Bayesian Multivariate Logistic Regression for Superiority and Inferiority Decision-Making under Observable Treatment Heterogeneity.

The effects of treatments may differ between persons with different characteristics. Addressing such treatment heterogeneity is crucial to investigate whether patients with specific characteristics are likely to benefit from a new treatment. The current paper presents a novel Bayesian method for superiority decision-making in the context of randomized controlled trials with multivariate binary responses and heterogeneous treatment effects. The framework is based on three elements: a) Bayesian multivariate logistic regression analysis with a Pólya-Gamma expansion; b) a transformation procedure to transfer obtained regression coefficients to a more intuitive multivariate probability scale (i.e., success probabilities and the differences between them); and c) a compatible decision procedure for treatment comparison with prespecified decision error rates. Procedures for a priori sample size estimation under a non-informative prior distribution are included. A numerical evaluation demonstrated that decisions based on a priori sample size estimation resulted in anticipated error rates among the trial population as well as subpopulations. Further, average and conditional treatment effect parameters could be estimated unbiasedly when the sample was large enough. Illustration with the International Stroke Trial dataset revealed a trend toward heterogeneous effects among stroke patients: Something that would have remained undetected when analyses were limited to average treatment effects.

Bayesian multilevel multivariate logistic regression for superiority decision-making under observable treatment heterogeneity.

BACKGROUND: In medical, social, and behavioral research we often encounter datasets with a multilevel structure and multiple correlated dependent variables. These data are frequently collected from a study population that distinguishes several subpopulations with different (i.e., heterogeneous) effects of an intervention. Despite the frequent occurrence of such data, methods to analyze them are less common and researchers often resort to either ignoring the multilevel and/or heterogeneous structure, analyzing only a single dependent variable, or a combination of these. These analysis strategies are suboptimal: Ignoring multilevel structures inflates Type I error rates, while neglecting the multivariate or heterogeneous structure masks detailed insights. METHODS: To analyze such data comprehensively, the current paper presents a novel Bayesian multilevel multivariate logistic regression model. The clustered structure of multilevel data is taken into account, such that posterior inferences can be made with accurate error rates. Further, the model shares information between different subpopulations in the estimation of average and conditional average multivariate treatment effects. To facilitate interpretation, multivariate logistic regression parameters are transformed to posterior success probabilities and differences between them. RESULTS: A numerical evaluation compared our framework to less comprehensive alternatives and highlighted the need to model the multilevel structure: Treatment comparisons based on the multilevel model had targeted Type I error rates, while single-level alternatives resulted in inflated Type I errors. Further, the multilevel model was more powerful than a single-level model when the number of clusters was higher. A re-analysis of the Third International Stroke Trial data illustrated how incorporating a multilevel structure, assessing treatment heterogeneity, and combining dependent variables contributed to an in-depth understanding of treatment effects. Further, we demonstrated how Bayes factors can aid in the selection of a suitable model. CONCLUSION: The method is useful in prediction of treatment effects and decision-making within subpopulations from multiple clusters, while taking advantage of the size of the entire study sample and while properly incorporating the uncertainty in a principled probabilistic manner using the full posterior distribution.

Bayes factor testing of equality and order constraints on measures of association in social research.

Measures of association play a central role in the social sciences to quantify the strength of a linear relationship between the variables of interest. In many applications researchers can translate scientific expectations to hypotheses with equality and/or order constraints on these measures of association. In this paper a Bayes factor test is proposed for testing multiple hypotheses with constraints on the measures of association between ordinal and/or continuous variables, possibly after correcting for certain covariates. This test can be used to obtain a direct answer to the research question how much evidence there is in the data for a social science theory relative to competing theories. The stand-alone software package 'BCT' allows users to apply the methodology in an easy manner. The methodology will also be available in the R package 'BFpack'. An empirical application from leisure studies about the associations between life, leisure and relationship satisfaction and an application about the differences about egalitarian justice beliefs across countries are used to illustrate the methodology.

Discovering trends of social interaction behavior over time: An introduction to relational event modeling : Trends of social interaction.

Real-life social interactions occur in continuous time and are driven by complex mechanisms. Each interaction is not only affected by the characteristics of individuals or the environmental context but also by the history of interactions. The relational event framework provides a flexible approach to studying the mechanisms that drive how a sequence of social interactions evolves over time. This paper presents an introduction of this new statistical framework and two of its extensions for psychological researchers. The relational event framework is illustrated with an exemplary study on social interactions between freshmen students at the start of their new studies. We show how the framework can be used to study: (a) which predictors are important drivers of social interactions between freshmen students who start interacting at zero acquaintance; (b) how the effects of predictors change over time as acquaintance increases; and (c) the dynamics between the different settings in which students interact. Findings show that patterns of interaction developed early in the freshmen student network and remained relatively stable over time. Furthermore, clusters of interacting students formed quickly, and predominantly within a specific setting for interaction. Extraversion predicted rates of social interaction, and this effect was particularly pronounced on the weekends. These results illustrate how the relational event framework and its extensions can lead to new insights on social interactions and how they are affected both by the interacting individuals and the dynamic social environment.

A review of applications of the Bayes factor in psychological research.

The last 25 years have shown a steady increase in attention for the Bayes factor as a tool for hypothesis evaluation and model selection. The present review highlights the potential of the Bayes factor in psychological research. We discuss six types of applications: Bayesian evaluation of point null, interval, and informative hypotheses, Bayesian evidence synthesis, Bayesian variable selection and model averaging, and Bayesian evaluation of cognitive models. We elaborate what each application entails, give illustrative examples, and provide an overview of key references and software with links to other applications. The article is concluded with a discussion of the opportunities and pitfalls of Bayes factor applications and a sketch of corresponding future research lines. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Dynamic relational event modeling: Testing, exploring, and applying.

The relational event model (REM) facilitates the study of network evolution in relational event history data, i.e., time-ordered sequences of social interactions. In real-life social networks it is likely that network effects, i.e., the parameters that quantify the relative importance of drivers of these social interaction sequences, change over time. In these networks, the basic REM is not appropriate to understand what drives network evolution. This research extends the REM framework with approaches for testing and exploring time-varying network effects. First, we develop a Bayesian approach to test whether network effects change during the study period. We conduct a simulation study that illustrates that the Bayesian test accurately quantifies the evidence between a basic ('static') REM or a dynamic REM. Secondly, in the case of the latter, time-varying network effects can be studied by means of a moving window that slides over the relational event history. A simulation study was conducted that illustrates that the accuracy and precision of the estimates depend on the window width: narrower windows result in greater accuracy at the cost of lower precision. Third, we develop a Bayesian approach for determining window widths using the empirical network data and conduct a simulation study that illustrates that estimation with empirically determined window widths achieves both good accuracy for time intervals with important changes and good precision for time intervals with hardly any changes in the effects. Finally, in an empirical application, we illustrate how the approaches in this research can be used to test for and explore time-varying network effects of face-to-face contacts at the workplace.

Bayesian One-Sided Variable Selection.

This paper presents a novel Bayesian variable selection approach that accounts for the sign of the regression coefficients based on multivariate one-sided tests. We propose a truncated g prior to specify a prior distribution of coefficients with anticipated signs in a given model. Informative priors for the direction of the effects can be incorporated into prior model probabilities. The best subset of variables is selected by comparing the posterior probabilities of the possible models. The new Bayesian one-sided variable selection procedure has higher chance to include relevant variables and therefore select the best model, if the anticipated direction is accurate. For a large number of candidate variables, we present an adaptation of a Bayesian model search method for the one-sided variable selection problem to ensure fast computation. In addition, a fully Bayesian approach is used to adjust the prior inclusion probability of each one-sided model to correct for multiplicity. The performance of the proposed method is investigated using several simulation studies and two real data examples.

Bayesian hypothesis testing and estimation under the marginalized random-effects meta-analysis model.

Meta-analysis methods are used to synthesize results of multiple studies on the same topic. The most frequently used statistical model in meta-analysis is the random-effects model containing parameters for the overall effect, between-study variance in primary study's true effect size, and random effects for the study-specific effects. We propose Bayesian hypothesis testing and estimation methods using the marginalized random-effects meta-analysis (MAREMA) model where the study-specific true effects are regarded as nuisance parameters which are integrated out of the model. We propose using a flat prior distribution on the overall effect size in case of estimation and a proper unit information prior for the overall effect size in case of hypothesis testing. For the between-study variance (which can attain negative values under the MAREMA model), a proper uniform prior is placed on the proportion of total variance that can be attributed to between-study variability. Bayes factors are used for hypothesis testing that allow testing point and one-sided hypotheses. The proposed methodology has several attractive properties. First, the proposed MAREMA model encompasses models with a zero, negative, and positive between-study variance, which enables testing a zero between-study variance as it is not a boundary problem. Second, the methodology is suitable for default Bayesian meta-analyses as it requires no prior information about the unknown parameters. Third, the proposed Bayes factors can even be used in the extreme case when only two studies are available because Bayes factors are not based on large sample theory. We illustrate the developed methods by applying it to two meta-analyses and introduce easy-to-use software in the R package BFpack to compute the proposed Bayes factors.

Bayesian Testing of Scientific Expectations under Multivariate Normal Linear Models.

The multivariate normal linear model is one of the most widely employed models for statistical inference in applied research. Special cases include (multivariate) t testing, (M)AN(C)OVA, (multivariate) multiple regression, and repeated measures analysis. Statistical criteria for a model selection problem where models may have equality as well as order constraints on the model parameters based on scientific expectations are limited however. This paper presents a default Bayes factor for this inference problem using fractional Bayes methodology. Group specific fractions are used to properly control prior information. Furthermore the fractional prior is centered on the boundary of the constrained space to properly evaluate order-constrained models. The criterion enjoys various important properties under a broad set of testing problems. The methodology is readily usable via the R package 'BFpack'. Applications from the social and medical sciences are provided to illustrate the methodology.

Bayesian Network Structure and Predictability of Autistic Traits.

The aim of this work is to explore the construct of autistic traits through the lens of network analysis with recently introduced Bayesian methods. A conditional dependence network structure was estimated from a data set composed of 649 university students that completed an autistic traits questionnaire. The connectedness of the network is also explored, as well as sex differences among female and male subjects in regard to network connectivity. The strongest connections in the network are found between items that measure similar autistic traits. Traits related to social skills are the most interconnected items in the network. Sex differences are found between female and male subjects. The Bayesian network analysis offers new insight on the connectivity of autistic traits as well as confirms several findings in the autism literature.

Beneath the surface: Unearthing within-person variability and mean relations with Bayesian mixed models.

Mixed-effects models are becoming common in psychological science. Although they have many desirable features, there is still untapped potential. It is customary to view homogeneous variance as an assumption to satisfy. We argue to move beyond that perspective, and to view modeling within-person variance as an opportunity to gain a richer understanding of psychological processes. The technique to do so is based on the mixed-effects location scale model that can simultaneously estimate mixed-effects submodels to both the mean (location) and within-person variance (scale). We develop a framework that goes beyond assessing the submodels in isolation of one another and introduce a novel Bayesian hypothesis test for mean-variance correlations in the distribution of random effects. We first present a motivating example, which makes clear how the model can characterize mean-variance relations. We then apply the method to reaction times (RTs) gathered from 2 cognitive inhibition tasks. We find there are more individual differences in the within-person variance than the mean structure, as well as a complex web of structural mean-variance relations. This stands in contrast to the dominant view of within-person variance (i.e., "noise"). The results also point toward paradoxical within-person, as opposed to between-person, effects: several people had slower and less variable incongruent responses. This contradicts the typical pattern, wherein larger means tend to be associated with more variability. We conclude with future directions, spanning from methodological to theoretical inquires, that can be answered with the presented methodology. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

Decision-making with multiple correlated binary outcomes in clinical trials.

Clinical trials often evaluate multiple outcome variables to form a comprehensive picture of the effects of a new treatment. The resulting multidimensional insight contributes to clinically relevant and efficient decision-making about treatment superiority. Common statistical procedures to make these superiority decisions with multiple outcomes have two important shortcomings, however: (1) Outcome variables are often modeled individually, and consequently fail to consider the relation between outcomes; and (2) superiority is often defined as a relevant difference on a single, on any, or on all outcome(s); and lacks a compensatory mechanism that allows large positive effects on one or multiple outcome(s) to outweigh small negative effects on other outcomes. To address these shortcomings, this paper proposes (1) a Bayesian model for the analysis of correlated binary outcomes based on the multivariate Bernoulli distribution; and (2) a flexible decision criterion with a compensatory mechanism that captures the relative importance of the outcomes. A simulation study demonstrates that efficient and unbiased decisions can be made while Type I error rates are properly controlled. The performance of the framework is illustrated for (1) fixed, group sequential, and adaptive designs; and (2) non-informative and informative prior distributions.

Comparing Gaussian graphical models with the posterior predictive distribution and Bayesian model selection.

Gaussian graphical models are commonly used to characterize conditional (in)dependence structures (i.e., partial correlation networks) of psychological constructs. Recently attention has shifted from estimating single networks to those from various subpopulations. The focus is primarily to detect differences or demonstrate replicability. We introduce two novel Bayesian methods for comparing networks that explicitly address these aims. The first is based on the posterior predictive distribution, with a symmetric version of Kullback-Leibler divergence as the discrepancy measure, that tests differences between two (or more) multivariate normal distributions. The second approach makes use of Bayesian model comparison, with the Bayes factor, and allows for gaining evidence for invariant network structures. This overcomes limitations of current approaches in the literature that use classical hypothesis testing, where it is only possible to determine whether groups are significantly different from each other. With simulation we show the posterior predictive method is approximately calibrated under the null hypothesis (α = .05) and has more power to detect differences than alternative approaches. We then examine the necessary sample sizes for detecting invariant network structures with Bayesian hypothesis testing, in addition to how this is influenced by the choice of prior distribution. The methods are applied to posttraumatic stress disorder symptoms that were measured in 4 groups. We end by summarizing our major contribution, that is proposing 2 novel methods for comparing Gaussian graphical models (GGMs), which extends beyond the social-behavioral sciences. The methods have been implemented in the R package BGGM. (PsycInfo Database Record (c) 2020 APA, all rights reserved).

A tutorial on testing hypotheses using the Bayes factor.

Learning about hypothesis evaluation using the Bayes factor could enhance psychological research. In contrast to null-hypothesis significance testing it renders the evidence in favor of each of the hypotheses under consideration (it can be used to quantify support for the null-hypothesis) instead of a dichotomous reject/do-not-reject decision; it can straightforwardly be used for the evaluation of multiple hypotheses without having to bother about the proper manner to account for multiple testing; and it allows continuous reevaluation of hypotheses after additional data have been collected (Bayesian updating). This tutorial addresses researchers considering to evaluate their hypotheses by means of the Bayes factor. The focus is completely applied and each topic discussed is illustrated using Bayes factors for the evaluation of hypotheses in the context of an ANOVA model, obtained using the R package bain. Readers can execute all the analyses presented while reading this tutorial if they download bain and the R-codes used. It will be elaborated in a completely nontechnical manner: what the Bayes factor is, how it can be obtained, how Bayes factors should be interpreted, and what can be done with Bayes factors. After reading this tutorial and executing the associated code, researchers will be able to use their own data for the evaluation of hypotheses by means of the Bayes factor, not only in the context of ANOVA models, but also in the context of other statistical models. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Bayesian evaluation of informative hypotheses for multiple populations.

The software package Bain can be used for the evaluation of informative hypotheses with respect to the parameters of a wide range of statistical models. For pairs of hypotheses the support in the data is quantified using the approximate adjusted fractional Bayes factor (BF). Currently, the data have to come from one population or have to consist of samples of equal size obtained from multiple populations. If samples of unequal size are obtained from multiple populations, the BF can be shown to be inconsistent. This paper examines how the approach implemented in Bain can be generalized such that multiple-population data can properly be processed. The resulting multiple-population approximate adjusted fractional Bayes factor is implemented in the R package Bain.

Computing Bayes factors from data with missing values.

The Bayes factor is increasingly used for the evaluation of hypotheses. These may be traditional hypotheses specified using equality constraints among the parameters of the statistical model of interest or informative hypotheses specified using equality and inequality constraints. Thus far, no attention has been given to the computation of Bayes factors from data with missing values. A key property of such a Bayes factor should be that it is only based on the information in the observed values. This article will show that such a Bayes factor can be obtained using multiple imputations of the missing values. After introduction of the general framework elaborations for Bayes factors based on default or subjective prior distributions and Bayes factors based on priors specified using training data will be given. It will be illustrated that the approach proposed can be applied using R packages for multiple imputation in combination with the Bayes factor packages Bain and BayesFactor. It will furthermore be illustrated that Bayes factors computed using a single imputation of the data are very inaccurate approximations of the correct Bayes factor. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

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.

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.

Prior sensitivity analysis in default Bayesian structural equation modeling.

Bayesian structural equation modeling (BSEM) has recently gained popularity because it enables researchers to fit complex models and solve some of the issues often encountered in classical maximum likelihood estimation, such as nonconvergence and inadmissible solutions. An important component of any Bayesian analysis is the prior distribution of the unknown model parameters. Often, researchers rely on default priors, which are constructed in an automatic fashion without requiring substantive prior information. However, the prior can have a serious influence on the estimation of the model parameters, which affects the mean squared error, bias, coverage rates, and quantiles of the estimates. In this article, we investigate the performance of three different default priors: noninformative improper priors, vague proper priors, and empirical Bayes priors-with the latter being novel in the BSEM literature. Based on a simulation study, we find that these three default BSEM methods may perform very differently, especially with small samples. A careful prior sensitivity analysis is therefore needed when performing a default BSEM analysis. For this purpose, we provide a practical step-by-step guide for practitioners to conducting a prior sensitivity analysis in default BSEM. Our recommendations are illustrated using a well-known case study from the structural equation modeling literature, and all code for conducting the prior sensitivity analysis is available in the online supplemental materials. (PsycINFO Database Record