Bayesian P-Values for Testing Independence in 2 × 2 Contingency Tables

This article considers Bayesian p-values for testing independence in 2 × 2 contingency tables with cell counts observed from the two independent binomial sampling scheme and the multinomial sampling scheme. From the frequentist perspective, Fisher's p-value (p _F ) is the most commonly used p-value but it can be conservative for small to moderate sample sizes. On the other hand, from the Bayesian perspective, Bayarri and Berger (2000 Bayarri , M. J. , Berger , J. O. ( 2000 ). P-values for composite null models (with discussion) . J. Amer. Statist. Assoc. 95 : 1127 – 1170 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) first proposed the partial posterior predictive p-value (p _PPOST ), which can avoid the double use of the data that occurs in another Bayesian p-value proposed by Guttman (1967 Guttman , I. ( 1967 ). The use of the concept of a future observation in goodness-of-fit problems . J. Roy. Statist. Soc. Ser. B 29 : 83 – 100 . [Google Scholar]) and Rubin (1984 Rubin , D. B. ( 1984 ). Bayesianly justifiable and relevant frequency calculations for the applied statistician . Ann. Statist. 12 : 1151 – 1172 .[Crossref], [Web of Science ®] , [Google Scholar]), called the posterior predictive p-value (p _POST ). The subjective and objective Bayesian p-values in terms of p _POST and p _PPOST are derived under the beta prior and the (noninformative) Jeffreys prior, respectively. Numerical comparisons among p _F , p _POST , and p _PPOST reveal that p _PPOST performs much better than p _F and p _POST for small to moderate sample sizes from the frequentist perspective.     

Improved P-Values for Testing Marginal Homogeneity in 2 × 2 Contingency Tables

This article considers the problem of testing marginal homogeneity in a 2 × 2 contingency table. We first review some well-known conditional and unconditional p-values appeared in the statistical literature. Then we treat the p-value as the test statistic and use the unconditional approach to obtain the modified p-value, which is shown to be valid. For a given nominal level, the rejection region of the modified p-value test contains that of the original p-value test. Some nice properties of the modified p-value are given. Especially, under mild conditions the rejection region of the modified p-value test is shown to be the Barnard convex set as described by Barnard (1947 Barnard , G. A. ( 1947 ). Significance tests for 2 × 2 tables . Biometrika 34 : 123 – 138 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]). If the one-sided null hypothesis has two nuisance parameters, we show that this result can reduce the dimension of the nuisance parameter space from two to one for computing modified p-values and sizes of tests. Numerical studies including an illustrative example are given. Numerical comparisons show that the sizes of the modified p-value tests are closer to a nominal level than those of the original p-value tests for many cases, especially in the case of small to moderate sample sizes.     

Wilson Confidence Intervals for the Two-Sample Log-Odds-Ratio in Stratified 2 × 2 Contingency Tables

Large-sample Wilson-type confidence intervals (CIs) are derived for a parameter of interest in many clinical trials situations: the log-odds-ratio, in a two-sample experiment comparing binomial success proportions, say between cases and controls. The methods cover several scenarios: (i) results embedded in a single 2 × 2 contingency table; (ii) a series of K 2 × 2 tables with common parameter; or (iii) K tables, where the parameter may change across tables under the influence of a covariate. The calculations of the Wilson CI require only simple numerical assistance, and for example are easily carried out using Excel. The main competitor, the exact CI, has two disadvantages: It requires burdensome search algorithms for the multi-table case and results in strong over-coverage associated with long confidence intervals. All the application cases are illustrated through a well-known example. A simulation study then investigates how the Wilson CI performs among several competing methods. The Wilson interval is shortest, except for very large odds ratios, while maintaining coverage similar to Wald-type intervals. An alternative to the Wald CI is the Agresti-Coull CI, calculated from the Wilson and Wald CIs, which has same length as the Wald CI but improved coverage.     

The Maximum Probability 2 × c Contingency Tables and the Maximum Probability Points of the Multivariate Hypergeometric Distribution

Abstract

The problem of obtaining the maximum probability 2 × c contingency table with fixed marginal sums, R  = (R ₁, R ₂) and C  = (C ₁, … , C _c ), and row and column independence is equivalent to the problem of obtaining the maximum probability points (mode) of the multivariate hypergeometric distribution MH(R ₁; C ₁, … , C _c ). The most simple and general method for these problems is Joe's (Joe, H. (1988 Joe, H. 1988. Extreme probabilities for contingency tables under row and column independence with application to Fisher's exact test. Commun. Statist. Theory Meth., 17(11): 3677–3685. [Taylor & Francis Online], [Web of Science ®] , [Google Scholar]). Extreme probabilities for contingency tables under row and column independence with application to Fisher's exact test. Commun. Statist. Theory Meth. 17(11):3677–3685.) In this article we study a family of MH's in which a connection relationship is defined between its elements. Based on this family and on a characterization of the mode described in Requena and Martín (Requena, F., Martín, N. (2000 Requena, F. and Martín, N. 2000. Characterization of maximum probability points in the multivariate hypergeometric distribution. Statist. Probab. Lett., 50: 39–47.  [Google Scholar]). Characterization of maximum probability points in the multivariate hypergeometric distribution. Statist. Probab. Lett. 50:39–47.), we develop a new method for the above problems, which is completely general, non recursive, very simple in practice and more efficient than the Joe's method. Also, under weak conditions (which almost always hold), the proposed method provides a simple explicit solution to these problems. In addition, the well-known expression for the mode of a hypergeometric distribution is just a particular case of the method in this article.     

Tables for the Lilliefors and Modified Cramer–von Mises Tests of Normality

We present new tabulations of the Lilliefors distribution and the modified Cramer–von Mises distribution, which are used to test for normality when the population mean and variance are unknown. Some practical remarks and an example are given.     

Chance-Corrected Measures of Reliability and Validity in 2 × 2 Tables

It is customary to use two groups of indices to evaluate a diagnostic method with a binary outcome: validity indices with a standard rater (sensitivity, specificity, and positive or negative predictive values) and reliability indices (positive, negative and overall agreements) without a standard rater. However neither of these classic indices is chance-corrected, and this may distort the analysis of the problem (especially in comparative studies). One way of chance-correcting these indices is by using the Delta model (an alternative to the Kappa model), but this means having to use a computer program to work out the calculations. This paper gives an asymptotic version of the Delta model, thus allowing simple expressions to be obtained for the estimator of each of the above-mentioned chance-corrected indices (as well as for its standard error).     

Simultaneous Logit-Based Confidence Intervals for Odds Ratios in 2 × k Classification Tables with a Fixed Reference Level

In this article, we consider the problem of constructing simultaneous confidence intervals for odds ratios in 2 × k classification tables with a fixed reference level. We discuss six methods designed to control the familywise error rate and investigate these methods in terms of simultaneous coverage probability and mean interval length. We illustrate the importance and the implementation of these methods using two {sc hiv} public health studies.     

Tests of significance for the odds ratio in a 2×2 table based on the ratio of two independent F-variates

Following Gart (1966) a test of significance for the odds ratio in a 2×2 table is developed based on a semi-empirical method of approximating discrete distributions by their continuous analogues. The distribution of the test statistic (W), the ratio of two independent F-variates, is derived. This approximate technique is compared with the "exact" test, uncorrected X test, and a normal approximation based on lnW.     

Exact distributions associated with an i×j×k contingency table

In this paper an exact distributional framework is developed for analysing an IxJxK contingency table. It is shown that for the case of hypotheses H₀:P_ijk=P_i..P._j./K and H₀:P_ijk =P_i..P._j.P.._k the exact distributional results do not follow as simple extensions of the corresponding results obtained for an I×J table under the hypothesis of independence. From the factorial moment generating functions, expressions for the covariance matrices in terms of the Kronecker products of matrices, are presented. These expressions give indications whether or not Pearson's chi-square statistic should be corrected by the factor (n?1)/n or not. Marginal and conditional distributions are considered briefly and important differences with regard to the resuits for marginal and conditional distributions for an IxJ table are mentioned.     

Simple,exact inference for 2 × 2 tables

Exact inference for odds-ratio tests and confidence intervals relies on sophisticated algorithms, typically found only in the specialize software. This tends to discourage the use of exact methods in the analyses of 2 × 2 tables. We show that by first devolving each corresponding hypergeometric random variable into independent Bernoulli variates, simple and efficient algorithms emerge that are easily programmed in the commonly available software.     

Multiplicative-interaction logit models for i×j×2 three-way tables

Multiplicative-interaction (M-I) logit models are proposed for three-way IxJx2 contingency tables where the third variable constitutes a binary response. Models are derived by assigning unknown scores to the categories and forming product interactions from them. Asymptotic results under special sampling constraints are derived for maximum likelihood estimates and the goodness-of-fit statistics. The class of models proposed in this paper are found to be useful when no obvious scores are available. An example is included.     

Homogeneity Test of Risk Differences of Marginal and Conditional Probabilities in Several Incomplete Correlated 2 × 2 Tables

This article considers K pairs of incomplete correlated 2 × 2 tables in which the interesting measurement is the risk difference between marginal and conditional probabilities. A Wald-type statistic and a score-type statistic are presented to test the homogeneity hypothesis about risk differences across strata. Powers and sample size formulae based on the above two statistics are deduced. Figures about sample size against risk difference (or marginal probability) are given. A real example is used to illustrate the proposed methods.     

Odds ratio for a single 2 × 2 table with correlated binomials for two margins

While analyzing 2 × 2 contingency tables, the log odds ratio for measuring the strength of association is often approximated by a normal distribution with some variance. We show that the expression of that variance needs to be modified in the presence of correlation between two binomial distributions of the contingency table. In the present paper, we derive a correlation-adjusted variance of the limiting normal distribution of log odds ratio. We also propose a correlation adjusted test based on the standard odds ratio for analyzing matched-pair studies and any other study settings that induce correlated binary outcomes. We demonstrate that our proposed test outperforms the classical McNemar’s test. Simulation studies show the gains in power are especially manifest when sample size is small and strong correlation is present. Two examples of real data sets are used to demonstrate that the proposed method may lead to conclusions significantly different from those reached using McNemar’s test.     

Structural properties of UMPU-tests for 2×2 tables and some applications

The paper is concerned with structural properties of the acceptance regions of uniformly most powerful unbiased tests (UMPU-tests) for one- and two-sided hypotheses for 2×2 tables as, for instance, the comparison of two proportions or testing for association. These tests can be considered as randomized versions of Fisher's exact tests. A series of monotonicity and unimodality properties will be proved. These properties are equivalent to a symmetry and convexity condition often required for powerful unconditional tests. Knowledge of such properties allows a fast and in some sense recursive calculation of the critical values of the UMPU-tests which is important if a repeated calculation of all critical values for different sample sizes or different levels is required. This is, for example, the case if the unconditional power has to be controlled over a certain subset of the alternative, or, if one is interested in powerful unconditional non-randomized tests generated by a UMPU-test. Our results also imply some useful properties of the two-dimensional unconditional power function. On the other hand, we found some less nice properties of the UMPU-tests, too.     

A new C(α) test for 2×2 tables

Two by two contingency tables which arise from experiments in which each subject serves as a self control are examined, Two types of experimental design are discussed: the confounded design and the counterbalanced design. In the case of the counterbalanced design, the locally asymptotically optimal C(α) test is compared with the binomial test for symmetry in a 2×2 contingency table. The binomial test is found to be less efficient than the C(α) test.     

Inference using attributable risk for a 2×2 case–control study

Asymptotic variance plays an important role in the inference using interval estimate of attributable risk. This paper compares asymptotic variances of attributable risk estimate using the delta method and the Fisher information matrix for a 2×2 case–control study due to the practicality of applications. The expressions of these two asymptotic variance estimates are shown to be equivalent. Because asymptotic variance usually underestimates the standard error, the bootstrap standard error has also been utilized in constructing the interval estimates of attributable risk and compared with those using asymptotic estimates. A simulation study shows that the bootstrap interval estimate performs well in terms of coverage probability and confidence length. An exact test procedure for testing independence between the risk factor and the disease outcome using attributable risk is proposed and is justified for the use with real-life examples for a small-sample situation where inference using asymptotic variance may not be valid.     

Optimal correction for continuity in the chi-squared test in 2×2 tables

The most common asymptotic procedure for analyzing a 2 × 2 table (under the conditioning principle) is the ‰ chi-squared test with correction for continuity (c.f.c). According to the way this is applied, up to the present four methods have been obtained: one for one-tailed tests (Yates') and three for two-tailed tests (those of Mantel, Conover and Haber). In this paper two further methods are defined (one for each case), the 6 resulting methods are grouped in families, their individual behaviour studied and the optimal is selected. The conclusions are established on the assumption that the method studied is applied indiscriminately (without being subjected to validity conditions), and taking a basis of 400,000 tables (with the values of sample size n between 20 and 300 and exact P-values between 1% and 10%) and a criterion of evaluation based on the percentage of times in which the approximate P-value differs from the exact (Fisher's exact test) by an excessive amount. The optimal c.f.c. depends on n, on E (the minimum quantity expected) and on the error α to be used, but the rule of selection is not complicated and the new methods proposed are frequently selected. In the paper we also study what occurs when E ≥ 5, as well as whether the chi-squared by factor (n-1).     

Minimal Markov Basis for Tests of Main Effect Models for 2p-1 Fractional Factorial Designs of Resolution p

We consider conditional exact tests of factor effects in design of experiments for discrete response variables. Similarly to the analysis of contingency tables, Markov chain Monte Carlo methods can be used to perform exact tests, especially when large-sample approximations of the null distributions are poor and the enumeration of the conditional sample space is infeasible. In order to construct a connected Markov chain over the appropriate sample space, one approach is to compute a Markov basis. Theoretically, a Markov basis can be characterized as a generator of a well-specified toric ideal in a polynomial ring and is computed by computational algebraic software. However, the computation of a Markov basis sometimes becomes infeasible, even for problems of moderate sizes. In the present article, we obtain the closed-form expression of minimal Markov bases for the main effect models of 2^{p ? 1} fractional factorial designs of resolution p.