A dependent Dirichlet process model for survival data with competing risks

In this paper, we first propose a dependent Dirichlet process (DDP) model using a mixture of Weibull models with each mixture component resembling a Cox model for survival data. We then build a Dirichlet process mixture model for competing risks data without regression covariates. Next we extend this model to a DDP model for competing risks regression data by using a multiplicative covariate effect on subdistribution hazards in the mixture components. Though built on proportional hazards (or subdistribution hazards) models, the proposed nonparametric Bayesian regression models do not require the assumption of constant hazard (or subdistribution hazard) ratio. An external time-dependent covariate is also considered in the survival model. After describing the model, we discuss how both cause-specific and subdistribution hazard ratios can be estimated from the same nonparametric Bayesian model for competing risks regression. For use with the regression models proposed, we introduce an omnibus prior that is suitable when little external information is available about covariate effects. Finally we compare the models’ performance with existing methods through simulations. We also illustrate the proposed competing risks regression model with data from a breast cancer study. An R package “DPWeibull” implementing all of the proposed methods is available at CRAN.

     

Confidence intervals for the difference between independent binomial proportions: comparison using a graphical approach and moving averages

This paper uses graphical methods to illustrate and compare the coverage properties of a number of methods for calculating confidence intervals for the difference between two independent binomial proportions. We investigate both small‐sample and large‐sample properties of both two‐sided and one‐sided coverage, with an emphasis on asymptotic methods. In terms of aligning the smoothed coverage probability surface with the nominal confidence level, we find that the score‐based methods on the whole have the best two‐sided coverage, although they have slight deficiencies for confidence levels of 90% or lower. For an easily taught, hand‐calculated method, the Brown‐Li ‘Jeffreys’ method appears to perform reasonably well, and in most situations, it has better one‐sided coverage than the widely recommended alternatives. In general, we find that the one‐sided properties of many of the available methods are surprisingly poor. In fact, almost none of the existing asymptotic methods achieve equal coverage on both sides of the interval, even with large sample sizes, and consequently if used as a non‐inferiority test, the type I error rate (which is equal to the one‐sided non‐coverage probability) can be inflated. The only exception is the Gart‐Nam ‘skewness‐corrected’ method, which we express using modified notation in order to include a bias correction for improved small‐sample performance, and an optional continuity correction for those seeking more conservative coverage. Using a weighted average of two complementary methods, we also define a new hybrid method that almost matches the performance of the Gart‐Nam interval. Copyright © 2014 John Wiley & Sons, Ltd.     

Probabilistic cost-effectiveness analysis of HIV prevention. Comparing a Bayesian approach with traditional deterministic sensitivity analysis

In cost-effectiveness analysis, the incremental cost-effectiveness ratio is used to measure economic efficiency of a new intervention, relative to an existing one. However, costs and effects are seldom known with certainty. Uncertainty arises from two main sources: uncertainty regarding correct values of intervention-related parameters and uncertainty associated with sampling variation. Recently, attention has focused on Bayesian techniques for quantifying uncertainty. We computed the Bayesian-based 95% credible interval estimates of the incremental cost-effectiveness ratio of several related HIV prevention interventions and compared these results with univariate sensitivity analyses. The conclusions were comparable, even though the probabilistic technique provided additional information.     

Semiparametric inference for survival models with step process covariates

The authors consider Bayesian methods for fitting three semiparametric survival models, incorporating time‐dependent covariates that are step functions. In particular, these are models due to Cox [Cox ( 1972 ) Journal of the Royal Statistical Society, Series B, 34, 187–208], Prentice & Kalbfleisch and Cox & Oakes [Cox & Oakes ( 1984 ) Analysis of Survival Data, Chapman and Hall, London]. The model due to Prentice & Kalbfleisch [Prentice & Kalbfleisch ( 1979 ) Biometrics, 35, 25–39], which has seen very limited use, is given particular consideration. The prior for the baseline distribution in each model is taken to be a mixture of Polya trees and posterior inference is obtained through standard Markov chain Monte Carlo methods. They demonstrate the implementation and comparison of these three models on the celebrated Stanford heart transplant data and the study of the timing of cerebral edema diagnosis during emergency room treatment of diabetic ketoacidosis in children. An important feature of their overall discussion is the comparison of semi‐parametric families, and ultimate criterion based selection of a family within the context of a given data set. The Canadian Journal of Statistics 37: 60–79; © 2009 Statistical Society of Canada     

On the estimation of female births missing due to prenatal sex selection

This research note is prompted by a paper by Kashyap (Is prenatal sex selection associated with lower female child mortality? Population Studies 73(1): 57–78). Kashyap’s paper, which provides 40 original estimates of missing female births, relies on an alternative definition of missing female births, leading to estimates of about half the magnitude of other estimates. There appears, therefore, a real need to take stock of the concept of missing female births widely used by statisticians around the world for assessing the demographic consequences of prenatal sex selection. This research note starts with a brief review of the history of the concept and the difference between Amartya Sen’s original method and the alternative method found elsewhere to compute missing female births. We then put forward three different arguments (deterministic and probabilistic approaches, and consistency analysis) in support of the original computation procedure based on the number of observed male births and the expected sex ratio at birth.     

Bayesian Nonparametric Inference for Random Distributions and Related Functions

In recent years, Bayesian nonparametric inference, both theoretical and computational, has witnessed considerable advances. However, these advances have not received a full critical and comparative analysis of their scope, impact and limitations in statistical modelling; many aspects of the theory and methods remain a mystery to practitioners and many open questions remain. In this paper, we discuss and illustrate the rich modelling and analytic possibilities that are available to the statistician within the Bayesian nonparametric and/or semiparametric framework.