Frailty models and copulas: similarities and differences

Copulas and frailty models are important tools to model bivariate survival data. Equivalence between Archimedean copula models and shared frailty models, e.g. between the Clayton-Oakes copula model and the shared gamma frailty model, has often been claimed in the literature. In this note we show that, in both the models, there is indeed a well-known equivalence between the copula functions; the modeling of the marginal survival functions, however, is quite different. The latter fact leads to different joint survival functions.     

Vine copula models with GLM and sparsity

Vine copula provides a flexible tool to capture asymmetry in modeling multivariate distributions. Nevertheless, its flexibility is achieved at the expense of exponentially increasing complexity of the model. To alleviate this issue, the simplifying assumption (SA) is commonly adapted in specific applications of vine copula models. In this paper, generalized linear models (GLMs) are proposed for the parameters in conditional bivariate copulas to relax the SA. In the spirit of the principle of parsimony, a regularization methodology is developed to control the number of parameters, leading to sparse vine copula models. The conventional vine copula with the SA, the proposed GLM-based vine copula, and the sparse vine copula are applied to several financial datasets, and the results show that our proposed models outperform the one with SA significantly in terms of the Bayesian information criterion.     

Copula directed acyclic graphs

A new methodology for selecting a Bayesian network for continuous data outside the widely used class of multivariate normal distributions is developed. The ‘copula DAGs’ combine directed acyclic graphs and their associated probability models with copula C/D-vines. Bivariate copula densities introduce flexibility in the joint distributions of pairs of nodes in the network. An information criterion is studied for graph selection tailored to the joint modeling of data based on graphs and copulas. Examples and simulation studies show the flexibility and properties of the method.     

Asymmetric Forecast Densities for U.S. Macroeconomic Variables from a Gaussian Copula Model of Cross-Sectional and Serial Dependence

Most existing reduced-form macroeconomic multivariate time series models employ elliptical disturbances, so that the forecast densities produced are symmetric. In this article, we use a copula model with asymmetric margins to produce forecast densities with the scope for severe departures from symmetry. Empirical and skew t distributions are employed for the margins, and a high-dimensional Gaussian copula is used to jointly capture cross-sectional and (multivariate) serial dependence. The copula parameter matrix is given by the correlation matrix of a latent stationary and Markov vector autoregression (VAR). We show that the likelihood can be evaluated efficiently using the unique partial correlations, and estimate the copula using Bayesian methods. We examine the forecasting performance of the model for four U.S. macroeconomic variables between 1975:Q1 and 2011:Q2 using quarterly real-time data. We find that the point and density forecasts from the copula model are competitive with those from a Bayesian VAR. During the recent recession the forecast densities exhibit substantial asymmetry, avoiding some of the pitfalls of the symmetric forecast densities from the Bayesian VAR. We show that the asymmetries in the predictive distributions of GDP growth and inflation are similar to those found in the probabilistic forecasts from the Survey of Professional Forecasters. Last, we find that unlike the linear VAR model, our fitted Gaussian copula models exhibit nonlinear dependencies between some macroeconomic variables. This article has online supplementary material.     

Semi-parametric survival analysis via Dirichlet process mixtures of the First Hitting Time model

Time-to-event data often violate the proportional hazards assumption inherent in the popular Cox regression model. Such violations are especially common in the sphere of biological and medical data where latent heterogeneity due to unmeasured covariates or time varying effects are common. A variety of parametric survival models have been proposed in the literature which make more appropriate assumptions on the hazard function, at least for certain applications. One such model is derived from the First Hitting Time (FHT) paradigm which assumes that a subject’s event time is determined by a latent stochastic process reaching a threshold value. Several random effects specifications of the FHT model have also been proposed which allow for better modeling of data with unmeasured covariates. While often appropriate, these methods often display limited flexibility due to their inability to model a wide range of heterogeneities. To address this issue, we propose a Bayesian model which loosens assumptions on the mixing distribution inherent in the random effects FHT models currently in use. We demonstrate via simulation study that the proposed model greatly improves both survival and parameter estimation in the presence of latent heterogeneity. We also apply the proposed methodology to data from a toxicology/carcinogenicity study which exhibits nonproportional hazards and contrast the results with both the Cox model and two popular FHT models.

     

Simultaneous inference in structured additive conditional copula regression models: a unifying Bayesian approach

While most regression models focus on explaining distributional aspects of one single response variable alone, interest in modern statistical applications has recently shifted towards simultaneously studying multiple response variables as well as their dependence structure. A particularly useful tool for pursuing such an analysis are copula-based regression models since they enable the separation of the marginal response distributions and the dependence structure summarised in a specific copula model. However, so far copula-based regression models have mostly been relying on two-step approaches where the marginal distributions are determined first whereas the copula structure is studied in a second step after plugging in the estimated marginal distributions. Moreover, the parameters of the copula are mostly treated as a constant not related to covariates and most regression specifications for the marginals are restricted to purely linear predictors. We therefore propose simultaneous Bayesian inference for both the marginal distributions and the copula using computationally efficient Markov chain Monte Carlo simulation techniques. In addition, we replace the commonly used linear predictor by a generic structured additive predictor comprising for example nonlinear effects of continuous covariates, spatial effects or random effects and furthermore allow to make the copula parameters covariate-dependent. To facilitate Bayesian inference, we construct proposal densities for a Metropolis–Hastings algorithm relying on quadratic approximations to the full conditionals of regression coefficients avoiding manual tuning. The performance of the resulting Bayesian estimates is evaluated in simulations comparing our approach with penalised likelihood inference, studying the choice of a specific copula model based on the deviance information criterion, and comparing a simultaneous approach with a two-step procedure. Furthermore, the flexibility of Bayesian conditional copula regression models is illustrated in two applications on childhood undernutrition and macroecology.     

A Comparison of Frailty and Other Models for Bivariate Survival Data

Multivariate survival data arise when eachstudy subject may experience multiple events or when study subjectsare clustered into groups. Statistical analyses of such dataneed to account for the intra-cluster dependence through appropriatemodeling. Frailty models are the most popular for such failuretime data. However, there are other approaches which model thedependence structure directly. In this article, we compare thefrailty models for bivariate data with the models based on bivariateexponential and Weibull distributions. Bayesian methods providea convenient paradigm for comparing the two sets of models weconsider. Our techniques are illustrated using two examples.One simulated example demonstrates model choice methods developedin this paper and the other example, based on a practical dataset of onset of blindness among patients with diabetic Retinopathy,considers Bayesian inference using different models.     

Copula Density Estimation by Total Variation Penalized Likelihood

Copulas are full measures of dependence among random variables. They are increasingly popular among academics and practitioners in financial econometrics for modeling comovements between markets, risk factors, and other relevant variables. A copula's hidden dependence structure that couples a joint distribution with its marginals makes a parametric copula non-trivial. An approach to bivariate copula density estimation is introduced that is based on a penalized likelihood with a total variation penalty term. Adaptive choice of the amount of regularization is based on approximate Bayesian Information Criterion (BIC) type scores. Performance are evaluated through the Monte Carlo simulation.     

Bayesian bivariate survival analysis using the power variance function copula

Copula models have become increasingly popular for modelling the dependence structure in multivariate survival data. The two-parameter Archimedean family of Power Variance Function (PVF) copulas includes the Clayton, Positive Stable (Gumbel) and Inverse Gaussian copulas as special or limiting cases, thus offers a unified approach to fitting these important copulas. Two-stage frequentist procedures for estimating the marginal distributions and the PVF copula have been suggested by Andersen (Lifetime Data Anal 11:333–350, 2005), Massonnet et al. (J Stat Plann Inference 139(11):3865–3877, 2009) and Prenen et al. (J R Stat Soc Ser B 79(2):483–505, 2017) which first estimate the marginal distributions and conditional on these in a second step to estimate the PVF copula parameters. Here we explore an one-stage Bayesian approach that simultaneously estimates the marginal and the PVF copula parameters. For the marginal distributions, we consider both parametric as well as semiparametric models. We propose a new method to simulate uniform pairs with PVF dependence structure based on conditional sampling for copulas and on numerical approximation to solve a target equation. In a simulation study, small sample properties of the Bayesian estimators are explored. We illustrate the usefulness of the methodology using data on times to appendectomy for adult twins in the Australian NH&MRC Twin registry. Parameters of the marginal distributions and the PVF copula are simultaneously estimated in a parametric as well as a semiparametric approach where the marginal distributions are modelled using Weibull and piecewise exponential distributions, respectively.     

The copula directional dependence by stochastic volatility models

This paper proposes a copula directional dependence by using a bivariate Gaussian copula beta regression with Stochastic Volatility (SV) models for marginal distributions. With the asymmetric copula generated by the composition of two Plackett copulas, we show that our SV copula directional dependence by the Gaussian copula beta regression model is superior to the Kim and Hwang (2016) copula directional dependence by an asymmetric GARCH model in terms of the percent relative efficiency of bias and mean squared error. To validate our proposed method with the real data, we use Brent Crude Daily Price (BRENT), West Texas Intermediate Daily Price (WTI), the Standard & Poor’s 500 (SP) and US 10-Year Treasury Constant Maturity Rate (TCM) so that our copula SV directional dependence is overall superior to the Kim and Hwang (2016) copula directional dependence by an asymmetric GARCH model in terms of precision by the percent relative efficiency of mean squared error. In terms of forecasting using the real financial data, we also show that the Bayesian SV model of the uniform transformed data by a copula conditional distribution yields an improvement on the volatility models such as GARCH and SV.     

Bayesian variable selection in a class of mixture models for ordinal data: a comparative study

In this paper, we consider a special finite mixture model named Combination of Uniform and shifted Binomial (CUB), recently introduced in the statistical literature to analyse ordinal data expressing the preferences of raters with regards to items or services. Our aim is to develop a variable selection procedure for this model using a Bayesian approach. Bayesian methods for variable selection and model choice have become increasingly popular in recent years, due to advances in Markov chain Monte Carlo computational algorithms. Several methods have been proposed in the case of linear and generalized linear models (GLM). In this paper, we adapt to the CUB model some of these algorithms: the Kuo–Mallick method together with its ‘metropolized’ version and the Stochastic Search Variable Selection method. Several simulated examples are used to illustrate the algorithms and to compare their performance. Finally, an application to real data is introduced.     

Predictive assessment of copula models

Copulas are powerful explanatory tools for studying dependence patterns in multivariate data. While the primary use of copula models is in multivariate dependence modelling, they also offer predictive value for regression analysis. This article investigates the utility of copula models for model‐based predictions from two angles. We assess whether, where, and by how much various copula models differ in their predictions of a conditional mean and conditional quantiles. From a model selection perspective, we then evaluate the predictive discrepancy between copula models using in‐sample and out‐of‐sample predictions both in bivariate and higher‐dimensional settings. Our findings suggest that some copula models are more difficult to distinguish in terms of their overall predictive power than others, and depending on the quantity of interest, the differences in predictions can be detected only in some targeted regions. The situations where copula‐based regression approaches would be advantageous over traditional ones are discussed using simulated and real data. The Canadian Journal of Statistics 47: 8–26; 2019 © 2018 Statistical Society of Canada     

Max‐infinitely divisible models and inference for spatial extremes

For many environmental processes, recent studies have shown that the dependence strength is decreasing when quantile levels increase. This implies that the popular max‐stable models are inadequate to capture the rate of joint tail decay, and to estimate joint extremal probabilities beyond observed levels. We here develop a more flexible modeling framework based on the class of max‐infinitely divisible processes, which extend max‐stable processes while retaining dependence properties that are natural for maxima. We propose two parametric constructions for max‐infinitely divisible models, which relax the max‐stability property but remain close to some popular max‐stable models obtained as special cases. The first model considers maxima over a finite, random number of independent observations, while the second model generalizes the spectral representation of max‐stable processes. Inference is performed using a pairwise likelihood. We illustrate the benefits of our new modeling framework on Dutch wind gust maxima calculated over different time units. Results strongly suggest that our proposed models outperform other natural models, such as the Student‐t copula process and its max‐stable limit, even for large block sizes.     

Power and sample size calculation for paired right-censored data based on survival copula models

Sample size determination is essential during the planning phases of clinical trials. To calculate the required sample size for paired right-censored data, the structure of the within-paired correlations needs to be pre-specified. In this article, we consider using popular parametric copula models, including the Clayton, Gumbel, or Frank families, to model the distribution of joint survival times. Under each copula model, we derive a sample size formula based on the testing framework for rank-based tests and non-rank-based tests (i.e., logrank test and Kaplan–Meier statistic, respectively). We also investigate how the power or the sample size was affected by the choice of testing methods and copula model under different alternative hypotheses. In addition to this, we examine the impacts of paired-correlations, accrual times, follow-up times, and the loss to follow-up rates on sample size estimation. Finally, two real-world studies are used to illustrate our method and R code is available to the user.     

Nonparametric Bayesian survival analysis using mixtures of Weibull distributions

Bayesian nonparametric methods have been applied to survival analysis problems since the emergence of the area of Bayesian nonparametrics. However, the use of the flexible class of Dirichlet process mixture models has been rather limited in this context. This is, arguably, to a large extent, due to the standard way of fitting such models that precludes full posterior inference for many functionals of interest in survival analysis applications. To overcome this difficulty, we provide a computational approach to obtain the posterior distribution of general functionals of a Dirichlet process mixture. We model the survival distribution employing a flexible Dirichlet process mixture, with a Weibull kernel, that yields rich inference for several important functionals. In the process, a method for hazard function estimation emerges. Methods for simulation-based model fitting, in the presence of censoring, and for prior specification are provided. We illustrate the modeling approach with simulated and real data.     

The Copula Information Criteria

We derive two types of Akaike information criterion (AIC)‐like model‐selection formulae for the semiparametric pseudo‐maximum likelihood procedure. We first adapt the arguments leading to the original AIC formula, related to empirical estimation of a certain Kullback–Leibler information distance. This gives a significantly different formula compared with the AIC, which we name the copula information criterion. However, we show that such a model‐selection procedure cannot exist for copula models with densities that grow very fast near the edge of the unit cube. This problem affects most popular copula models. We then derive what we call the cross‐validation copula information criterion, which exists under weak conditions and is a first‐order approximation to exact cross validation. This formula is very similar to the standard AIC formula but has slightly different motivation. A brief illustration with real data is given.     

Bayesian estimation and stochastic model specification search for dynamic survival models

Dynamic survival models are a useful extension of the popular Cox model as the effects of explanatory variables are allowed to change over time. In this paper a new auxiliary mixture sampler for Bayesian estimation of the model parameters is introduced. This sampler forms the basis of a model space MCMC method for stochastic model specification search in dynamic survival models, which involves selection of covariates to include in the model as well as specification of effects as time-varying or constant. The method is applied to two well-known data sets from the literature.     

Regression in a copula model for bivariate count data

In many cases of modeling bivariate count data, the interest lies on studying the association rather than the marginal properties. We form a flexible regression copula-based model where covariates are used not only for the marginal but also for the copula parameters. Since copula measures the association, the use of covariates in its parameters allow for direct modeling of association. A real-data application related to transaction market basket data is used. Our goal is to refine and understand whether the association between the number of purchases of certain product categories depends on particular demographic customers’ characteristics. Such information is important for decision making for marketing purposes.     

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.     

The FGM Long-Term Bivariate Survival Copula Model: Modeling,Bayesian Estimation,and Case Influence Diagnostics

In this article, we propose a bivariate long-term distribution based on the Farlie-Gumbel-Morgenstern copula model. The proposed model allows for the presence of censored data and covariates. For inferential purposes, a Bayesian approach via Markov Chain Monte Carlo (MCMC) were considered. Further, some discussions on the model selection criteria are given. In order to examine outlying and influential observations, we present a Bayesian case deletion influence diagnostics based on the Kullback-Leibler divergence. The newly developed procedures are illustrated on artificial and real data.