Catanova for Two-Way Contingency Tables with Ordinal Variables Using Orthogonal Polynomials

ABSTRACT

The analysis of variance of cross-classified (categorical) data (CATANOVA) is a technique designed to identify the variation between treatments of interest to the researcher. There are well-established links between CATANOVA and the Goodman and Kruskal tau statistic as well as the Light and Margolin R ² for the purposes of the graphical identification of this variation.

The aim of this article is to present a partition of the numerator of the tau statistic, or equivalently, the BSS measure in the CATANOVA framework, into location, dispersion, and higher order components. Even if a CATANOVA identifies an overall lack of variation, by considering this partition and calculations derived from them, it is possible to identify hidden, but statistically significant, sources of variation.     

Multiscale Bayesian state-space model for Granger causality analysis of brain signal

Modelling time-varying and frequency-specific relationships between two brain signals is becoming an essential methodological tool to answer theoretical questions in experimental neuroscience. In this article, we propose to estimate a frequency Granger causality statistic that may vary in time in order to evaluate the functional connections between two brain regions during a task. We use for that purpose an adaptive Kalman filter type of estimator of a linear Gaussian vector autoregressive model with coefficients evolving over time. The estimation procedure is achieved through variational Bayesian approximation and is extended for multiple trials. This Bayesian State Space (BSS) model provides a dynamical Granger-causality statistic that is quite natural. We propose to extend the BSS model to include the à trous Haar decomposition. This wavelet-based forecasting method is based on a multiscale resolution decomposition of the signal using the redundant à trous wavelet transform and allows us to capture short- and long-range dependencies between signals. Equally importantly it allows us to derive the desired dynamical and frequency-specific Granger-causality statistic. The application of these models to intracranial local field potential data recorded during a psychological experimental task shows the complex frequency-based cross-talk between amygdala and medial orbito-frontal cortex.     

Testing equality of proportions with incomplete correlated data

Let (ψ_i,φ_i) be independent, identically distributed pairs of zero-one random variables with (possible) dependence of ψ_i and φ_i within the pair. For n pairs, both variables are observed, but for m₁ additional pairs only ψ_i is observed and for m₂ others φ_i is observed. If π_1· = P{ψ_i = 1} and π_·1=P{φ_i, the problem is to test π_1·=π_·1. Maximum likelihood estimates of π_1· and π_·1 are obtained via the EM algorithm. A test statistic is developed whose null distribution is asymptotically chi-square with one degree of freedom (as n and either m₁ or m₂ tend to infinity). If m₁ = m₂ = 0 the statistic reduces to that of McNemar's test; if n = 0, it is equivalent to the statistic for testing equality of two independent proportions. This test is compared with other tests by means of Pitman efficiency. Examples are presented.     

Correspondence Analysis of Cumulative Frequencies Using a Decomposition of Taguchi's Statistic

Taguchi's statistic has long been known to be a more appropriate measure of association for ordinal variables than the Pearson chi-squared statistic. Therefore, there is some advantage in using Taguchi's statistic for performing correspondence analysis when a two-way contingency table consists of one ordinal categorical variable. This article will explore the development of correspondence analysis using a decomposition of Taguchi's statistic.     

Cumulative correspondence analysis using orthogonal polynomials

Taguchi's statistic has long been known to be a more appropriate measure of association of the dependence for ordinal variables compared to the Pearson chi-squared statistic. Therefore, there is some advantage in using Taguchi's statistic in the correspondence analysis context when a two-way contingency table consists at least of an ordinal categorical variable. The aim of this paper, considering the contingency table with two ordinal categorical variables, is to show a decomposition of Taguchi's index into linear, quadratic and higher-order components. This decomposition has been developed using Emerson's orthogonal polynomials. Moreover, two case studies to explain the methodology have been analyzed.     

Tolerance intervals for exponentiated scale family of distributions

In this article we provide an asymptotic upper β-expectation and β-content γ-level tolerance intervals for a new family of distributions, namely the Exponentiated Scale family of distributions. Expected coverage of a proposed β-expectation Tolerance Interval is obtained. Bootstrap-based tolerance limits are obtained for data arising from an exponentiated exponential distribution.     

A comparative study of correlation coefficients in spatially MRSI-observed neurochemicals from multiple sclerosis patients

In measuring the association between magnetic resonance spectroscopic imaging (MRSI)-observed neurochemicals from multiple sclerosis (MS) patients, the classic correlation coefficients such as the Pearson's r, Spearman's ρand Kendall's τdo not take into account the spatial dependence of the observations. This paper reports a comparative study on these classic correlation coefficients (Pearson's r, Spearman's ρand Kendall's τ) and some more recent correlation coefficients (Tjostheim's a, the modified t) that take into account the spatial dependence of the intensities of the concentrations of several neurochemicals in MS patients. Our study indicates that the use of the classic correlation coefficients that ignores the spatial dependence of the observations may overestimate the statistical significance of the results.     

A note on the Zhang omnibus test for normality based on the Q statistic

A discussion about the estimators proposed by Zhang (1999) for the true standard deviation σof a normal distribution is presented. Those estimators, called by Zhang q 1 and q 2 , are functions of the expected values of the order statistics from a standard normal distribution and they were the basis of the Q statistic used in the derivation of a new test for normality proposed by Zhang. Although the type I error and the power of the test was discussed by Zhang, no study was performed to test the reliability of q 1 and q 2 as estimators of σ. In this paper, it is shown that q 1 is a very poor estimator for σespecially when σis large. On the other hand, the estimator q 2 has a performance very similar to the well-known sample standard deviation S. When some correlation is introduced among the sample units it can be seen that the estimator q 1 is much more affected than the estimators q 2 and S.     

Catanova for multidimensional contingency tables: Nominal-scale response

This paper extends an analysis of variance for categorical data (CATANOVA) procedure to multidimensional contingency tables involving several factors and a response variable measured on a nominal scale. Using an appropriate measure of total variation for multinomial data, partial and multiple association measures are developed as R² quantities which parallel the analogous statistics in multiple linear regression for quantitative data. In addition, test statistics are derived in terms of these R² criteria. Finally, this CATANOVA approach is illustrated within the context of 2 three-way contingency table from a multicenter clinicaltrial.     

Testing equality of mean vectors in a one-way MANOVA with monotone missing data

In this study, testing the equality of mean vectors in a one-way multivariate analysis of variance (MANOVA) is considered when each dataset has a monotone pattern of missing observations. The likelihood ratio test (LRT) statistic in a one-way MANOVA with monotone missing data is given. Furthermore, the modified test (MT) statistic based on likelihood ratio (LR) and the modified LRT (MLRT) statistic with monotone missing data are proposed using the decomposition of the LR and an asymptotic expansion for each decomposed LR. The accuracy of the approximation for the Chi-square distribution is investigated using a Monte Carlo simulation. Finally, an example is given to illustrate the methods.     

Simple and multiple correspondence analysis for ordinal-scale variables using orthogonal polynomials

Correspondence analysis (CA) has gained a reputation for being a very useful statistical technique for determining the nature of association between two or more categorical variables. For simple and multiple CA, the singular value decomposition (SVD) is the primary tool used and allows the user to construct a low-dimensional space to visualize this association. As an alternative to SVD, one may consider the bivariate moment decomposition (BMD), a method of decomposition that involves using orthogonal polynomials to reflect the structure of ordered categorical responses. When the features of BMD are combined with SVD, a hybrid decomposition (HD) is formed. The aim of this paper is to show the applicability of HD when performing simple and multiple CA.     

Bayesian optimization analysis with ML-II ε-contaminated prior

In this paper we derive the predictive density function of a future observation when prior distribution for unknown mean of a normal population is a Type-II maximum likelihood ε-contaminated prior. The derived predictive distribution is applied to the problem of optimization of a regression nature in the decisive prediction framework.     

Random stopping sets in a sequential analysis of random measures and fields

A random stopping set is defined and some of its properties are proved. Namely, we prove the theorem on the absolute continuity of measures on a σ-algebra F_τ connected with a random stopping set τ, which can be applied to the sequential analysis of random measures and fields.     

An Improved Method on Wilcoxon Rank Sum Test for Gene Selection from Microarray Experiments

Selecting a small subset out of the thousands of genes in microarray data is important for accurate classification of phenotypes. In this paper, we propose a flexible rank-based nonparametric procedure for gene selection from microarray data. In the method we propose a statistic for testing whether area under receiver operating characteristic curve (AUC) for each gene is equal to 0.5 allowing different variance for each gene. The contribution to this “single gene” statistic is the studentization of the empirical AUC, which takes into account the variances associated with each gene in the experiment. Delong et al. proposed a nonparametric procedure for calculating a consistent variance estimator of the AUC. We use their variance estimation technique to get a test statistic, and we focus on the primary step in the gene selection process, namely, the ranking of genes with respect to a statistical measure of differential expression. Two real datasets are analyzed to illustrate the methods and a simulation study is carried out to assess the relative performance of different statistical gene ranking measures. The work includes how to use the variance information to produce a list of significant targets and assess differential gene expressions under two conditions. The proposed method does not involve complicated formulas and does not require advanced programming skills. We conclude that the proposed methods offer useful analytical tools for identifying differentially expressed genes for further biological and clinical analysis.     

Self-affine time series: measures of weak and strong persistence

In this paper, we examine self-affine time series and their persistence. Time series are defined to be self-affine if their power-spectral density scales as a power of their frequency. Persistence can be classified in terms of range, short or long range, and in terms of strength, weak or strong. Self-affine time series are scale-invariant, thus they always exhibit long-range persistence. Synthetic self-affine time series are generated using the Fourier power-spectral method. We generate fractional Gaussian noises (fGns), −1β1, where β is the power-spectral exponent. These are summed to give fractional Brownian motions (fBms), 1β3, where the series are self-affine fractals with fractal dimension 1D2; β=2 is a Brownian motion. With β>1, the time series are non-stationary and moments of the time series depend upon its length; with β<1 the time series are stationary. We define self-affine time series with β>1 to have strong persistence and with β<1 to have weak persistence. We use a variety of techniques to quantify the strength of persistence of synthetic self-affine time series with −3β5. These techniques are effective in the following ranges: (1) semivariograms, 1β3, (2) rescaled-range (R/S) analyses, −1β1, (3) Fourier spectral techniques, all values of β, and (4) wavelet variance analyses, all values of β. Wavelet variance analyses lack many of the inherent problems that are found in Fourier power-spectral analysis.     

Randomization procedures for analyzing clinical trial data with treatment related withdrawals

The problem of treatment related withdrawals has not been fully addressed in the statistical literature. Statistical procedures which compare efficacies of treatments when withdrawals may occur prior to the conclusion of a study are discussed. A unified test statistic which incorporates all available data, not just the last values and adjusts for withdrawal patterns, proportion of withdrawals, and level of response prior to withdrawal has been developed with the help of data- dependent scoring schemes. A randomization technique has been developed to compute an empirical significance level for each scoring system under both the Fulldata and Endpoint data for a specified parameter configuration. The proposed methods have been applied to a subset (Allen Park Hospital) of the VA study 127.     

A Remark on the Zhang Omnibus Test for Normality

Zhang (1999) proposed a novel test statistic Q for testing normality based on the ratio of two unbiased standard deviation estimators, q₁ and q₂, for the true population standard deviation σ. Mingoti & Neves (2003) discussed some properties of q₁ and q₂ and showed that the variance of q₁ increases as the true population variance increases. In this paper, we show that the distribution of q₁ is not normal. As a result, normality percentage points for Q are not appropriate. In this paper, percentage points of Q are obtained using simulations. Monte Carlo simulations are provided to evaluate the performance of the new method and Zhang's method.     

A note on a parametric extension of rank tests to the analysis of multifactor experiments within blocks

A general rank test procedure based on an underlying multinomial distribution is suggested for randomized block experiments with multifactor treatment combinations within each block. The Wald statistic for the multinomial is used to test hypotheses about the within–block rankings. This statistic is shown to be related to the one–sample Hotellingt's T² statistic, suggesting a method for computing the test statistic using the standard statistical computer packages.     

A simple diagnostic method of outlier detection for stationary Gaussian time series

In this paper we present a "model free' method of outlier detection for Gaussian time series by using the autocorrelation structure of the time series. We also present a graphic diagnostic method in order to distinguish an additive outlier (AO) from an innovation outlier (IO). The test statistic for detecting the outlier has a χ ² distribution with one degree of freedom. We show that this method works well when the time series contain either one type of the outliers or both additive and innovation type outliers, and this method has the advantage that no time series model needs to be estimated from the data. Simulation evidence shows that different types of outliers can be graphically distinguished by using the techniques proposed.