Bayesian analysis of contingency tables: a simulation and graphics-based approach

In this paper we present a simulation and graphics-based model checking and model comparison methodology for the Bayesian analysis of contingency tables. We illustrate the approach by testing the hypotheses of independence and symmetry on complete and incomplete simulated tables.     

A bayesian test for a two-way contingency table using independence priors

One method of testing for independence in a two-way table is based on the Bayes factor, the ratio of the likelihoods under the independence hypothesis H and the alternative hypothesis H. The main difficulty in this approach is the specification of prior distributions on the composite hypotheses H and H. A new Bayesian test statistic is constructed by using a prior distribution on H that is concentrated about the “independence surface” H. Approximations are proposed which simplify the computation of the test statistic. The values of the Bayes factor are compared with values of statistics proposed by Gunel and Dickey (1974), Good and Crook (1987), and Spiegelhalter and Smith (1982) for a number of two-way tables. This investigation suggests a strong relationship between the new statistic and the p-value.     

Logratio approach to statistical analysis of 2×2 compositional tables

Compositional tables represent a continuous counterpart to well-known contingency tables. Their cells contain quantitatively expressed relative contributions of a whole, carrying exclusively relative information and are popularly represented in proportions or percentages. The resulting factors, corresponding to rows and columns of the table, can be inspected similarly as with contingency tables, e.g. for their mutual independent behaviour. The nature of compositional tables requires a specific geometrical treatment, represented by the Aitchison geometry on the simplex. The properties of the Aitchison geometry allow a decomposition of the original table into its independent and interactive parts. Moreover, the specific case of 2×2 compositional tables allows the construction of easily interpretable orthonormal coordinates (resulting from the isometric logratio transformation) for the original table and its decompositions. Consequently, for a sample of compositional tables both explorative statistical analysis like graphical inspection of the independent and interactive parts or any statistical inference (odds-ratio-like testing of independence) can be performed. Theoretical advancements of the presented approach are demonstrated using two economic applications.     

The Tale of Cochran's Rule: My Contingency Table has so Many Expected Values Smaller than 5, What Am I to Do?

In an informal way, some dilemmas in connection with hypothesis testing in contingency tables are discussed. The body of the article concerns the numerical evaluation of Cochran's Rule about the minimum expected value in r × c contingency tables with fixed margins when testing independence with Pearson's X² statistic using the χ² distribution.     

Universal codes as a basis for time series testing

We suggest a new approach to hypothesis testing for ergodic and stationary processes. In contrast to standard methods, the suggested approach gives a possibility to make tests, based on any lossless data compression method even if the distribution law of the codeword lengths is not known. We apply this approach to the following four problems: goodness-of-fit testing (or identity testing), testing for independence, testing of serial independence and homogeneity testing and suggest nonparametric statistical tests for these problems. It is important to note that practically used so-called archivers can be used for suggested testing.     

Likelihood Ratio Test Against Stochastic Order in Three Way Contingency Tables

Trend tests in dose-response have been central problems in medicine. The likelihood ratio test is often used to test hypotheses involving a stochastic order. Stratified contingency tables are common in practice. The distribution theory of likelihood ratio test has not been full developed for stratified tables and more than two stochastically ordered distributions. Under c strata of m × r tables, for testing the conditional independence against simple stochastic order alternative, this article introduces a model-free test method and gives the asymptotic distribution of the test statistic, which is a chi-bar-squared distribution. A real data set concerning an ordered stratified table will be used to show the validity of this test method.     

Testing independence of several groups of variables

The null distribution of Wilks' likelihood-ratio criterion for testing independence of several groups of variables in a multivariate normal population is derived. Percentage points are tabulated for various values of the sample sizeN and partitions of p, the number of variables. This paper extends Mathai and Katiya's (1979) “sphericity” results and tables.     

Partitioning chi-squape in contingency tables: A teaching approach

A representation of sums and differences of the form 2n log n, the lnn function, is introduced to express likelihood-ratio chi-square test statistics in contingency table analysis. This is a concise explicit form to display when partitioning chi-square statistics in accordance with hierarchical models. The lnn representation gives students insights into the construction of test statistics, and assists in relating identical forms under differing model sets. Hierarchies are presented for independence and equi-probability in two-way tables, for symmetry in correlated square tables, for independence-and-homogeneity of two-way responses across levels of a factor, and for mutual independence in three-way tables, along with relevant partitions of chi-square.     

Convergence rates and powers of six power-divergence statistics for testing independence in 2 by 2 contingency table

Several tests for testing independence of 2 by 2 contingency tables have been proposed over the years. Cressie and Read (1984) identified several of these tests as members of a power-divergence family, and much of the characteristics for these tests are unified. However, the question of which test is best is still not fully understood. This paper provides algorithms for chi-square estimates and investigates the convergence rates and powers of these chi-square tests.     

Extended and updated tables for the Friedman rank test

The Friedman's test is used for assessing the independence of repeated experiments resulting in ranks, summarized as a table of integer entries ranging from 1 to k, with k columns and N rows. For its practical use, the hypothesis testing can be derived either from published tables with exact values for small k and N, or using an asymptotic analytical approximation valid for large N or large k. The quality of the approximation, measured as the relative difference of the true critical values with respect those arising from the asymptotic approximation is simply not known. The literature review shows cases where the wrong conclusion could have been drawn using it, although it may not be the only cause of opposite decisions. By Monte Carlo simulation we conclude that published tables do not cover a large enough set of (k, N) values to assure adequate accuracy. Our proposal is to systematically extend existing tables for k and N values, so that using the analytical approximation for values outside it will have less than a prescribed relative error. For illustration purposes some of the tables have been included in the paper, but the complete set is presented as a source code valid for Octave/Matlab/Scilab etc., and amenable to be ported to other programming languages.     

A Bootstrap Approach for Testing Marginal Independence Between Two Categorical Variables When Subjects Have Repeated Responses

To assess independence in two-way contingency tables, the Pearson chi-square test or Fisher’s exact test are typically used. These tests assume that each subject contributes at most one count to only one table cell (e.g., sex versus blood type). In other situations, each subject may have more than one count contributing to the table and these counts may occur in different cells of the table. One may wish to test independence, adjusting for the within-subject correlation. We provide a simple nonparametric bootstrap approach and assess its performance through simulation studies. The method is illustrated on subjects with multiple mental health presentations to Emergency Departments.     

Tests of independence in incomplete multi-way tables using likelihood functions

Kang (2006) and Kang and Larsen (in press) used the log likelihood function with Lagrangian multipliers for estimation of cell probabilities in two-way incomplete contingency tables. This paper extends results and simulations to three-way and multi-way tables. Numerous studies cross-classify subjects by three or more categorical factors. Constraints on cell probabilities are incorporated through Lagrangian multipliers. Variances of the MLEs are derived from the matrix of second derivatives of the log likelihood with respect to cell probabilities and the Lagrange multiplier. Wald and likelihood ratio tests of independence are derived using the estimates and estimated variances. In simulation results in Kang and Larsen (in press), for data missing at random, maximum likelihood estimation (MLE) produced more efficient estimates of population proportions than either multiple imputation (MI) based on data augmentation or complete case (CC) analysis. Neither MLE nor MI, however, lead to an improvement over CC analysis with respect to power of tests for independence in two-way tables. Results are extended to multidimensional tables with arbitrary patterns of missing data when the variables are recorded on individual subjects. In three-way and higher-way tables, however, there is information relevant for judging independence in partially classified information, as long as two or more variables are jointly observed. Simulations study three-dimensional tables with three patterns of association and two levels of missing information.     

Algebraic Markov Bases and MCMC for Two-Way Contingency Tables

ABSTRACT.  The Diaconis–Sturmfels algorithm is a method for sampling from conditional distributions, based on the algebraic theory of toric ideals. This algorithm is applied to categorical data analysis through the notion of Markov basis. An application of this algorithm is a non-parametric Monte Carlo approach to the goodness of fit tests for contingency tables. In this paper, we characterize or compute the Markov bases for some log-linear models for two-way contingency tables using techniques from Computational Commutative Algebra, namely Gröbner bases. This applies to a large set of cases including independence, quasi-independence, symmetry, quasi-symmetry. Three examples of quasi-symmetry and quasi-independence from Fingleton ( Models of category counts , Cambridge University Press, Cambridge, 1984) and Agresti ( An Introduction to categorical data analysis , Wiley, New York, 1996) illustrate the practical applicability and the relevance of this algebraic methodology.     

Marginal homogeneity,symmetry, and independence

A contingency table of the mc form provides a convenient summary of data when c individuals in a matched set9 each belonging to a different one of c classifications, are identified as belonging to one of m categories, A study in which matched sets (c=3) of 1 case, 1 hospital control, and 1 neighborhood control are classified into one of m=4 occupational categories would be an example, Independence in the cxm tables for each of the matched sets implies symmetry in the summary mc table with consequent marginal homogeneity. Adaptation of the Mantel-Haenszel procedure for testing independence to the case of many cxm tables so as to yield a chi square with (cl)(ml) degrees of freedom (DF) provides a test of marginal homogeneity in the summary mc table. This can be viewed as a test of symmetry directed against alternatives which would make for marginal inhomogeneity and can differ     

The Standard Error of the Mean and the Difference between Means for Finite Populations

This article discusses a representation of Pearson's chi-square for independence in two-way contingency tables in terms of conditional probabilities of two categorical random variables and proposes a functional interpretation of Pearson's chi-square. This representation is suggested for use in the teaching of statistical independence between categorical variables.     

A martingale-based test for independence of time to failure and cause of failure for competing risks models

In this article, we introduce a class of tests, using a martingale approach, for testing independence of failure time and cause of failure for competing risks data. Asymptotic distribution of the proposed test statistic is derived. The procedure is illustrated with a real-life data. A simulation study is carried out to assess the level and power of the test.     

Independence in Contingency Tables Using Simplicial Geometry

Frequently, contingency tables are generated in a multinomial sampling. Multinomial probabilities are then organized in a table assigning probabilities to each cell. A probability table can be viewed as an element in the simplex. The Aitchison geometry of the simplex identifies independent probability tables as a linear subspace. An important consequence is that, given a probability table, the nearest independent table is obtained by orthogonal projection onto the independent subspace. The nearest independent table is identified as that obtained by the product of geometric marginals, which do not coincide with the standard marginals, except in the independent case. The original probability table is decomposed into orthogonal tables, the independent and the interaction tables. The underlying model is log-linear, and a procedure to test independence of a contingency table, based on a multinomial simulation, is developed. Its performance is studied on an illustrative example.     

A Test of Independence in Two-Way Contingency Tables Based on Maximal Correlation

Maximal correlation has several desirable properties as a measure of dependence, including the fact that it vanishes if and only if the variables are independent. Except for a few special cases, it is hard to evaluate maximal correlation explicitly. We focus on two-dimensional contingency tables and discuss a procedure for estimating maximal correlation, which we use for constructing a test of independence. We compare the maximal correlation test with other tests of independence by Monte Carlo simulations. When the underlying continuous variables are dependent but uncorrelated, we point out some cases for which the new test is more powerful.     

Exact Tests for 2 × 2 Contingency Tables

Fisher's exact test, difference in proportions, log odds ratio, Pearson's chi-squared, and likelihood ratio are compared as test statistics for testing independence of two dichotomous factors when the associated p values are computed by using the conditional distribution given the marginals. The statistics listed above that can be used for a one-sided alternative give identical p values. For a two-sided alternative, many of the above statistics lead to different p values. The p values are shown to differ only by which tables in the opposite tail from the observed table are considered more extreme than the observed table.     

A Unified Approach to Estimating and Testing Income Distributions With Grouped Data

We propose a unified approach that is flexibly applicable to various types of grouped data for estimating and testing parametric income distributions. To simplify the use of our approach, we also provide a parametric bootstrap method and show its asymptotic validity. We also compare this approach with existing methods for grouped income data, and assess their finite-sample performance by a Monte Carlo simulation. For empirical demonstrations, we apply our approach to recovering China's income/consumption distributions from a sequence of income/consumption share tables and the U.S. income distributions from a combination of income shares and sample quantiles. Supplementary materials for this article are available online.