Efficient algorithms for exact inference in 2 × 2 contingency tables

We propose a simple and robust algorithm for exact inference in 2 × 2 contingency tables. It is based on recursive relations allowing efficient computation of odds-ratio estimates, confidence limits and p-values for Fisher's test. A factor of 3–10 is gained in terms of computer time compared with the classical algorithm of Thomas.     

The exact unconditional z-pooled test for equality of two binomial probabilities: optimal choice of the Berger and Boos confidence coefficient

Exact unconditional tests for comparing two binomial probabilities are generally more powerful than conditional tests like Fisher's exact test. Their power can be further increased by the Berger and Boos confidence interval method, where a p-value is found by restricting the common binomial probability under H ₀ to a 1?γ confidence interval. We studied the average test power for the exact unconditional z-pooled test for a wide range of cases with balanced and unbalanced sample sizes, and significance levels 0.05 and 0.01. The detailed results are available online on the web. Among the values 10^?3, 10^?4, …, 10^?10, the value γ=10^?4 gave the highest power, or close to the highest power, in all the cases we looked at, and can be given as a general recommendation as an optimal γ.     

Editor's Report

There are two common methods for statistical inference on 2 × 2 contingency tables. One is the widely taught Pearson chi-square test, which uses the well-known χ²statistic. The chi-square test is appropriate for large sample inference, and it is equivalent to the Z-test that uses the difference between the two sample proportions for the 2 × 2 case. Another method is Fisher’s exact test, which evaluates the likelihood of each table with the same marginal totals. This article mathematically justifies that these two methods for determining extreme do not completely agree with each other. Our analysis obtains one-sided and two-sided conditions under which a disagreement in determining extreme between the two tests could occur. We also address the question whether or not their discrepancy in determining extreme would make them draw different conclusions when testing homogeneity or independence. Our examination of the two tests casts light on which test should be trusted when the two tests draw different conclusions.     

Comparison of exact tests for association in unordered contingency tables using standard,mid-p,and randomized test versions

Pearson’s chi-square (Pe), likelihood ratio (LR), and Fisher (Fi)–Freeman–Halton test statistics are commonly used to test the association of an unordered r×c contingency table. Asymptotically, these test statistics follow a chi-square distribution. For small sample cases, the asymptotic chi-square approximations are unreliable. Therefore, the exact p-value is frequently computed conditional on the row- and column-sums. One drawback of the exact p-value is that it is conservative. Different adjustments have been suggested, such as Lancaster’s mid-p version and randomized tests. In this paper, we have considered 3×2, 2×3, and 3×3 tables and compared the exact power and significance level of these test’s standard, mid-p, and randomized versions. The mid-p and randomized test versions have approximately the same power and higher power than that of the standard test versions. The mid-p type-I error probability seldom exceeds the nominal level. For a given set of parameters, the power of Pe, LR, and Fi differs approximately the same way for standard, mid-p, and randomized test versions. Although there is no general ranking of these tests, in some situations, especially when averaged over the parameter space, Pe and Fi have the same power and slightly higher power than LR. When the sample sizes (i.e., the row sums) are equal, the differences are small, otherwise the observed differences can be 10% or more. In some cases, perhaps characterized by poorly balanced designs, LR has the highest power.     

Partial Round-Robin Comparisons with Perfect Rankings

In teaching the development of uniformly most powerful unbiased (UMPU) tests, one rarely discusses the performance of alternative biased tests. It is shown, through the comparison of two independent Bernoulli proportions, that a biased test (the Z test) can be more powerful than the UMPU test (Fisher's exact test—randomized) in a large region of the alternative parameter space. A more general example is also given.     

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.     

Fast and Stable Algorithms for Computing and Sampling From the Noncentral Hypergeometric Distribution

Although the noncentral hypergeometric distribution underlies conditional inference for 2 × 2 tables, major statistical packages lack support for this distribution. This article introduces fast and stable algorithms for computing the noncentral hypergeometric distribution and for sampling from it. The algorithms avoid the expensive and explosive combinatorial numbers by using a recursive relation. The algorithms also take advantage of the sharp concentration of the distribution around its mode to save computing time. A modified inverse method substantially reduces the number of searches in generating a random deviate. The algorithms are implemented in a Java class, Hypergeometric, available on the World Wide Web.     

Large sample results for permutation tests of association

This paper deals with the asymptotics of permutation tests based on a certain rather general class of measures of association for R by C contingency tables, given marginal totals. This class includes the classical chi-square test, the T _b and γ indices of Goodman and Kruskall (1954) and the popular Rand (1971) index. The asymptotic distribution of this class of permutation tests for association is a weighted sum of non-central (gen-erally speaking) chi-squares. The formulae for the asymptotic moments of such tests are also given. If non-centrality holds under the null hypothe-sis of independence, the distribution in question converges to the normal distribution. The efficacies for such measures of association are obtained. Several applications are analysed in detail, including the above mentioned indices. Approximations to the permutation distribution are also discussed.     

Testing for Serial Independence: Beyond the Portmanteau Approach

Portmanteau tests are typically used to test serial independence even if, by construction, they are generally powerful only in presence of pairwise dependence between lagged variables. In this article, we present a simple statistic defining a new serial independence test, which is able to detect more general forms of dependence. In particular, differently from the Portmanteau tests, the resulting test is powerful also under a dependent process characterized by pairwise independence. A diagram, based on p-values from the proposed test, is introduced to investigate serial dependence. Finally, the effectiveness of the proposal is evaluated in a simulation study and with an application on financial data. Both show that the new test, used in synergy with the existing ones, helps in the identification of the true data-generating process. Supplementary materials for this article are available online.     

A nonparametric procedure for testing partially ranked data

In consumer preference studies, it is common to seek a complete ranking of a variety of, say N, alternatives or treatments. Unfortunately, as N increases, it becomes progressively more confusing and undesirable for respondents to rank all N alternatives simultaneously. Moreover, the investigators may only be interested in consumers’ top few choices. Therefore, it is desirable to accommodate the setting where each survey respondent ranks only her/his most preferred k (k?N) alternatives. In this paper, we propose a simple procedure to test the independence of N alternatives and the top-k ranks, such that the value of k can be predetermined before securing a set of partially ranked data or be at the discretion of the investigator in the presence of complete ranking data. The asymptotic distribution of the proposed test under root-n local alternatives is established. We demonstrate our procedure with two real data sets.     

Outlier detection in contingency tables using decomposable graphical models

For high-dimensional data, it is a tedious task to determine anomalies such as outliers. We present a novel outlier detection method for high-dimensional contingency tables. We use the class of decomposable graphical models to model the relationship among the variables of interest, which can be depicted by an undirected graph called the interaction graph. Given an interaction graph, we derive a closed-form expression of the likelihood ratio test (LRT) statistic and an exact distribution for efficient simulation of the test statistic. An observation is declared an outlier if it deviates significantly from the approximated distribution of the test statistic under the null hypothesis. We demonstrate the use of the LRT outlier detection framework on genetic data modeled by Chow–Liu trees.     

Contingency tables with fuzzy information

ABSTRACT

This paper extends the classical methods of analysis of a two-way contingency table to the fuzzy environment for two cases: (1) when the available sample of observations is reported as imprecise data, and (2) the case in which we prefer to categorize the variables based on linguistic terms rather than as crisp quantities. For this purpose, the α-cuts approach is used to extend the usual concepts of the test statistic and p-value to the fuzzy test statistic and fuzzy p-value. In addition, some measures of association are extended to the fuzzy version in order to evaluate the dependence in such contingency tables. Some practical examples are provided to explain the applicability of the proposed methods in real-world problems.     

Marginal information for expectation parameters

The authors consider a special case of inference in the presence of nuisance parameters. They show that when the orthogonalized score function is a function of a statistic S, no Fisher information for the interest parameter is lost by using the marginal distribution of S rather than the full distribution of the observations. Therefore, no information for the interest parameter is recovered by conditioning on an ancillary statistic, and information will be lost by conditioning on an approximate ancillary statistic. This is the case for regular multivariate exponential families when the interest parameter is a subvector of the expectation parameter and the statistic is the maximum likelihood estimate of the interest parameter. Several examples are considered, including the 2 × 2 table.     

Quasi-asymmetry model for square tables with nominal categories

For an R×R square contingency table with nominal categories, the present paper proposes a model which indicates that the absolute values of log odds of the odds ratio for rows i and j and columns j and R to the corresponding symmetric odds ratio for rows j and R and columns i and j are constant for every i<j<R. The model is an extension of the quasi-symmetry model and states a structure of asymmetry of odds ratios. An example is given.     

Adjusted Wilcoxon signed rank test tables for ratio of percentiles

The ordinary Wilcoxon signed rank test table provides confidence intervals for the median of one population. Adjusted Wilcoxon signed rank test tables which can provide confidence intervals for the median and the 10th percentile of one population are created in this paper. Base-(n + 1) number system and theorems about property of symmetry of the adjusted Wilcoxon signed rank test statistic are derived for programming. Theorem 1 states that the adjusted Wilcoxon signed rank test statistic are symmetric around n(n + 1)/4. Theorem 2 states that the adjusted Wilcoxon signed rank test statistic with the same number of negative ranks m are symmetric around m(n+1)/2. 87.5% and 85% confidence intervals of the median are given in the table for n = 12, 13,…, 29 to create approximated 95% confidence intervals of the ratio of medians for two independent populations. 95% and 92.5% confidence intervals of the 10th percentile are given in the table for n = 26, 27, 28, 29 to create approximated 95% confidence regions of the ratio of the 10th percentiles for two independent populations. Finally two large datasets from wood industry will be partitioned to verify the correctness of adjusted Wilcoxon signed rank test tables for small samples.     

Likelihood-Based Inference for Weak Exogeneity in I(2) Cointegrated VAR Models

This article develops limit theory for likelihood analysis of weak exogeneity in I(2) cointegrated vector autoregressive (VAR) models incorporating deterministic terms. Conditions for weak exogeneity in I(2) VAR models are reviewed, and the asymptotic properties of conditional maximum likelihood estimators and a likelihood-based weak exogeneity test are then investigated. It is demonstrated that weak exogeneity in I(2) VAR models allows us to conduct asymptotic conditional inference based on mixed Gaussian distributions. It is then proved that a log-likelihood ratio test statistic for weak exogeneity in I(2) VAR models is asymptotically χ² distributed. The article also presents an empirical illustration of the proposed test for weak exogeneity using Japan's macroeconomic data.     

One‐Way anova for Functional Data via Globalizing the Pointwise F‐test

In this paper, we propose and study a new global test, namely, GPF test, for the one‐way anova problem for functional data, obtained via globalizing the usual pointwise F‐test. The asymptotic random expressions of the test statistic are derived, and its asymptotic power is investigated. The GPF test is shown to be root‐n consistent. It is much less computationally intensive than a parametric bootstrap test proposed in the literature for the one‐way anova for functional data. Via some simulation studies, it is found that in terms of size‐controlling and power, the GPF test is comparable with two existing tests adopted for the one‐way anova problem for functional data. A real data example illustrates the GPF test.     

A new test for the mean vector in large dimension and small samples

In this article, we consider the problem of testing the mean vector in the multivariate normal distribution, where the dimension p is greater than the sample size N. We propose a new test T_Block and obtain its asymptotic distribution. We also compare the proposed test with other two tests. The simulation results suggest that the performance of the new test is comparable to the existing two tests, and under some circumstances it may have higher power. Therefore, the new statistic can be employed in practice as an alternative choice.     

Statistical inference of risk difference in K correlated 2×2 tables with structural zero

K correlated 2×2 tables with structural zero are commonly encountered in infectious disease studies. A hypothesis test for risk difference is considered in K independent 2×2 tables with structural zero in this paper. Score statistic, likelihood ratio statistic and Wald‐type statistic are proposed to test the hypothesis on the basis of stratified data and pooled data. Sample size formulae are derived for controlling a pre‐specified power or a pre‐determined confidence interval width. Our empirical results show that score statistic and likelihood ratio statistic behave better than Wald‐type statistic in terms of type I error rate and coverage probability, sample sizes based on stratified test are smaller than those based on the pooled test in the same design. A real example is used to illustrate the proposed methodologies. Copyright © 2009 John Wiley & Sons, Ltd.     

A REMARK ON TESTING SIGNIFICANCE OF AN OBSERVED CORRELATION MATRIX

A simple test for the diagonality of the covariance matrix of a multi-variate normal population is proposed. The test, which is based upon the sum of squares of the z-transforms of the sample correlations, is seen to compare well with the current tests in terms of both the null distribution approximations and the powers.