Adaptive procedure for generalized familywise error rate control

This article considers multiple hypotheses testing with the generalized familywise error rate k-FWER control, which is the probability of at least k false rejections. We first assume the p-values corresponding to the true null hypotheses are independent, and propose adaptive generalized Bonferroni procedure with k-FWER control based on the estimation of the number of true null hypotheses. Then, we assume the p-values are dependent, satisfying block dependence, and propose adaptive procedure with k-FWER control. Extensive simulations compare the performance of the adaptive procedures with different estimators.     

Expected Power for the False Discovery Rate with Independence

The Benjamini–Hochberg procedure is widely used in multiple comparisons. Previous power results for this procedure have been based on simulations. This article produces theoretical expressions for expected power. To derive them, we make assumptions about the number of hypotheses being tested, which null hypotheses are true, which are false, and the distributions of the test statistics under each null and alternative. We use these assumptions to derive bounds for multiple dimensional rejection regions. With these bounds and a permanent based representation of the joint density function of the largest p-values, we use the law of total probability to derive the distribution of the total number of rejections. We derive the joint distribution of the total number of rejections and the number of rejections when the null hypothesis is true. We give an analytic expression for the expected power for a false discovery rate procedure that assumes the hypotheses are independent.     

Two new estimators for the proportion of true null hypotheses in multiple test

In multiple hypothesis test, an important problem is estimating the proportion of true null hypotheses. Existing methods are mainly based on the p-values of the single tests. In this paper, we propose two new estimations for this proportion. One is a natural extension of the commonly used methods based on p-values and the other is based on a mixed distribution. Simulations show that the first method is comparable with existing methods and performs better under some cases. And the method based on a mixed distribution can get accurate estimators even if the variance of data is large or the difference between the null hypothesis and alternative hypothesis is very small.     

Generalized Inference for a Class of Linear Models Under Heteroscedasticity

In this article we study inferences for a class of linear models under heteroscedasticity. Using the generalized inference approach, we obtain the generalized p-values of two-sided hypotheses for the multi-dimensional location parameters and one-sided hypotheses for the scale parameters, respectively. Some frequentist properties in small-sample cases and large-sample cases are proven.     

The adaptive calibration of testing p-values

Abstract

In statistical hypothesis testing, a p-value is expected to be distributed as the uniform distribution on the interval (0, 1) under the null hypothesis. However, some p-values, such as the generalized p-value and the posterior predictive p-value, cannot be assured of this property. In this paper, we propose an adaptive p-value calibration approach, and show that the calibrated p-value is asymptotically distributed as the uniform distribution. For Behrens–Fisher problem and goodness-of-fit test under a normal model, the calibrated p-values are constructed and their behavior is evaluated numerically. Simulations show that the calibrated p-values are superior than original ones.     

Estimating the proportion of true null hypotheses using the pattern of observed p-values

Estimating the proportion of true null hypotheses, π₀, has attracted much attention in the recent statistical literature. Besides its apparent relevance for a set of specific scientific hypotheses, an accurate estimate of this parameter is key for many multiple testing procedures. Most existing methods for estimating π₀ in the literature are motivated from the independence assumption of test statistics, which is often not true in reality. Simulations indicate that most existing estimators in the presence of the dependence among test statistics can be poor, mainly due to the increase of variation in these estimators. In this paper, we propose several data-driven methods for estimating π₀ by incorporating the distribution pattern of the observed p-values as a practical approach to address potential dependence among test statistics. Specifically, we use a linear fit to give a data-driven estimate for the proportion of true-null p-values in (λ, 1] over the whole range [0, 1] instead of using the expected proportion at 1?λ. We find that the proposed estimators may substantially decrease the variance of the estimated true null proportion and thus improve the overall performance.     

Distribution of the Λ-Criterion for Sphericity Test and Its Connection to a Generalized Dirichlet Model

It is shown that the exact null distribution of the likelihood ratio criterion for sphericity test in the p-variate normal case and the marginal distribution of the first component of a (p ? 1)-variate generalized Dirichlet model with a given set of parameters are identical. The exact distribution of the likelihood ratio criterion so obtained has a general format for every p. A novel idea is introduced here through which the complicated exact null distribution of the sphericity test criterion in multivariate statistical analysis is converted into an easily tractable marginal density in a generalized Dirichlet model. It provides a direct and easiest method of computation of p-values. The computation of p-values and a table of critical points corresponding to p = 3 and 4 are also presented.     

Controlling the familywise error rate with plug-in estimator for the proportion of true null hypotheses

Summary.  Estimation of the number or proportion of true null hypotheses in multiple-testing problems has become an interesting area of research. The first important work in this field was performed by Schweder and Spjøtvoll. Among others, they proposed to use plug-in estimates for the proportion of true null hypotheses in multiple-test procedures to improve the power. We investigate the problem of controlling the familywise error rate FWER when such estimators are used as plug-in estimators in single-step or step-down multiple-test procedures. First we investigate the case of independent p -values under the null hypotheses and show that a suitable choice of plug-in estimates leads to control of FWER in single-step procedures. We also investigate the power and study the asymptotic behaviour of the number of false rejections. Although step-down procedures are more difficult to handle we briefly consider a possible solution to this problem. Anyhow, plug-in step-down procedures are not recommended here. For dependent p -values we derive a condition for asymptotic control of FWER and provide some simulations with respect to FWER and power for various models and hypotheses.     

Testing Homogeneity of Inverse Gaussian Scale Parameters Based on Generalized Likelihood Ratio

This article presents a new procedure for testing homogeneity of scale parameters from k independent inverse Gaussian populations. Based on the idea of generalized likelihood ratio method, a new generalized p-value is derived. Some simulation results are presented to compare the performance of the proposed method and existing methods. Numerical results show that the proposed test has good size and power performance.     

Comparing multiple treatments to both positive and negative controls

In the past, most comparison to control problems have dealt with comparing k test treatments to either positive or negative controls. Dasgupta et al. [2006. Using numerical methods to find the least favorable configuration when comparing k test treatments to both positive and negative controls. Journal of Statistical Computation and Simulation 76, 251–265] enumerate situations where it is imperative to compare several test treatments to both a negative as well as a positive control simultaneously. Specifically, the aim is to see if the test treatments are worse than the negative control, or if they are better than the positive control when the two controls are sufficiently apart. To find critical regions for this problem, one needs to find the least favorable configuration (LFC) under the composite null. In their paper, Dasgupta et al. [2006. Using numerical methods to find the least favorable configuration when comparing k test treatments to both positive and negative controls. Journal of Statistical Computation and Simulation 76, 251–265] came up with a numerical technique to find the LFC. In this paper we verify their result analytically. Via Monte Carlo simulation we compare the proposed method to the logical single step alternatives: Dunnett's [1955. A multiple comparison procedure for comparing several treatments with a control. Journal of the American Statistical Association 50, 1096–1121] or the Bonferroni correction. The proposed method is superior in terms of both the Type I error and the marginal power.     

Editorial Collaborators

Abstract

The present note explores sources of misplaced criticisms of P-values, such as conflicting definitions of “significance levels” and “P-values” in authoritative sources, and the consequent misinterpretation of P-values as error probabilities. It then discusses several properties of P-values that have been presented as fatal flaws: That P-values exhibit extreme variation across samples (and thus are “unreliable”), confound effect size with sample size, are sensitive to sample size, and depend on investigator sampling intentions. These properties are often criticized from a likelihood or Bayesian framework, yet they are exactly the properties P-values should exhibit when they are constructed and interpreted correctly within their originating framework. Other common criticisms are that P-values force users to focus on irrelevant hypotheses and overstate evidence against those hypotheses. These problems are not however properties of P-values but are faults of researchers who focus on null hypotheses and overstate evidence based on misperceptions that p?=?0.05 represents enough evidence to reject hypotheses. Those problems are easily seen without use of Bayesian concepts by translating the observed P-value p into the Shannon information (S-value or surprisal) –log₂(p).     

A Proposed Hybrid Effect Size Plus p-Value Criterion: Empirical Evidence Supporting its Use

ABSTRACT

When the editors of Basic and Applied Social Psychology effectively banned the use of null hypothesis significance testing (NHST) from articles published in their journal, it set off a fire-storm of discussions both supporting the decision and defending the utility of NHST in scientific research. At the heart of NHST is the p-value which is the probability of obtaining an effect equal to or more extreme than the one observed in the sample data, given the null hypothesis and other model assumptions. Although this is conceptually different from the probability of the null hypothesis being true, given the sample, p-values nonetheless can provide evidential information, toward making an inference about a parameter. Applying a 10,000-case simulation described in this article, the authors found that p-values’ inferential signals to either reject or not reject a null hypothesis about the mean (α?=?0.05) were consistent for almost 70% of the cases with the parameter’s true location for the sampled-from population. Success increases if a hybrid decision criterion, minimum effect size plus p-value (MESP), is used. Here, rejecting the null also requires the difference of the observed statistic from the exact null to be meaningfully large or practically significant, in the researcher’s judgment and experience. The simulation compares performances of several methods: from p-value and/or effect size-based, to confidence-interval based, under various conditions of true location of the mean, test power, and comparative sizes of the meaningful distance and population variability. For any inference procedure that outputs a binary indicator, like flagging whether a p-value is significant, the output of one single experiment is not sufficient evidence for a definitive conclusion. Yet, if a tool like MESP generates a relatively reliable signal and is used knowledgeably as part of a research process, it can provide useful information.     

p-Values,Bayes Factors,and Sufficiency

ABSTRACT

Various approaches can be used to construct a model from a null distribution and a test statistic. I prove that one such approach, originating with D. R. Cox, has the property that the p-value is never greater than the Generalized Likelihood Ratio (GLR). When combined with the general result that the GLR is never greater than any Bayes factor, we conclude that, under Cox’s model, the p-value is never greater than any Bayes factor. I also provide a generalization, illustrations for the canonical Normal model, and an alternative approach based on sufficiency. This result is relevant for the ongoing discussion about the evidential value of small p-values, and the movement among statisticians to “redefine statistical significance.”     

Exact Tests in Panel Data Using Generalized p-Values

In this article, we consider exact tests in panel data regression model with one-way and two-way error component for which no exact tests are available. Exact inferences using generalized p-values are obtained. When there are several groups of panel data, test for equal coefficients under one-way and two-way error component are derived.     

A generalized p-value approach to inference on the performance measures of an M/Ek/1 queueing system

Abstract

The hypothesis tests of performance measures for an M/E_k/1 queueing system are considered. With pivotal models deduced from sufficient statistics for the unknown parameters, a generalized p-value approach to derive tests about parametric functions are proposed. The focus is on derivation of the p-values of hypothesis testing for five popular performance measures of the system in the steady state. Given a sample T, let p(T) be the p values we developed. We derive a closed form expression to show that, for small samples, the probability P(p(T) ? γ) is approximately equal to γ, for 0 ? γ ? 1.     

One-way ANOVA with Unequal Variances

We consider the one-way ANOVA problem of testing the equality of several normal means when the variances are not assumed to be equal. This is a generalization of the Behrens-Fisher problem, but even in this special case there is no exact test and the actual size of any test depends on the values of the nuisance parameters. Therefore, controlling the actual size of the test is of main concern. In this article, we first consider a test using the concept of generalized p-value. Extensive simulation studies show that the actual size of this test does not exceed the nominal level, for practically all values of the nuisance parameters, but the test is not too conservative either, in the sense that the actual size of the test can be very close to the nominal level for some values of the nuisance parameters. We then use this test to propose a simple F-test, which has similar properties but avoids the computations associated with generalized p-values. Because of its simplicity, both conceptually as well as computationally, this F-test may be more useful in practice, since one-way ANOVA is widely used by practitioners who may not be familiar with the generalized p-value and its computational aspects.     

Inferences on the Coefficients of Variation in a Multivariate Normal Population

In this article, the problem of testing the equality of coefficients of variation in a multivariate normal population is considered, and an asymptotic approach and a generalized p-value approach based on the concepts of generalized test variable are proposed. Monte Carlo simulation studies show that the proposed generalized p-value test has good empirical sizes, and it is better than the asymptotic approach. In addition, the problem of hypothesis testing and confidence interval for the common coefficient variation of a multivariate normal population are considered, and a generalized p-value and a generalized confidence interval are proposed. Using Monte Carlo simulation, we find that the coverage probabilities and expected lengths of this generalized confidence interval are satisfactory, and the empirical sizes of the generalized p-value are close to nominal level. We illustrate our approaches using a real data.     

Blending Bayesian and Classical Tools to Define Optimal Sample-Size-Dependent Significance Levels

ABSTRACT

This article argues that researchers do not need to completely abandon the p-value, the best-known significance index, but should instead stop using significance levels that do not depend on sample sizes. A testing procedure is developed using a mixture of frequentist and Bayesian tools, with a significance level that is a function of sample size, obtained from a generalized form of the Neyman–Pearson Lemma that minimizes a linear combination of α, the probability of rejecting a true null hypothesis, and β, the probability of failing to reject a false null, instead of fixing α and minimizing β. The resulting hypothesis tests do not violate the Likelihood Principle and do not require any constraints on the dimensionalities of the sample space and parameter space. The procedure includes an ordering of the entire sample space and uses predictive probability (density) functions, allowing for testing of both simple and compound hypotheses. Accessible examples are presented to highlight specific characteristics of the new tests.     

Bayesian Analysis of Contingency Tables

ABSTRACT

The display of the data by means of contingency tables is used in different approaches to statistical inference, for example, to broach the test of homogeneity of independent multinomial distributions. We develop a Bayesian procedure to test simple null hypotheses versus bilateral alternatives in contingency tables. Given independent samples of two binomial distributions and taking a mixed prior distribution, we calculate the posterior probability that the proportion of successes in the first population is the same as in the second. This posterior probability is compared with the p-value of the classical method, obtaining a reconciliation between both results, classical and Bayesian. The obtained results are generalized for r × s tables.     

Three Recommendations for Improving the Use of p-Values

ABSTRACT

Researchers commonly use p-values to answer the question: How strongly does the evidence favor the alternative hypothesis relative to the null hypothesis? p-Values themselves do not directly answer this question and are often misinterpreted in ways that lead to overstating the evidence against the null hypothesis. Even in the “post p?<?0.05 era,” however, it is quite possible that p-values will continue to be widely reported and used to assess the strength of evidence (if for no other reason than the widespread availability and use of statistical software that routinely produces p-values and thereby implicitly advocates for their use). If so, the potential for misinterpretation will persist. In this article, we recommend three practices that would help researchers more accurately interpret p-values. Each of the three recommended practices involves interpreting p-values in light of their corresponding “Bayes factor bound,” which is the largest odds in favor of the alternative hypothesis relative to the null hypothesis that is consistent with the observed data. The Bayes factor bound generally indicates that a given p-value provides weaker evidence against the null hypothesis than typically assumed. We therefore believe that our recommendations can guard against some of the most harmful p-value misinterpretations. In research communities that are deeply attached to reliance on “p?<?0.05,” our recommendations will serve as initial steps away from this attachment. We emphasize that our recommendations are intended merely as initial, temporary steps and that many further steps will need to be taken to reach the ultimate destination: a holistic interpretation of statistical evidence that fully conforms to the principles laid out in the ASA statement on statistical significance and p-values.