Comparison of correlated proportions based on paired binary data from clustered samples

In this article, we explore hypothesis testing problems related to correlated proportions from clustered matched-pair binary data. Null hypotheses of equality in proportions, homogeneity, and non-inferiority of one to another are similar testing problems of linear contrasts of correlated proportions with suitable transformation. The covariance estimators of the test statistics are based on moment estimation under the null hypotheses. We present a general framework for testing linear contrasts of the correlated proportions from clustered matched-pair data based upon a class of unbiased estimators of the proportions. The corresponding testing procedures do not impose structure assumptions on the correlation matrix and are easy to use. Simulation results suggest that the proposed method is more likely to maintain the proper significance level and to improve power than the test proposed by Obuchowski.     

Exact methods for testing homogeneity of proportions for multiple groups of paired binary data

We consider four exact procedures to test the homogeneity of proportions for correlated multiple clustered data. Exact procedures are compared with the asymptotic approach based on the score statistic. We use a real example from a double-blind clinical trial studying the treatment of otitis media to illustrate the various test procedures and provide extensive numerical studies to compare procedures with regards to Type I error rates and powers under the unconditional framework. The exact unconditional procedure based on estimation followed by maximization is generally more powerful than other procedures.     

Testing homogeneity of difference of two proportions for stratified correlated paired binary data

In ophthalmologic or otolaryngologic study, each subject may contribute paired organs measurements to the analysis. A number of statistical methods have been proposed on bilateral correlated data. In practice, it is important to detect confounding effect by treatment interaction, since ignoring confounding effect may lead to unreliable conclusion. Therefore, stratified data analysis can be considered to adjust the effect of confounder on statistical inference. In this article, we investigate and derive three test procedures for testing homogeneity of difference of two proportions for stratified correlated paired binary data in the basis of equal correlation model assumption. The performance of proposed test procedures is examined through Monte Carlo simulation. The simulation results show that the Score test is usually robust on type I error control with high power, and therefore is recommended among the three methods. One example from otolaryngologic study is given to illustrate the three test procedures.     

Testing the homogeneity of risk differences with sparse count data

ABSTRACT

In this paper, we consider testing the homogeneity of risk differences in independent binomial distributions especially when data are sparse. We point out some drawback of existing tests in either controlling a nominal size or obtaining powers through theoretical and numerical studies. The proposed test is designed to avoid the drawbacks of existing tests. We present the asymptotic null distribution and asymptotic power function for the proposed test. We also provide numerical studies including simulations and real data examples showing the proposed test has reliable results compared to existing testing procedures.     

Inference on effect size indices from several two-armed experiments

The statistical inference problem on effect size indices is addressed using a series of independent two-armed experiments from k arbitrary populations. The effect size parameter simply quantifies the difference between two groups. It is a meaningful index to be used when data are measured on different scales. In the context of bivariate statistical models, we define estimators of the effect size indices and propose large sample testing procedures to test the homogeneity of these indices. The null and non-null distributions of the proposed testing procedures are derived and their performance is evaluated via Monte Carlo simulation. Further, three types of interval estimation of the proposed indices are considered for both combined and uncombined data. Lower and upper confidence limits for the actual effect size indices are obtained and compared via bootstrapping. It is found that the length of the intervals based on the combined effect size estimator are almost half the length of the intervals based on the uncombined effect size estimators. Finally, we illustrate the proposed procedures for hypothesis testing and interval estimation using a real data set.     

Improved tests for homogeneity of variances

Equality of variances is one of the key assumptions of analysis of variances (ANOVA). There are several testing procedures available to validate this assumption, but it is rare to find a test procedure which controls the type I error rate while providing high statistical power. In this article, we introduce a bootstrap test based on the ratio of mean absolute deviances (RMD). We also propose a two-stage testing procedure where we first quantify the skewness of the distributions and then choose an appropriate test for homogeneity of variances. The performances of these test procedures are studied via a simulation study.     

Performance of and software for a modified mantel-haenszel statistic for correlated data

This paper presents the results of a small sample simulation study designed to evaluate the performance of a recently proposed test statistic for the analysis of correlated binary data. The new statistic is an adjusted Mantel-Haenszel test, which may be used in testing for association between a binary exposure and a binary outcome of interest across several fourfold tables when the data have been collected under a cluster sampling design. Al- though originally developed for the analysis of periodontal data, the proposed method may be applied to clustered binary data arising in a variety of settings, including longitu- dinal studies, family studies, and school-based research. The features of the simulation are intended to mimic those of a research study of periodontal health, in which a large number of observations is made on each of a relatively small number of patients. The simulation reveals that the adjusted test statistic performs well in finite samples, having empirical type I error rates close to nominal and empirical power similar to that of more complicated marginal regression methods. Software for computing the adjusted statistic is also provided.     

Notes on Test Homogeneity of the Odds Ratio in Matched Pairs Under Stratified Sampling: A Monte Carlo Evaluation

Using Monte Carlo simulation, we compare the performance of five asymptotic test procedures and a randomized permutation test procedure for testing the homogeneity of odds ratio under the stratified matched-pair design. We note that the weighted-least-square test procedure is liberal, while Pearson's goodness-of-fit (PGF) test procedure with the continuity correction is conservative. We note that PGF without the continuity correction, the conditional likelihood ratio test procedure, and the randomized permutation test procedure can generally perform well with respect to Type I error. We use the data taken from a case–control study regarding the endometrial cancer incidence published elsewhere to illustrate the use of these test procedures.     

Testing for violations of the homogeneity needed for conditional logistic regression

In epidemiologic studies where the outcome is binary, the data often arise as clusters, as when siblings, friends or neighbors are used as matched controls in a case-control study. Conditional logistic regression (CLR) is typically used for such studies to estimate the odds ratio for an exposure of interest. However, CLR assumes the exposure coefficient is the same in every cluster, and CLR-based inference can be badly biased when homogeneity is violated. Existing methods for testing goodness-of-fit for CLR are not designed to detect such violations. Good alternative methods of analysis exist if one suspects there is heterogeneity across clusters. However, routine use of alternative robust approaches when there is no appreciable heterogeneity could cause loss of precision and be computationally difficult, particularly if the clusters are small. We propose a simple non-parametric test, the test of heterogeneous susceptibility (THS), to assess the assumption of homogeneity of a coefficient across clusters. The test is easy to apply and provides guidance as to the appropriate method of analysis. Simulations demonstrate that the THS has reasonable power to reveal violations of homogeneity. We illustrate by applying the THS to a study of periodontal disease.     

Order restricted inference for multivariate binary data with application to toxicology

In many applications researchers collect multivariate binary response data under two or more, naturally ordered, experimental conditions. In such situations one is often interested in using all binary outcomes simultaneously to detect an ordering among the experimental conditions. To make such comparisons we develop a general methodology for testing for the multivariate stochastic order between K ≥ 2 multivariate binary distributions. The proposed test uses order restricted estimators which, according to our simulation study, are more efficient than the unrestricted estimators in terms of mean squared error. The power of the proposed test was compared with several alternative tests. These included procedures which combine individual univariate tests for order, such as union intersection tests and a Bonferroni based test. We also compared the proposed test with unrestricted Hotelling's T(2) type test. Our simulations suggest that the proposed method competes well with these alternatives. The gain in power is often substantial. The proposed methodology is illustrated by applying it to a two-year rodent cancer bioassay data obtained from the US National Toxicology Program (NTP). Supplemental materials are available online.     

Tests for homogeneity of variance

Six procedures which convert tests of homogeneity of variance into tests for mean equality for independent groups are compared. The tests are the analysis of variance (ANOVA) and Welch F statistics. The Welch statistics are included since it was anticipated that ANOVA would not provide a robust test when samples of unequal sizes are obtained from non-normal populations. However, the Welch tests are not found to be uniformly preferrable. In addition, a prior recommendation for Miller's jackknife procedure is not supported for the unequal sample size case. The data indicates that the current tests for variance heterogeneity are either sensitive to non-normality or, if robust, lacking in power. Therefore, these tests cannot be recommended for the purpose of testing the validity of the ANOVA homogeneity assumption.     

Estimation and test of several multivariate normal means under an order restriction when the dimension is larger than two

Suppose that an order restriction is imposed among several p-variate normal mean vectors. We are interested in the problems of estimating these mean vectors and testing their homogeneity under this restriction. These problems are multivariate extensions of Bartholomew's (1959) ones. For the bivariate case, these problems have been studied by Sasabuchi et al. (1983) and (1998) and some others. In the present paper we examine the convergence of an iterative algorithm for computing the maximum likelihood estimator when p is larger than two. We also study some test procedures for testing homogeneity when p is larger than two.     

Diagonal latent block model for binary data

This paper addresses the problem of co-clustering binary data in the latent block model framework with diagonal constraints for resulting data partitions. We consider the Bernoulli generative mixture model and present three new methods differing in the assumptions made about the degree of homogeneity of diagonal blocks. The proposed models are parsimonious and allow to take into account the structure of a data matrix when reorganizing it into homogeneous diagonal blocks. We derive algorithms for each of the presented models based on the classification expectation-maximization algorithm which maximizes the complete data likelihood. We show that our contribution can outperform other state-of-the-art (co)-clustering methods on synthetic sparse and non-sparse data. We also prove the efficiency of our approach in the context of document clustering, by using real-world benchmark data sets.     

Clustering and classification problems in genetics through U-statistics

ABSTRACT

Genetic data are frequently categorical and have complex dependence structures that are not always well understood. For this reason, clustering and classification based on genetic data, while highly relevant, are challenging statistical problems. Here we consider a versatile U-statistics-based approach for non-parametric clustering that allows for an unconventional way of solving these problems. In this paper we propose a statistical test to assess group homogeneity taking into account multiple testing issues and a clustering algorithm based on dissimilarities within and between groups that highly speeds up the homogeneity test. We also propose a test to verify classification significance of a sample in one of two groups. We present Monte Carlo simulations that evaluate size and power of the proposed tests under different scenarios. Finally, the methodology is applied to three different genetic data sets: global human genetic diversity, breast tumour gene expression and Dengue virus serotypes. These applications showcase this statistical framework's ability to answer diverse biological questions in the high dimension low sample size scenario while adapting to the specificities of the different datatypes.     

Testing for structural change in cointegrated regression models: some comparisons and generalizations

This paper compares and generalizes some testing procedures for structural change in the context of cointegrated regression models. The Lagrange Multiplier (LM) tests proposod by Hansen (1992) are generalized to testing for partial structural change. An exponential average LM test is also suggested following the idea of Andrews and Ploberger (1992). In particular, an optimal test for cointegration is developed. We also propose a new cointegration test which is robust to a possible one-time discrete jump in the intercept. We tabulate the asymptotic critical values for the above tests and conduct a small Monte Carlo simulation to investigate their finite sample performance.     

Testing for structural change in cointegrated regression models: some comparisons and generalizations

This paper compares and generalizes some testing procedures for structural change in the context of cointegrated regression models. The Lagrange Multiplier (LM) tests proposod by Hansen (1992) are generalized to testing for partial structural change. An exponential average LM test is also suggested following the idea of Andrews and Ploberger (1992). In particular, an optimal test for cointegration is developed. We also propose a new cointegration test which is robust to a possible one-time discrete jump in the intercept. We tabulate the asymptotic critical values for the above tests and conduct a small Monte Carlo simulation to investigate their finite sample performance.     

Non parametric multiple comparisons of non nested rival models

The practice for testing homogeneity of several rival models is of interest. In this article, we consider a non parametric multiple test for non nested distributions in the context of the model selection. Based on the linear sign rank test, and the known union–intersection principle, we let the magnitude of the data to give a better performance to the test statistic. We consider the sample and the non nested rival models as blocks and treatments, respectively, and introduce the extended Friedman test version to compare with the results of the test based on the linear sign rank test. A real dataset based on the waiting time to earthquake is considered to illustrate the results.     

On sequential closed testing dose groups with a control

Methods for a sequential test of a dose-response effect in pre-clinical studies are investigated. The objective of the test procedure is to compare several dose groups with a zero-dose control. The sequential testing is conducted within a closed family of one-sided tests. The procedures investigated are based on a monotonicity assumption. These closed procedures strongly control the familywise error rate while providing information about the shape of the dose-responce relationship. Performance of sequential testing procedures are compared via a Monte Carlo simulation study. We illustrae the procedures by application to a real data set.     

Hypothesis Testing for Various Familial Dependence Structures

This work compares various hypothesis testing procedures in the case of familial clustered data. Specifically, we use likelihood ratio and Wald's tests for maximum likelihood estimators, and Wald-type tests for moment and quasi-least squares estimators. Using simulations, we estimate significance levels for various hypotheses concerning the one-parent auto-regressive and two-parent equi-correlated dependence structures. We show that the likelihood ratio test performs best for certain simple hypotheses in the one-parent case, whereas the Wald-type test for the quasi-least squares procedure is optimal in the more complex two-parent case.     

Power and stability comparisons of multiple testing procedures with false discovery rate control

High-throughput data analyses are widely used for examining differential gene expression, identifying single nucleotide polymorphisms, and detecting methylation loci. False discovery rate (FDR) has been considered a proper type I error rate to control for discovery-based high-throughput data analysis. Various multiple testing procedures have been proposed to control the FDR. The power and stability properties of some commonly used multiple testing procedures have not been extensively investigated yet, however. Simulation studies were conducted to compare power and stability properties of five widely used multiple testing procedures at different proportions of true discoveries for various sample sizes for both independent and dependent test statistics. Storey's two linear step-up procedures showed the best performance among all tested procedures considering FDR control, power, and variance of true discoveries. Leukaemia and ovarian cancer microarray studies were used to illustrate the power and stability characteristics of these five multiple testing procedures with FDR control.