Bayesian analysis of the Box-Cox transformation model based on left-truncated and right-censored data

In this paper, we discuss the inference problem about the Box-Cox transformation model when one faces left-truncated and right-censored data, which often occur in studies, for example, involving the cross-sectional sampling scheme. It is well-known that the Box-Cox transformation model includes many commonly used models as special cases such as the proportional hazards model and the additive hazards model. For inference, a Bayesian estimation approach is proposed and in the method, the piecewise function is used to approximate the baseline hazards function. Also the conditional marginal prior, whose marginal part is free of any constraints, is employed to deal with many computational challenges caused by the constraints on the parameters, and a MCMC sampling procedure is developed. A simulation study is conducted to assess the finite sample performance of the proposed method and indicates that it works well for practical situations. We apply the approach to a set of data arising from a retirement center.     

A class of mixed models for recurrent event data

In this article, we propose a class of mixed models for recurrent event data. The new models include the proportional rates model and Box–Cox transformation rates models as special cases, and allow the effects of covariates on the rate functions of counting processes to be proportional or convergent. For inference on the model parameters, estimating equation approaches are developed. The asymptotic properties of the resulting estimators are established and the finite sample performance of the proposed procedure is evaluated through simulation studies. A real example with data taken from a clinic study on chronic granulomatous disease (CGD) is also illustrated for the use of the proposed methodology. The Canadian Journal of Statistics 39: 578–590; 2011. © 2011 Statistical Society of Canada     

基于贝叶斯方法的比例数据分位数推断及其应用

为了尝试使用贝叶斯方法研究比例数据的分位数回归统计推断问题,首先基于Tobit模型给出了分位数回归建模方法,然后通过选取合适的先验分布得到了贝叶斯层次模型,进而给出了各参数的后验分布并用于Gibbs抽样。数值模拟分析验证了所提出的贝叶斯推断方法对于比例数据分析的有效性。最后,将贝叶斯方法应用于美国加州海洛因吸毒数据,在不同的分位数水平下揭示了吸毒频率的影响因素。     

Bayesian analysis of generalized odds-rate hazards models for survival data

In the analysis of censored survival data Cox proportional hazards model (1972) is extremely popular among the practitioners. However, in many real-life situations the proportionality of the hazard ratios does not seem to be an appropriate assumption. To overcome such a problem, we consider a class of nonproportional hazards models known as generalized odds-rate class of regression models. The class is general enough to include several commonly used models, such as proportional hazards model, proportional odds model, and accelerated life time model. The theoretical and computational properties of these models have been re-examined. The propriety of the posterior has been established under some mild conditions. A simulation study is conducted and a detailed analysis of the data from a prostate cancer study is presented to further illustrate the proposed methodology.     

Marginal Analysis For Clustered Failure Time Data

Clustered failure time data are commonly encountered in biomedical research where the study subjects from the same cluster (e.g., family) share the common genetic and/or environmental factors such that the failure times within the same cluster are correlated. Two approaches that are commonly used to account for the intra-cluster association are frailty models and marginal models. In this paper, we study the marginal proportional hazards model, where the structure of dependence between individuals within a cluster is unspecified. An estimation procedure is developed based on a pseudo-likelihood approach, and a risk set sampling method is proposed for the formulation of the pseudo-likelihood. The asymptotic properties of the proposed estimators are studied, and the related issues regarding the statistical efficiencies are discussed. The performances of the proposed estimator are demonstrated by the simulation studies. A data example from a child vitamin A supplementation trial in Nepal (Nepal Nutrition Intervention Project-Sarlahi, or NNIPS) is used to illustrate this methodology.     

A class of partially linear transformation models for recurrent gap times

In this article, we propose a general class of partially linear transformation models for recurrent gap time data, which extends the linear transformation models by incorporating non linear covariate effects and includes the partially linear proportional hazards and the partially linear proportional odds models as special cases. Both global and local estimating equations are developed to estimate the parametric and non parametric covariate effects, and the asymptotic properties of the resulting estimators are established. The finite-sample behavior of the proposed estimators is evaluated through simulation studies, and an application to a clinic study on chronic granulomatous disease is provided.     

Inference on semiparametric transformation model with general interval-censored failure time data

Failure time data occur in many areas and in various censoring forms and many models have been proposed for their regression analysis such as the proportional hazards model and the proportional odds model. Another choice that has been discussed in the literature is a general class of semiparmetric transformation models, which include the two models above and many others as special cases. In this paper, we consider this class of models when one faces a general type of censored data, case K informatively interval-censored data, for which there does not seem to exist an established inference procedure. For the problem, we present a two-step estimation procedure that is quite flexible and can be easily implemented, and the consistency and asymptotic normality of the proposed estimators of regression parameters are established. In addition, an extensive simulation study is conducted and suggests that the proposed procedure works well for practical situations. An application is also provided.     

Analysis of transformation models with right-truncated data

In many applications, statistical data are frequently observed subject to a retrospective sampling criterion resulting in right-truncated data. In this article, a general class of semiparametric transformation models that include proportional hazards model and proportional odds model as special cases is studied for the analysis of right-truncated data. We proposed two estimators for regression coefficients. The first estimator is based on martingale estimating equations. The second estimator is based on the conditional likelihood function given the truncation times. The asymptotic properties of both estimators are derived. The finite sample performance is examined through a simulation study.     

Fitting and testing the Marshall–Olkin extended Weibull model with randomly censored data

The random censorship model (RCM) is commonly used in biomedical science for modeling life distributions. The popular non-parametric Kaplan–Meier estimator and some semiparametric models such as Cox proportional hazard models are extensively discussed in the literature. In this paper, we propose to fit the RCM with the assumption that the actual life distribution and the censoring distribution have a proportional odds relationship. The parametric model is defined using Marshall–Olkin's extended Weibull distribution. We utilize the maximum-likelihood procedure to estimate model parameters, the survival distribution, the mean residual life function, and the hazard rate as well. The proportional odds assumption is also justified by the newly proposed bootstrap Komogorov–Smirnov type goodness-of-fit test. A simulation study on the MLE of model parameters and the median survival time is carried out to assess the finite sample performance of the model. Finally, we implement the proposed model on two real-life data sets.     

Assessing gamma frailty models for clustered failure time data

Proportional hazards frailty models use a random effect, so called frailty, to construct association for clustered failure time data. It is customary to assume that the random frailty follows a gamma distribution. In this paper, we propose a graphical method for assessing adequacy of the proportional hazards frailty models. In particular, we focus on the assessment of the gamma distribution assumption for the frailties. We calculate the average of the posterior expected frailties at several followup time points and compare it at these time points to 1, the known mean frailty. Large discrepancies indicate lack of fit. To aid in assessing the goodness of fit, we derive and estimate the standard error of the mean of the posterior expected frailties at each time point examined. We give an example to illustrate the proposed methodology and perform sensitivity analysis by simulations.     

A Class of Sampling Two Units with Probability Proportional to Size

A class of sampling two units without replacement with inclusion probability proportional to size is proposed in this article. Many different well known probability proportional to size sampling designs are special cases from this class. The first and second inclusion probabilities of this class satisfy important properties and provide a non-negative variance estimator of the Horvitz and Thompson estimator for the population total. Suitable choice for the first and second inclusion probabilities from this class can be used to reduce the variance estimator of the Horvitz and Thompson estimator. Comparisons between different proportional to size sampling designs through real data and artificial examples are given. Examples show that the minimum variance of the Horvitz and Thompson estimator obtained from the proposed design is not attainable for the most cases at any of the well known designs.     

A class of Box-Cox transformation models for recurrent event data

In this article, we propose a class of Box-Cox transformation models for recurrent event data, which includes the proportional means models as special cases. The new model offers great flexibility in formulating the effects of covariates on the mean functions of counting processes while leaving the stochastic structure completely unspecified. For the inference on the proposed models, we apply a profile pseudo-partial likelihood method to estimate the model parameters via estimating equation approaches and establish large sample properties of the estimators and examine its performance in moderate-sized samples through simulation studies. In addition, some graphical and numerical procedures are presented for model checking. An example of application on a set of multiple-infection data taken from a clinic study on chronic granulomatous disease (CGD) is also illustrated.     

Bayesian Proportional Odds Models for Analyzing Current Status Data: Univariate,Clustered, and Multivariate

Current status data commonly arise in many fields such as epidemiological studies and cross-sectional tumorigenicity studies. In this article, we propose a semiparametric Bayesian approach for analyzing current status data with the proportional odds model. The use of monotone splines for the baseline odds function and a novel data augmentation with Poisson latent variables enable simple updating all of the parameters in the posterior computation. The proposed approach shows good performance and is compared with the approach in Wang and Dunson (2010 Wang , L. , Dunson , D. B. ( 2010 ). Semiparametric Bayes proportional odds models for current status data with under-reporting . Biometrics. Online early, DOI: 10.1111/j.1541-0420.2010.01532.x [Web of Science ®] , [Google Scholar]) in a simulation study. We also generalize the proposed approach to analyze clustered and multivariate current status data under the frailty proportional odds models.     

Approximate Bayesian Computation for Exponential Random Graph Models for Large Social Networks

We consider the issue of sampling from the posterior distribution of exponential random graph (ERG) models and other statistical models with intractable normalizing constants. Existing methods based on exact sampling are either infeasible or require very long computing time. We study a class of approximate Markov chain Monte Carlo (MCMC) sampling schemes that deal with this issue. We also develop a new Metropolis–Hastings kernel to sample sparse large networks from ERG models. We illustrate the proposed methods on several examples.     

Smooth Semi‐nonparametric Analysis for Mixture Cure Models and Its Application to Breast Cancer

Mixture cure models are widely used when a proportion of patients are cured. The proportional hazards mixture cure model and the accelerated failure time mixture cure model are the most popular models in practice. Usually the expectation–maximisation (EM) algorithm is applied to both models for parameter estimation. Bootstrap methods are used for variance estimation. In this paper we propose a smooth semi‐nonparametric (SNP) approach in which maximum likelihood is applied directly to mixture cure models for parameter estimation. The variance can be estimated by the inverse of the second derivative of the SNP likelihood. A comprehensive simulation study indicates good performance of the proposed method. We investigate stage effects in breast cancer by applying the proposed method to breast cancer data from the South Carolina Cancer Registry.     

Proportional hazards regression for cancer screening data

The complication in analysing tumour data is that the tumours detected in a screening programme tend to be slowly progressive, which is the so-called left-truncated sampling that is inherent in screening studies. Under the assumption that all subjects have the same tumour growth function, Ghosh [Proportional hazards regression for cancer studies, Biometrics 64 (2008), pp. 141–148] developed estimation procedures for proportional hazards model. In this note, by modelling growth function as a function of covariates and parameterizing the distribution function of left truncation time, we demonstrate that Ghosh's approach can be extended to the case when each subject has a specific growth function. A simulation study is conducted to demonstrate the potential usefulness of the proposed estimators for the regression parameters in the proportional hazards model.     

A class of accelerated means regression models for recurrent event data

In this article, we propose a general class of accelerated means regression models for recurrent event data. The class includes the proportional means model, the accelerated failure time model and the accelerated rates model as special cases. The new model offers great flexibility in formulating the effects of covariates on the mean functions of counting processes while leaving the stochastic structure completely unspecified. For the inference on the model parameters, estimating equation approaches are developed and both large and final sample properties of the proposed estimators are established. In addition, some graphical and numerical procedures are presented for model checking. An illustration with multiple-infection data from a clinic study on chronic granulomatous disease is also provided.     

Cure rate models: A unified approach

The authors propose a novel class of cure rate models for right‐censored failure time data. The class is formulated through a transformation on the unknown population survival function. It includes the mixture cure model and the promotion time cure model as two special cases. The authors propose a general form of the covariate structure which automatically satisfies an inherent parameter constraint and includes the corresponding binomial and exponential covariate structures in the two main formulations of cure models. The proposed class provides a natural link between the mixture and the promotion time cure models, and it offers a wide variety of new modelling structures as well. Within the Bayesian paradigm, a Markov chain Monte Carlo computational scheme is implemented for sampling from the full conditional distributions of the parameters. Model selection is based on the conditional predictive ordinate criterion. The use of the new class of models is illustrated with a set of real data involving a melanoma clinical trial.     

Bayesian gamma frailty models for survival data with semi-competing risks and treatment switching

Motivated from a colorectal cancer study, we propose a class of frailty semi-competing risks survival models to account for the dependence between disease progression time, survival time, and treatment switching. Properties of the proposed models are examined and an efficient Gibbs sampling algorithm using the collapsed Gibbs technique is developed. A Bayesian procedure for assessing the treatment effect is also proposed. The deviance information criterion (DIC) with an appropriate deviance function and Logarithm of the pseudomarginal likelihood (LPML) are constructed for model comparison. A simulation study is conducted to examine the empirical performance of DIC and LPML and as well as the posterior estimates. The proposed method is further applied to analyze data from a colorectal cancer study.     

Bayesian estimation of a proportional hazards model for double-censored durations

Double-censored data consist of uncensored, left- and right-censored observations and occur in survival time analysis. In this paper, parametric Bayes estimation is investigated for a proportional hazards model with durations subject to double-censoring. We prove consistency and asymptotic normality of the posterior mean with the Bernstein–von Mises theorem. In addition, we estimate asymptotic standard errors. A simulation study shows that the finite-sample performance is similar to that of the maximum likelihood estimator. Finally, the proposed model is applied to rating transition data. The analysis suggests that an upgrade of a rating increases the duration in that class by about 10 days on average.