The Minimaxity of the Mid P-value under Linear and Squared Loss Functions

The mid-p is defined as the sum of the probabilities of all outcomes more extreme than an observed value, plus half of the probabilities of all outcomes exactly as extreme. On the one hand, it offers greater power than the standard p-value, but on the other, tests based on the mid-p statistic may have greater Type I error than their nominal level. This article investigates the mid p-value's properties under the estimated truth paradigm, which views p-values as estimators of the truth. The mid-p is shown to minimize the maximum risk for one-sided and two-sided tests.     

Modified p-Value of Two-Sided Test for Normal Distribution with Restricted Parameter Space

This article proposes a modified p-value for the two-sided test of the location of the normal distribution when the parameter space is restricted. A commonly used test for the two-sided test of the normal distribution is the uniformly most powerful unbiased (UMPU) test, which is also the likelihood ratio test. The p-value of the test is used as evidence against the null hypothesis. Note that the usual p-value does not depend on the parameter space but only on the observation and the assumption of the null hypothesis. When the parameter space is known to be restricted, the usual p-value cannot sufficiently utilize this information to make a more accurate decision. In this paper, a modified p-value (also called the rp-value) dependent on the parameter space is proposed, and the test derived from the modified p-value is also shown to be the UMPU test.     

Two-Tailed p-Values and Coherent Measures of Evidence

ABSTRACT

In a test of significance, it is common practice to report the p-value as one way of summarizing the incompatibility between a set of data and a proposed model for the data constructed under a set of assumptions together with a null hypothesis. However, the p-value does have some flaws, one being in general its definition for two-sided tests and a related serious logical one of incoherence, in its interpretation as a statistical measure of evidence for its respective null hypothesis. We shall address these two issues in this article.     

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.     

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.     

A Bayesian analysis for the multivariate point null testing problem

A Bayesian test for the point null testing problem in the multivariate case is developed. A procedure to get the mixed distribution using the prior density is suggested. For comparisons between the Bayesian and classical approaches, lower bounds on posterior probabilities of the null hypothesis, over some reasonable classes of prior distributions, are computed and compared with the p-value of the classical test. With our procedure, a better approximation is obtained because the p-value is in the range of the Bayesian measures of evidence.     

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.     

The p-Value Requires Context,Not a Threshold

Abstract

It is widely recognized by statisticians, though not as widely by other researchers, that the p-value cannot be interpreted in isolation, but rather must be considered in the context of certain features of the design and substantive application, such as sample size and meaningful effect size. I consider the setting of the normal mean and highlight the information contained in the p-value in conjunction with the sample size and meaningful effect size. The p-value and sample size jointly yield 95% confidence bounds for the effect of interest, which can be compared to the predetermined meaningful effect size to make inferences about the true effect. I provide simple examples to demonstrate that although the p-value is calculated under the null hypothesis, and thus seemingly may be divorced from the features of the study from which it arises, its interpretation as a measure of evidence requires its contextualization within the study. This implies that any proposal for improved use of the p-value as a measure of the strength of evidence cannot simply be a change to the threshold for significance.     

Abandon Statistical Significance

ABSTRACT

We discuss problems the null hypothesis significance testing (NHST) paradigm poses for replication and more broadly in the biomedical and social sciences as well as how these problems remain unresolved by proposals involving modified p-value thresholds, confidence intervals, and Bayes factors. We then discuss our own proposal, which is to abandon statistical significance. We recommend dropping the NHST paradigm—and the p-value thresholds intrinsic to it—as the default statistical paradigm for research, publication, and discovery in the biomedical and social sciences. Specifically, we propose that the p-value be demoted from its threshold screening role and instead, treated continuously, be considered along with currently subordinate factors (e.g., related prior evidence, plausibility of mechanism, study design and data quality, real world costs and benefits, novelty of finding, and other factors that vary by research domain) as just one among many pieces of evidence. We have no desire to “ban” p-values or other purely statistical measures. Rather, we believe that such measures should not be thresholded and that, thresholded or not, they should not take priority over the currently subordinate factors. We also argue that it seldom makes sense to calibrate evidence as a function of p-values or other purely statistical measures. We offer recommendations for how our proposal can be implemented in the scientific publication process as well as in statistical decision making more broadly.     

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.     

P-Value Precision and Reproducibility

P-values are useful statistical measures of evidence against a null hypothesis. In contrast to other statistical estimates, however, their sample-to-sample variability is usually not considered or estimated, and therefore not fully appreciated. Via a systematic study of log-scale p-value standard errors, bootstrap prediction bounds, and reproducibility probabilities for future replicate p-values, we show that p-values exhibit surprisingly large variability in typical data situations. In addition to providing context to discussions about the failure of statistical results to replicate, our findings shed light on the relative value of exact p-values vis-a-vis approximate p-values, and indicate that the use of *, **, and *** to denote levels 0.05, 0.01, and 0.001 of statistical significance in subject-matter journals is about the right level of precision for reporting p-values when judged by widely accepted rules for rounding statistical estimates.     

Interval-wise testing for functional data

In the framework of null hypothesis significance testing for functional data, we propose a procedure able to select intervals of the domain imputable for the rejection of a null hypothesis. An unadjusted p-value function and an adjusted one are the output of the procedure, namely interval-wise testing. Depending on the sort and level α of type-I error control, significant intervals can be selected by thresholding the two p-value functions at level α. We prove that the unadjusted (adjusted) p-value function point-wise (interval-wise) controls the probability of type-I error and it is point-wise (interval-wise) consistent. To enlighten the gain in terms of interpretation of the phenomenon under study, we applied the interval-wise testing to the analysis of a benchmark functional data set, i.e. Canadian daily temperatures. The new procedure provides insights that current state-of-the-art procedures do not, supporting similar advantages in the analysis of functional data with less prior knowledge.     

Statistical evidence and surprise unified under possibility theory

Sander Greenland argues that reported results of hypothesis tests should include the surprisal, the base-2 logarithm of the reciprocal of a p-value. The surprisal measures how many bits of evidence in the data warrant rejecting the null hypothesis. A generalization of surprisal also can measure how much the evidence justifies rejecting a composite hypothesis such as the complement of a confidence interval. That extended surprisal, called surprise, quantifies how many bits of astonishment an agent believing a hypothesis would experience upon observing the data. While surprisal is a function of a point in hypothesis space, surprise is a function of a subset of hypothesis space. Satisfying the conditions of conditional min-plus probability, surprise inherits a wealth of tools from possibility theory. The equivalent compatibility function has been recently applied to the replication crisis, to adjusting p-values for prior information, and to comparing scientific theories.     

Significance test for linear regression: how to test without P-values?

The discussion on the use and misuse of p-values in 2016 by the American Statistician Association was a timely assertion that statistical concept should be properly used in science. Some researchers, especially the economists, who adopt significance testing and p-values to report their results, may felt confused by the statement, leading to misinterpretations of the statement. In this study, we aim to re-examine the accuracy of the p-value and introduce an alternative way for testing the hypothesis. We conduct a simulation study to investigate the reliability of the p-value. Apart from investigating the performance of p-value, we also introduce some existing approaches, Minimum Bayes Factors and Belief functions, for replacing p-value. Results from the simulation study confirm unreliable p-value in some cases and that our proposed approaches seem to be useful as the substituted tool in the statistical inference. Moreover, our results show that the plausibility approach is more accurate for making decisions about the null hypothesis than the traditionally used p-values when the null hypothesis is true. However, the MBFs of Edwards et al. [Bayesian statistical inference for psychological research. Psychol. Rev. 70(3) (1963), pp. 193–242]; Vovk [A logic of probability, with application to the foundations of statistics. J. Royal Statistical Soc. Series B (Methodological) 55 (1993), pp. 317–351] and Sellke et al. [Calibration of p values for testing precise null hypotheses. Am. Stat. 55(1) (2001), pp. 62–71] provide more reliable results compared to all other methods when the null hypothesis is false.KEYWORDS: Ban of P-value, Minimum Bayes Factors, belief functions     

The discrepancy of P-values and posterior probability: Two-sided hypothesis of variance of normal distribution with unknown mean

This article is concerned with the comparison of P-value and Bayesian measure in point null hypothesis for the variance of Normal distribution with unknown mean. First, using fixed prior for test parameter, the posterior probability is obtained and compared with the P-value when an appropriate prior is used for the mean parameter. In the second, lower bounds of the posterior probability of H₀ under a reasonable class of prior are compared with the P-value. It has been shown that even in the presence of nuisance parameters, these two approaches can lead to different results in the statistical inference.     

The Use of Posterior Predictive P-Values in Testing Goodness-of-Fit

In this article, we introduce two goodness-of-fit tests for testing normality through the concept of the posterior predictive p-value. The discrepancy variables selected are the Kolmogorov-Smirnov (KS) and Berk-Jones (BJ) statistics and the prior chosen is Jeffreys’ prior. The constructed posterior predictive p-values are shown to be distributed independently of the unknown parameters under the null hypothesis, thus they can be taken as the test statistics. It emerges from the simulation that the new tests are more powerful than the corresponding classical tests against most of the alternatives concerned.     

A more powerful unconditional exact test of homogeneity for 2 × c contingency table analysis

The classical unconditional exact p-value test can be used to compare two multinomial distributions with small samples. This general hypothesis requires parameter estimation under the null which makes the test severely conservative. Similar property has been observed for Fisher's exact test with Barnard and Boschloo providing distinct adjustments that produce more powerful testing approaches. In this study, we develop a novel adjustment for the conservativeness of the unconditional multinomial exact p-value test that produces nominal type I error rate and increased power in comparison to all alternative approaches. We used a large simulation study to empirically estimate the 5th percentiles of the distributions of the p-values of the exact test over a range of scenarios and implemented a regression model to predict the values for two-sample multinomial settings. Our results show that the new test is uniformly more powerful than Fisher's, Barnard's, and Boschloo's tests with gains in power as large as several hundred percent in certain scenarios. Lastly, we provide a real-life data example where the unadjusted unconditional exact test wrongly fails to reject the null hypothesis and the corrected unconditional exact test rejects the null appropriately.     

Estimating the Proportion of True Null Hypotheses in Nonparametric Exponential Mixture Model with Appication to the Leukemia Gene Expression Data

We revisit the problem of estimating the proportion π of true null hypotheses where a large scale of parallel hypothesis tests are performed independently. While the proportion is a quantity of interest in its own right in applications, the problem has arisen in assessing or controlling an overall false discovery rate. On the basis of a Bayes interpretation of the problem, the marginal distribution of the p-value is modeled in a mixture of the uniform distribution (null) and a non-uniform distribution (alternative), so that the parameter π of interest is characterized as the mixing proportion of the uniform component on the mixture. In this article, a nonparametric exponential mixture model is proposed to fit the p-values. As an alternative approach to the convex decreasing mixture model, the exponential mixture model has the advantages of identifiability, flexibility, and regularity. A computation algorithm is developed. The new approach is applied to a leukemia gene expression data set where multiple significance tests over 3,051 genes are performed. The new estimate for π with the leukemia gene expression data appears to be about 10% lower than the other three estimates that are known to be conservative. Simulation results also show that the new estimate is usually lower and has smaller bias than the other three estimates.     

A Condition to Obtain the Same Decision in the Homogeneity Testing Problem from the Frequentist and Bayesian Point of View

We develop a Bayesian procedure for the homogeneity testing problem of r populations using r × s contingency tables. The posterior probability of the homogeneity null hypothesis is calculated using a mixed prior distribution. The methodology consists of choosing an appropriate value of π₀ for the mass assigned to the null and spreading the remainder, 1 ? π₀, over the alternative according to a density function. With this method, a theorem which shows when the same conclusion is reached from both frequentist and Bayesian points of view is obtained. A sufficient condition under which the p-value is less than a value α and the posterior probability is also less than 0.5 is provided.     

The p-values for one-sided hypothesis testing in univariate linear calibration

In this article, we focus on the one-sided hypothesis testing for the univariate linear calibration, where a normally distributed response variable and an explanatory variable are involved. The observations of the response variable corresponding to known values of the explanatory variable are used to make inferences on a single unknown value of the explanatory variable. We apply the generalized inference to the calibration problem, and take the generalized p-value as the test statistic to develop a new p-value for one-sided hypothesis testing, which we refer to as the one-sided posterior predictive p-value. The behavior of the one-sided posterior predictive p-value is numerically compared with that of the generalized p-value, and simulations show that the proposed p-value is quite satisfactory in the frequentist performance.