Automatic Bayes Factors for Testing Equality- and Inequality-Constrained Hypotheses on Variances

In comparing characteristics of independent populations, researchers frequently expect a certain structure of the population variances. These expectations can be formulated as hypotheses with equality and/or inequality constraints on the variances. In this article, we consider the Bayes factor for testing such (in)equality-constrained hypotheses on variances. Application of Bayes factors requires specification of a prior under every hypothesis to be tested. However, specifying subjective priors for variances based on prior information is a difficult task. We therefore consider so-called automatic or default Bayes factors. These methods avoid the need for the user to specify priors by using information from the sample data. We present three automatic Bayes factors for testing variances. The first is a Bayes factor with equal priors on all variances, where the priors are specified automatically using a small share of the information in the sample data. The second is the fractional Bayes factor, where a fraction of the likelihood is used for automatic prior specification. The third is an adjustment of the fractional Bayes factor such that the parsimony of inequality-constrained hypotheses is properly taken into account. The Bayes factors are evaluated by investigating different properties such as information consistency and large sample consistency. Based on this evaluation, it is concluded that the adjusted fractional Bayes factor is generally recommendable for testing equality- and inequality-constrained hypotheses on variances.     

Bayesian model selection of informative hypotheses for repeated measurements

When analyzing repeated measurements data, researchers often have expectations about the relations between the measurement means. The expectations can often be formalized using equality and inequality constraints between (i) the measurement means over time, (ii) the measurement means between groups, (iii) the means adjusted for time-invariant covariates, and (iv) the means adjusted for time-varying covariates. The result is a set of informative hypotheses. In this paper, the Bayes factor is used to determine which hypothesis receives most support from the data. A pivotal element in the Bayesian framework is the specification of the prior. To avoid subjective prior specification, training data in combination with restrictions on the measurement means are used to obtain so-called constrained posterior priors. A simulation study and an empirical example from developmental psychology show that this prior results in Bayes factors with desirable properties.     

A prior predictive loss function for the evaluation of inequality constrained hypotheses

In many types of statistical modeling, inequality constraints are imposed between the parameters of interest. As we will show in this paper, the DIC (i.e., posterior Deviance Information Criterium as proposed as a Bayesian model selection tool by Spiegelhalter, Best, Carlin, & Van Der Linde, 2002) fails when comparing inequality constrained hypotheses. In this paper, we will derive the prior DIC and show that it also fails when comparing inequality constrained hypotheses. However, it will be shown that a modification of the prior predictive loss function that is minimized by the prior DIC renders a criterion that does have the properties needed in order to be able to compare inequality constrained hypotheses. This new criterion will be called the Prior Information Criterion (PIC) and will be illustrated and evaluated using simulated data and examples. The PIC has a close connection with the marginal likelihood in combination with the encompassing prior approach and both methods will be compared. All in all, the main message of the current paper is: (1) do not use the classical DIC when evaluating inequality constrained hypotheses, better use the PIC; and (2) the PIC is considered a proper model selection tool in the context of evaluating inequality constrained hypotheses.     

Bayesian data analysis as a tool for behavior analysts

Bayesian approaches to data analysis are considered within the context of behavior analysis. The paper distinguishes between Bayesian inference, the use of Bayes Factors, and Bayesian data analysis using specialized tools. Given the importance of prior beliefs to these approaches, the review addresses those situations in which priors have a big effect on the outcome (Bayes Factors) versus a smaller effect (parameter estimation). Although there are many advantages to Bayesian data analysis from a philosophical perspective, in many cases a behavior analyst can be reasonably well‐served by the adoption of traditional statistical tools as long as the focus is on parameter estimation and model comparison, not null hypothesis significance testing. A strong case for Bayesian analysis exists under specific conditions: When prior beliefs can help narrow parameter estimates (an especially important issue given the small sample sizes common in behavior analysis) and when an analysis cannot easily be conducted using traditional approaches (e.g., repeated measures censored regression).     

Modeling Dependence Structures for Response Times in a Bayesian Framework

A multivariate generalization of the log-normal model for response times is proposed within an innovative Bayesian modeling framework. A novel Bayesian Covariance Structure Model (BCSM) is proposed, where the inclusion of random-effect variables is avoided, while their implied dependencies are modeled directly through an additive covariance structure. This makes it possible to jointly model complex dependencies due to for instance the test format (e.g., testlets, complex constructs), time limits, or features of digitally based assessments. A class of conjugate priors is proposed for the random-effect variance parameters in the BCSM framework. They give support to testing the presence of random effects, reduce boundary effects by allowing non-positive (co)variance parameters, and support accurate estimation even for very small true variance parameters. The conjugate priors under the BCSM lead to efficient posterior computation. Bayes factors and the Bayesian Information Criterion are discussed for the purpose of model selection in the new framework. In two simulation studies, a satisfying performance of the MCMC algorithm and of the Bayes factor is shown. In comparison with parameter expansion through a half-Cauchy prior, estimates of variance parameters close to zero show no bias and undercoverage of credible intervals is avoided. An empirical example showcases the utility of the BCSM for response times to test the influence of item presentation formats on the test performance of students in a Latin square experimental design.

     

Incorporating prior theory in covariance structure analysis: A bayesian approach

A Bayesian approach to the testing of competing covariance structures is developed. The method provides approximate posterior probablities for each model under consideration without prior specification of individual parameter distributions. The method is based on ayesian updating using cross-validated pseudo-likelihoods. Given that the observed variables are the samefor all competing models, the approximate posterior probabilities may be obtained easily from the chi square values and other known constants, using only a hand calculator. The approach is illustrated using and example which illustrates how the prior probabilities can alter the results concerning which model specification is preferred.     

Bayesian inference for psychology,part IV: parameter estimation and Bayes factors

In the psychological literature, there are two seemingly different approaches to inference: that from estimation of posterior intervals and that from Bayes factors. We provide an overview of each method and show that a salient difference is the choice of models. The two approaches as commonly practiced can be unified with a certain model specification, now popular in the statistics literature, called spike-and-slab priors. A spike-and-slab prior is a mixture of a null model, the spike, with an effect model, the slab. The estimate of the effect size here is a function of the Bayes factor, showing that estimation and model comparison can be unified. The salient difference is that common Bayes factor approaches provide for privileged consideration of theoretically useful parameter values, such as the value corresponding to the null hypothesis, while estimation approaches do not. Both approaches, either privileging the null or not, are useful depending on the goals of the analyst.     

Seeking Confirmation Is Rational for Deterministic Hypotheses

The tendency to test outcomes that are predicted by our current theory (the confirmation bias) is one of the best‐known biases of human decision making. We prove that the confirmation bias is an optimal strategy for testing hypotheses when those hypotheses are deterministic, each making a single prediction about the next event in a sequence. Our proof applies for two normative standards commonly used for evaluating hypothesis testing: maximizing expected information gain and maximizing the probability of falsifying the current hypothesis. This analysis rests on two assumptions: (a) that people predict the next event in a sequence in a way that is consistent with Bayesian inference; and (b) when testing hypotheses, people test the hypothesis to which they assign highest posterior probability. We present four behavioral experiments that support these assumptions, showing that a simple Bayesian model can capture people's predictions about numerical sequences (Experiments 1 and 2), and that we can alter the hypotheses that people choose to test by manipulating the prior probability of those hypotheses (Experiments 3 and 4).     

Model inference or model selection: discussion of Klugkist, Laudy, and Hoijtink (2005)

I. Klugkist, O. Laudy, and H. Hoijtink (2005) presented a Bayesian approach to analysis of variance models with inequality constraints. Constraints may play 2 distinct roles in data analysis. They may represent prior information that allows more precise inferences regarding parameter values, or they may describe a theory to be judged against the data. In the latter case, the authors emphasized the use of Bayes factors and posterior model probabilities to select the best theory. One difficulty is that interpretation of the posterior model probabilities depends on which other theories are included in the comparison. The posterior distribution of the parameters under an unconstrained model allows one to quantify the support provided by the data for inequality constraints without requiring the model selection framework.     

Approximated adjusted fractional Bayes factors: A general method for testing informative hypotheses

Informative hypotheses are increasingly being used in psychological sciences because they adequately capture researchers’ theories and expectations. In the Bayesian framework, the evaluation of informative hypotheses often makes use of default Bayes factors such as the fractional Bayes factor. This paper approximates and adjusts the fractional Bayes factor such that it can be used to evaluate informative hypotheses in general statistical models. In the fractional Bayes factor a fraction parameter must be specified which controls the amount of information in the data used for specifying an implicit prior. The remaining fraction is used for testing the informative hypotheses. We discuss different choices of this parameter and present a scheme for setting it. Furthermore, a software package is described which computes the approximated adjusted fractional Bayes factor. Using this software package, psychological researchers can evaluate informative hypotheses by means of Bayes factors in an easy manner. Two empirical examples are used to illustrate the procedure.     

Properties of hypothesis testing techniques and (Bayesian) model selection for exploration‐based and theory‐based (order‐restricted) hypotheses

In this paper, the performance of six types of techniques for comparisons of means is examined. These six emerge from the distinction between the method employed (hypothesis testing, model selection using information criteria, or Bayesian model selection) and the set of hypotheses that is investigated (a classical, exploration‐based set of hypotheses containing equality constraints on the means, or a theory‐based limited set of hypotheses with equality and/or order restrictions). A simulation study is conducted to examine the performance of these techniques. We demonstrate that, if one has specific, a priori specified hypotheses, confirmation (i.e., investigating theory‐based hypotheses) has advantages over exploration (i.e., examining all possible equality‐constrained hypotheses). Furthermore, examining reasonable order‐restricted hypotheses has more power to detect the true effect/non‐null hypothesis than evaluating only equality restrictions. Additionally, when investigating more than one theory‐based hypothesis, model selection is preferred over hypothesis testing. Because of the first two results, we further examine the techniques that are able to evaluate order restrictions in a confirmatory fashion by examining their performance when the homogeneity of variance assumption is violated. Results show that the techniques are robust to heterogeneity when the sample sizes are equal. When the sample sizes are unequal, the performance is affected by heterogeneity. The size and direction of the deviations from the baseline, where there is no heterogeneity, depend on the effect size (of the means) and on the trend in the group variances with respect to the ordering of the group sizes. Importantly, the deviations are less pronounced when the group variances and sizes exhibit the same trend (e.g., are both increasing with group number).     

Scientific reasoning in a real‐world context: The effect of prior belief and outcome on children's hypothesis‐testing strategies

The impact of event outcome and prior belief on scientific reasoning was investigated within a real‐world oral health context. Participants (N= 144; ranging from 3 to 11 years) were given hypothesis‐testing tasks and asked to explain their answers. Participants were presented with information that was either consistent or inconsistent with their own beliefs. Each task consisted of scenarios in which the outcome was either good or bad oral health. When the information was belief consistent and the outcome was good, or when the information was belief inconsistent and the outcome was bad, children were more likely to choose scientifically appropriate tests of the stated hypothesis (i.e. manipulate only one variable). Evidence‐based explanations were associated with scientifically appropriate choices in the good‐outcome, belief‐inconsistent scenario and the belief‐consistent, bad‐outcome scenario. Participants' performance on these tasks is explained by considering the plausibility of causal variables. A control of variables strategy was used to test hypotheses in cases in which the evidence was consistent with participants' beliefs and knowledge of causal mechanisms. In contrast, when the evidence was inconsistent with participants' beliefs, children chose to manipulate behaviours likely to lead to a positive health outcome. These findings demonstrate that context and prior knowledge interact to play an important role in children's scientific reasoning.     

Evidence with uncertain likelihoods

An agent often has a number of hypotheses, and must choose among them based on observations, or outcomes of experiments. Each of these observations can be viewed as providing evidence for or against various hypotheses. All the attempts to formalize this intuition up to now have assumed that associated with each hypothesis h there is a likelihood function  μ _h , which is a probability measure that intuitively describes how likely each observation is, conditional on h being the correct hypothesis. We consider an extension of this framework where there is uncertainty as to which of a number of likelihood functions is appropriate, and discuss how one formal approach to defining evidence, which views evidence as a function from priors to posteriors, can be generalized to accommodate this uncertainty.     

The frequentist implications of optional stopping on Bayesian hypothesis tests

Null hypothesis significance testing (NHST) is the most commonly used statistical methodology in psychology. The probability of achieving a value as extreme or more extreme than the statistic obtained from the data is evaluated, and if it is low enough, the null hypothesis is rejected. However, because common experimental practice often clashes with the assumptions underlying NHST, these calculated probabilities are often incorrect. Most commonly, experimenters use tests that assume that sample sizes are fixed in advance of data collection but then use the data to determine when to stop; in the limit, experimenters can use data monitoring to guarantee that the null hypothesis will be rejected. Bayesian hypothesis testing (BHT) provides a solution to these ills because the stopping rule used is irrelevant to the calculation of a Bayes factor. In addition, there are strong mathematical guarantees on the frequentist properties of BHT that are comforting for researchers concerned that stopping rules could influence the Bayes factors produced. Here, we show that these guaranteed bounds have limited scope and often do not apply in psychological research. Specifically, we quantitatively demonstrate the impact of optional stopping on the resulting Bayes factors in two common situations: (1) when the truth is a combination of the hypotheses, such as in a heterogeneous population, and (2) when a hypothesis is composite—taking multiple parameter values—such as the alternative hypothesis in a t-test. We found that, for these situations, while the Bayesian interpretation remains correct regardless of the stopping rule used, the choice of stopping rule can, in some situations, greatly increase the chance of experimenters finding evidence in the direction they desire. We suggest ways to control these frequentist implications of stopping rules on BHT.     

Robust step‐down tests for multivariate independent group designs

A composite step‐down procedure, in which a set of step‐down tests are summarized collectively with Fisher's combination statistic, was considered to test for multivariate mean equality in two‐group designs. An approximate degrees of freedom (ADF) composite procedure based on trimmed/Winsorized estimators and a non‐pooled estimate of error variance is proposed, and compared to a composite procedure based on trimmed/Winsorized estimators and a pooled estimate of error variance. The step‐down procedures were also compared to Hotelling's T² and Johansen's ADF global procedure based on trimmed estimators in a simulation study. Type I error rates of the pooled step‐down procedure were sensitive to covariance heterogeneity in unbalanced designs; error rates were similar to those of Hotelling's T² across all of the investigated conditions. Type I error rates of the ADF composite step‐down procedure were insensitive to covariance heterogeneity and less sensitive to the number of dependent variables when sample size was small than error rates of Johansen's test. The ADF composite step‐down procedure is recommended for testing hypotheses of mean equality in two‐group designs except when the data are sampled from populations with different degrees of multivariate skewness.     

Prior distributions for random choice structures

We study various axioms of discrete probabilistic choice, measuring how restrictive they are, both alone and in the presence of other axioms, given a specific class of prior distributions over a complete collection of finite choice probabilities. We do this by using Monte Carlo simulation to compute, for a range of prior distributions, probabilities that various simple and compound axioms hold. For example, the probability of the triangle inequality is usually many orders of magnitude higher than the probability of random utility. While neither the triangle inequality nor weak stochastic transitivity imply the other, the conditional probability that one holds given the other holds is greater than the marginal probability, for all priors in the class we consider. The reciprocal of the prior probability that an axiom holds is an upper bound on the Bayes factor in favor of a restricted model, in which the axiom holds, against an unrestricted model. The relatively high prior probability of the triangle inequality limits the degree of support that data from a single decision maker can provide in its favor. The much lower probability of random utility implies that the Bayes factor in favor of it can be much higher, for suitable data.     

Bayesian t tests for accepting and rejecting the null hypothesis

Progress in science often comes from discovering invariances in relationships among variables; these invariances often correspond to null hypotheses. As is commonly known, it is not possible to state evidence for the null hypothesis in conventional significance testing. Here we highlight a Bayes factor alternative to the conventional t test that will allow researchers to express preference for either the null hypothesis or the alternative. The Bayes factor has a natural and straightforward interpretation, is based on reasonable assumptions, and has better properties than other methods of inference that have been advocated in the psychological literature. To facilitate use of the Bayes factor, we provide an easy-to-use, Web-based program that performs the necessary calculations.     

Gaussian model‐based partitioning using iterated local search

The emergence of Gaussian model‐based partitioning as a viable alternative to K‐means clustering fosters a need for discrete optimization methods that can be efficiently implemented using model‐based criteria. A variety of alternative partitioning criteria have been proposed for more general data conditions that permit elliptical clusters, different spatial orientations for the clusters, and unequal cluster sizes. Unfortunately, many of these partitioning criteria are computationally demanding, which makes the multiple‐restart (multistart) approach commonly used for K‐means partitioning less effective as a heuristic solution strategy. As an alternative, we propose an approach based on iterated local search (ILS), which has proved effective in previous combinatorial data analysis contexts. We compared multistart, ILS and hybrid multistart–ILS procedures for minimizing a very general model‐based criterion that assumes no restrictions on cluster size or within‐group covariance structure. This comparison, which used 23 data sets from the classification literature, revealed that the ILS and hybrid heuristics generally provided better criterion function values than the multistart approach when all three methods were constrained to the same 10‐min time limit. In many instances, these differences in criterion function values reflected profound differences in the partitions obtained.     

An overview of Bayesian reasoning in the analysis of delay‐discounting data

Statistical inference (including interval estimation and model selection) is increasingly used in the analysis of behavioral data. As with many other fields, statistical approaches for these analyses traditionally use classical (i.e., frequentist) methods. Interpreting classical intervals and p‐values correctly can be burdensome and counterintuitive. By contrast, Bayesian methods treat data, parameters, and hypotheses as random quantities and use rules of conditional probability to produce direct probabilistic statements about models and parameters given observed study data. In this work, we reanalyze two data sets using Bayesian procedures. We precede the analyses with an overview of the Bayesian paradigm. The first study reanalyzes data from a recent study of controls, heavy smokers, and individuals with alcohol and/or cocaine substance use disorder, and focuses on Bayesian hypothesis testing for covariates and interval estimation for discounting rates among various substance use disorder profiles. The second example analyzes hypothetical environmental delay‐discounting data. This example focuses on using historical data to establish prior distributions for parameters while allowing subjective expert opinion to govern the prior distribution on model preference. We review the subjective nature of specifying Bayesian prior distributions but also review established methods to standardize the generation of priors and remove subjective influence while still taking advantage of the interpretive advantages of Bayesian analyses. We present the Bayesian approach as an alternative paradigm for statistical inference and discuss its strengths and weaknesses.     

All for one or some for all? Evaluating informative hypotheses using multiple <Emphasis Type="Italic">N</Emphasis> = 1 studies

Analyses are mostly executed at the population level, whereas in many applications the interest is on the individual level instead of the population level. In this paper, multiple N =?1 experiments are considered, where participants perform multiple trials with a dichotomous outcome in various conditions. Expectations with respect to the performance of participants can be translated into so-called informative hypotheses. These hypotheses can be evaluated for each participant separately using Bayes factors. A Bayes factor expresses the relative evidence for two hypotheses based on the data of one individual. This paper proposes to “average” these individual Bayes factors in the gP-BF, the average relative evidence. The gP-BF can be used to determine whether one hypothesis is preferred over another for all individuals under investigation. This measure provides insight into whether the relative preference of a hypothesis from a pre-defined set is homogeneous over individuals. Two additional measures are proposed to support the interpretation of the gP-BF: the evidence rate (ER), the proportion of individual Bayes factors that support the same hypothesis as the gP-BF, and the stability rate (SR), the proportion of individual Bayes factors that express a stronger support than the gP-BF. These three statistics can be used to determine the relative support in the data for the informative hypotheses entertained. Software is available that can be used to execute the approach proposed in this paper and to determine the sensitivity of the outcomes with respect to the number of participants and within condition replications.