods are available to address this classic statistical problem, they are largely focused on inference for the reporting delay distribution, with inference about caseload of disease incidence based on estimates for the delay distribution. This approach limits the complexity of models for disease incidence to provide reliable estimates and projections of incidence. Also, many of the available methods lack robustness since they require parametric distribution assumptions. We propose a new approach to overcome such limitations by allowing for separate models for the incidence and the reporting delay in a distribution-free fashion, but with joint inference for both modeling components, based on functional response models. In addition, we discuss inference about projections of future disease incidence to help identify significant shifts in temporal trends modeled based on the observed data. This latter issue on detecting ‘change points’ is not sufficiently addressed in the literature, despite the fact that such warning signs of potential outbreak are critically important for prevention purposes. We illustrate the approach with both simulated and real data, with the latter involving data for suicide attempts from the Veteran Healthcare Administration.     

Approximate likelihood methods for estimating local recombination rates

Summary. There is currently great interest in understanding the way in which recombination rates vary, over short scales, across the human genome. Aside from inherent interest, an understanding of this local variation is essential for the sensible design and analysis of many studies aimed at elucidating the genetic basis of common diseases or of human population histories. Standard pedigree-based approaches do not have the fine scale resolution that is needed to address this issue. In contrast, samples of deoxyribonucleic acid sequences from unrelated chromosomes in the population carry relevant information, but inference from such data is extremely challenging. Although there has been much recent interest in the development of full likelihood inference methods for estimating local recombination rates from such data, they are not currently practicable for data sets of the size being generated by modern experimental techniques. We introduce and study two approximate likelihood methods. The first, a marginal likelihood, ignores some of the data. A careful choice of what to ignore results in substantial computational savings with virtually no loss of relevant information. For larger sequences, we introduce a 'composite' likelihood, which approximates the model of interest by ignoring certain long-range dependences. An informal asymptotic analysis and a simulation study suggest that inference based on the composite likelihood is practicable and performs well. We combine both methods to reanalyse data from the lipoprotein lipase gene, and the results seriously question conclusions from some earlier studies of these data.     

Overcoming biases and misconceptions in ecological studies

The aggregate data study design provides an alternative group level analysis to ecological studies in the estimation of individual level health risks. An aggregate model is derived by aggregating a plausible individual level relative rate model within groups, such that population-based disease rates are modelled as functions of individual level covariate data. We apply an aggregate data method to a series of fictitious examples from a review paper by Greenland and Robins which illustrated the problems that can arise when using the results of ecological studies to make inference about individual health risks. We use simulated data based on their examples to demonstrate that the aggregate data approach can address many of the sources of bias that are inherent in typical ecological analyses, even though the limited between-region covariate variation in these examples reduces the efficiency of the aggregate study. The aggregate method has the potential to estimate exposure effects of interest in the presence of non-linearity, confounding at individual and group levels, effect modification, classical measurement error in the exposure and non-differential misclassification in the confounder.     

Mixture of linear mixed models using multivariate t distribution

Linear mixed models are widely used when multiple correlated measurements are made on each unit of interest. In many applications, the units may form several distinct clusters, and such heterogeneity can be more appropriately modelled by a finite mixture linear mixed model. The classical estimation approach, in which both the random effects and the error parts are assumed to follow normal distribution, is sensitive to outliers, and failure to accommodate outliers may greatly jeopardize the model estimation and inference. We propose a new mixture linear mixed model using multivariate t distribution. For each mixture component, we assume the response and the random effects jointly follow a multivariate t distribution, to conveniently robustify the estimation procedure. An efficient expectation conditional maximization algorithm is developed for conducting maximum likelihood estimation. The degrees of freedom parameters of the t distributions are chosen data adaptively, for achieving flexible trade-off between estimation robustness and efficiency. Simulation studies and an application on analysing lung growth longitudinal data showcase the efficacy of the proposed approach.     

Automatic selection of the proper family for simultaneous confidence intervals

Statisticians often employ simultaneous confidence intervals to reduce the likelihood of their drawing false conclusions when they must make a number of comparisons. To do this properly, it is necessary to consider the family of comparisons over which simultaneous confidence must be assured. Sometimes it is not clear what family of comparisons is appropriate. We describe how computer software can monitor the types of contrasts a user examines, and select the smallest family of contrasts that is likely to be of interest. We also describe how to calculate simultaneous confidence intervals for these families using a hybrid of the Bonferroni and Scheffé methods. Our method is especially suitable for problems with discrete and continuous predictors.