Bayesian Analysis of Contingency Tables

ABSTRACT

The display of the data by means of contingency tables is used in different approaches to statistical inference, for example, to broach the test of homogeneity of independent multinomial distributions. We develop a Bayesian procedure to test simple null hypotheses versus bilateral alternatives in contingency tables. Given independent samples of two binomial distributions and taking a mixed prior distribution, we calculate the posterior probability that the proportion of successes in the first population is the same as in the second. This posterior probability is compared with the p-value of the classical method, obtaining a reconciliation between both results, classical and Bayesian. The obtained results are generalized for r × s tables.     

On the existence of a normal approximation to the distribution of the ratio of two independent normal random variables

The distribution of the ratio of two independent normal random variables X and Y is heavy tailed and has no moments. The shape of its density can be unimodal, bimodal, symmetric, asymmetric, and/or even similar to a normal distribution close to its mode. To our knowledge, conditions for a reasonable normal approximation to the distribution of Z = X/Y have been presented in scientific literature only through simulations and empirical results. A proof of the existence of a proposed normal approximation to the distribution of Z, in an interval I centered at β = E(X) /E(Y), is given here for the case where both X and Y are independent, have positive means, and their coefficients of variation fulfill some conditions. In addition, a graphical informative way of assessing the closeness of the distribution of a particular ratio X/Y to the proposed normal approximation is suggested by means of a receiver operating characteristic (ROC) curve.     

Consistency of non parametric estimators of the area under the ROC curve

ABSTRACT

The area under the receiver operating characteristic (ROC) curve is a popular summary index that measures the accuracy of a continuous-scale diagnostic test to measure its accuracy. Under certain conditions on estimators of distribution functions, we prove a theorem on strong consistency of the non parametric “plugin” estimators of the area under the ROC curve. Based on this theorem, we construct some new “plugin” consistent estimators. The performance of the non parametric estimators considered is illustrated numerically and the estimators are compared in terms of bias, variance, and mean square error.     

Estimation in Partially Linear Single-Index Models with Missing Covariates

In this article, we consider a partially linear single-index model Y = g(Z ^τθ₀) + X ^τβ₀ + ? when the covariate X may be missing at random. We propose weighted estimators for the unknown parametric and nonparametric part by applying weighted estimating equations. We establish normality of the estimators of the parameters and asymptotic expansion for the estimator of the nonparametric part when the selection probabilities are unknown. Simulation studies are also conducted to illustrate the finite sample properties of these estimators.     

A Condition to Obtain the Same Decision in the Homogeneity Testing Problem from the Frequentist and Bayesian Point of View

We develop a Bayesian procedure for the homogeneity testing problem of r populations using r × s contingency tables. The posterior probability of the homogeneity null hypothesis is calculated using a mixed prior distribution. The methodology consists of choosing an appropriate value of π₀ for the mass assigned to the null and spreading the remainder, 1 ? π₀, over the alternative according to a density function. With this method, a theorem which shows when the same conclusion is reached from both frequentist and Bayesian points of view is obtained. A sufficient condition under which the p-value is less than a value α and the posterior probability is also less than 0.5 is provided.     

Nonparametric estimation of the ROC curve based on smoothed empirical distribution functions

The receiver operating characteristic (ROC) curve is a graphical representation of the relationship between false positive and true positive rates. It is a widely used statistical tool for describing the accuracy of a diagnostic test. In this paper we propose a new nonparametric ROC curve estimator based on the smoothed empirical distribution functions. We prove its strong consistency and perform a simulation study to compare it with some other popular nonparametric estimators of the ROC curve. We also apply the proposed method to a real data set.     

Testing Serial Correlation in Partially Linear Single-Index Errors-in-Variables Models

In this article, we propose two test statistics for testing the underlying serial correlation in a partially linear single-index model Y = η(Z ^τα) + X ^τβ + ? when X is measured with additive error. The proposed test statistics are shown to have asymptotic normal or chi-squared distributions under the null hypothesis of no serial correlation. Monte Carlo experiments are also conducted to illustrate the finite sample performance of the proposed test statistics. The simulation results confirm that these statistics perform satisfactorily in both estimated sizes and powers.     

Applications of the Bootstrap in ROC Analysis

The problem of estimating standard errors for diagnostic accuracy measures might be challenging for many complicated models. We can address such a problem by using the Bootstrap methods to blunt its technical edge with resampled empirical distributions. We consider two cases where bootstrap methods can successfully improve our knowledge of the sampling variability of the diagnostic accuracy estimators. The first application is to make inference for the area under the ROC curve resulted from a functional logistic regression model which is a sophisticated modelling device to describe the relationship between a dichotomous response and multiple covariates. We consider using this regression method to model the predictive effects of multiple independent variables on the occurrence of a disease. The accuracy measures, such as the area under the ROC curve (AUC) are developed from the functional regression. Asymptotical results for the empirical estimators are provided to facilitate inferences. The second application is to test the difference of two weighted areas under the ROC curve (WAUC) from a paired two sample study. The correlation between the two WAUC complicates the asymptotic distribution of the test statistic. We then employ the bootstrap methods to gain satisfactory inference results. Simulations and examples are supplied in this article to confirm the merits of the bootstrap methods.     

Kshirsagar-Type Lower Bounds for Mean Squared Error of Prediction

Let Y be an observable random vector and Z be an unobserved random variable with joint density f(y, z | θ), where θ is an unknown parameter vector. Considering the problem of predicting Z based on Y, we derive Kshirsagar type lower bounds for the mean squared error of any predictor of Z. These bounds do not require the regularity conditions of Bhattacharyya bounds and hence are more widely applicable. Moreover, the new bounds are shown to be sharper than the corresponding Bhattacharyya bounds. The conditions for attaining the new lower bounds are useful for easy derivation of best unbiased predictors, which we illustrate with some examples.     

The roles of prior catchability assumptions and sample features on bayes estimates of the number of classes in a population

The object of this paper is to explain the role played by the catchability and sampling in the Bayesian estimation of k, the unknown number of classes in a multinomial population. It is shown that the posterior distribution of k increases as the capture probabilities of the classes become more unequal, and that the posterior distribution of k increases with the number of classes observed in the sample and decreases with the sample size. Moreover, it is shown that the posterior mean of k is consistent.     

A non-inferiority test for diagnostic accuracy in the absence of the golden standard test based on the paired partial areas under receiver operating characteristic curves

Non-inferiority tests are often measured for the diagnostic accuracy in medical research. The area under the receiver operating characteristic (ROC) curve is a familiar diagnostic measure for the overall diagnostic accuracy. Nevertheless, since it may not differentiate the diverse shapes of the ROC curves with different diagnostic significance, the partial area under the ROC (PAUROC) curve, another summary measure emerges for such diagnostic processes that require the false-positive rate to be in the clinically interested range. Traditionally, to estimate the PAUROC, the golden standard (GS) test on the true disease status is required. Nevertheless, the GS test may sometimes be infeasible. Besides, in a lot of research fields such as the epidemiology field, the true disease status of the patients may not be known or available. Under the normality assumption on diagnostic test results, based on the expectation-maximization algorithm in combination with the bootstrap method, we propose the heuristic method to construct a non-inferiority test for the difference in the paired PAUROCs without the GS test. Through the simulation study, although the proposed method might provide a liberal test, as a whole, the empirical size of the proposed method sufficiently controls the size at the significance level, and the empirical power of the proposed method in the absence of the GS is as good as that of the non-inferiority in the presence of the GS. The proposed method is illustrated with the published data.     

Linear Regression Models under Conditional Independence Restrictions

Maximum likelihood estimation is investigated in the context of linear regression models under partial independence restrictions. These restrictions aim to assume a kind of completeness of a set of predictors Z in the sense that they are sufficient to explain the dependencies between an outcome Y and predictors X: ?(Y|Z, X) = ?(Y|Z), where ?(·|·) stands for the conditional distribution. From a practical point of view, the former model is particularly interesting in a double sampling scheme where Y and Z are measured together on a first sample and Z and X on a second separate sample. In that case, estimation procedures are close to those developed in the study of double‐regression by Engel & Walstra (1991) and Causeur & Dhorne (1998) . Properties of the estimators are derived in a small sample framework and in an asymptotic one, and the procedure is illustrated by an example from the food industry context.     

Bayesian analysis of head and neck cancer data using generalized inverse Lindley stress–strength reliability model

In this article, we present the analysis of head and neck cancer data using generalized inverse Lindley stress–strength reliability model. We propose Bayes estimators for estimating P(X > Y), when X and Y represent survival times of two groups of cancer patients observed under different therapies. The X and Y are assumed to be independent generalized inverse Lindley random variables with common shape parameter. Bayes estimators are obtained under the considerations of symmetric and asymmetric loss functions assuming independent gamma priors. Since posterior becomes complex and does not possess closed form expressions for Bayes estimators, Lindley’s approximation and Markov Chain Monte Carlo techniques are utilized for Bayesian computation. An extensive simulation experiment is carried out to compare the performances of Bayes estimators with the maximum likelihood estimators on the basis of simulated risks. Asymptotic, bootstrap, and Bayesian credible intervals are also computed for the P(X > Y).     

Combining ROC curves using MAMSE weighted distributions

The receiver operating characteristic (ROC) curve can be used to evaluate the properties of a diagnostic test from the distribution of a variable on the healthy and diseased populations. The minimum averaged mean squared error (MAMSE) weights were developed to handle data from different sources by adjusting the relative contribution of each data source. The authors use the MAMSE weights to infer the ROC curve of a diagnostic test based on raw data from multiple studies. The proposed estimates are consistent and Monte Carlo simulations show favourable finite sample performance. The method is illustrated in a case study where progesterone level is used to detect ectopic pregnancies and abortions from other natural causes. The Canadian Journal of Statistics 46: 298–315; 2018 © 2018 Statistical Society of Canada     

Nonparametric covariate adjustment for receiver operating characteristic curves

The accuracy of a diagnostic test is typically characterized using the receiver operating characteristic (ROC) curve. Summarizing indexes such as the area under the ROC curve (AUC) are used to compare different tests as well as to measure the difference between two populations. Often additional information is available on some of the covariates which are known to influence the accuracy of such measures. The authors propose nonparametric methods for covariate adjustment of the AUC. Models with normal errors and possibly non‐normal errors are discussed and analyzed separately. Nonparametric regression is used for estimating mean and variance functions in both scenarios. In the model that relaxes the assumption of normality, the authors propose a covariate‐adjusted Mann–Whitney estimator for AUC estimation which effectively uses available data to construct working samples at any covariate value of interest and is computationally efficient for implementation. This provides a generalization of the Mann–Whitney approach for comparing two populations by taking covariate effects into account. The authors derive asymptotic properties for the AUC estimators in both settings, including asymptotic normality, optimal strong uniform convergence rates and mean squared error (MSE) consistency. The MSE of the AUC estimators was also assessed in smaller samples by simulation. Data from an agricultural study were used to illustrate the methods of analysis. The Canadian Journal of Statistics 38:27–46; 2010 © 2009 Statistical Society of Canada     

Estimation of P(Y < X) for the Three-Parameter Generalized Exponential Distribution

This article considers the estimation of R = P(Y < X) when X and Y are distributed as two independent three-parameter generalized exponential (GE) random variables with different shape parameters but having the same location and scale parameters. A modified maximum likelihood method and a Bayesian technique are used to estimate R on the basis of independent complete samples. The Bayes estimator cannot be obtained in explicit form, and therefore it has been determined using an importance sampling procedure. An analysis of a real life data set is presented for illustrative purposes.     

Estimation of Conditional Ranks and Tests of Exogeneity in Nonparametric Nonseparable Models

Consider a nonparametric nonseparable regression model Y = ?(Z, U), where ?(Z, U) is strictly increasing in U and U ～ U[0, 1]. We suppose that there exists an instrument W that is independent of U. The observable random variables are Y, Z, and W, all one-dimensional. We construct test statistics for the hypothesis that Z is exogenous, that is, that U is independent of Z. The test statistics are based on the observation that Z is exogenous if and only if V = F_Y|Z(Y|Z) is independent of W, and hence they do not require the estimation of the function ?. The asymptotic properties of the proposed tests are proved, and a bootstrap approximation of the critical values of the tests is shown to be consistent and to work for finite samples via simulations. An empirical example using the U.K. Family Expenditure Survey is also given. As a byproduct of our results we obtain the asymptotic properties of a kernel estimator of the distribution of V, which equals U when Z is exogenous. We show that this estimator converges to the uniform distribution at faster rate than the parametric n^{? 1/2}-rate.     

On implementation of the Gibbs sampler for estimating the accuracy of multiple diagnostic tests

Implementation of the Gibbs sampler for estimating the accuracy of multiple binary diagnostic tests in one population has been investigated. This method, proposed by Joseph, Gyorkos and Coupal, makes use of a Bayesian approach and is used in the absence of a gold standard to estimate the prevalence, the sensitivity and specificity of medical diagnostic tests. The expressions that allow this method to be implemented for an arbitrary number of tests are given. By using the convergence diagnostics procedure of Raftery and Lewis, the relation between the number of iterations of Gibbs sampling and the precision of the estimated quantiles of the posterior distributions is derived. An example concerning a data set of gastro-esophageal reflux disease patients collected to evaluate the accuracy of the water siphon test compared with 24 h pH-monitoring, endoscopy and histology tests is presented. The main message that emerges from our analysis is that implementation of the Gibbs sampler to estimate the parameters of multiple binary diagnostic tests can be critical and convergence diagnostic is advised for this method. The factors which affect the convergence of the chains to the posterior distributions and those that influence the precision of their quantiles are analyzed.     

A bayesian approach to a reliability problem: Theory,analysis and interesting numerics

We consider approximate Bayesian inference about the quantity R = P[Y₂> Y₁] when both the random variables Y₁, Y₂ have expectations that depend on certain explanatory variables. Our interest centers on certain characteristics of the posterior of R under Jeffreys's prior, such as its mean, variance and percentiles. Since the posterior of R is not available in closed form, several approximation procedures are introduced, and their relative performance is assessed using two real datasets.