Refining Bayesian hierarchical MPT modeling: Integrating prior knowledge and ordinal expectations.

Multinomial processing tree (MPT) models are a broad class of statistical models used to test sophisticated psychological theories. The research questions derived from these theories often go beyond simple condition effects on parameters and involve ordinal expectations (e.g., the same-direction effect on the memory parameter is stronger in one experimental condition than another) or disordinal expectations (e.g., the effect reverses in one experimental condition). Here, we argue that by refining common modeling practices, Bayesian hierarchical models are well suited to estimate and test these expectations. Concretely, we show that the default priors proposed in the literature lead to nonsensical predictions for individuals and the population distribution, leading to problems not only in model comparison but also in parameter estimation. Rather than relying on these priors, we argue that MPT modelers should determine priors that are consistent with their theoretical knowledge. In addition, we demonstrate how Bayesian model comparison may be used to test ordinal and disordinal interactions by means of Bayes factors. We apply the techniques discussed to empirical data from Bell et al. Journal of Experimental Psychology: Learning, Memory, and Cognition, 41, 456-472 (2015).

"This behavior strikes us as ideal": assessment and anticipations of Huisman (2022).

Huisman (Psychonomic Bulletin & Review, 1-10. 2022) argued that a valid measure of evidence should indicate more support in favor of a true alternative hypothesis when sample size is large than when it is small. Bayes factors may violate this pattern and hence Huisman concluded that Bayes factors are invalid as a measure of evidence. In this brief comment we call attention to the following: (1) Huisman's purported anomaly is in fact dictated by probability theory; (2) Huisman's anomaly has been discussed and explained in the statistical literature since 1939; the anomaly was also highlighted in the Psychonomic Bulletin & Review article by Rouder et al. (2009), who interpreted the anomaly as "ideal": an interpretation diametrically opposed to that of Huisman. We conclude that when intuition clashes with probability theory, chances are that it is intuition that needs schooling.

Reducing bias in secondary data analysis via an Explore and Confirm Analysis Workflow (ECAW): a proposal and survey of observational researchers.

Background. Although preregistration can reduce researcher bias and increase transparency in primary research settings, it is less applicable to secondary data analysis. An alternative method that affords additional protection from researcher bias, which cannot be gained from conventional forms of preregistration alone, is an Explore and Confirm Analysis Workflow (ECAW). In this workflow, a data management organization initially provides access to only a subset of their dataset to researchers who request it. The researchers then prepare an analysis script based on the subset of data, upload the analysis script to a registry, and then receive access to the full dataset. ECAWs aim to achieve similar goals to preregistration, but make access to the full dataset contingent on compliance. The present survey aimed to garner information from the research community where ECAWs could be applied-employing the Avon Longitudinal Study of Parents and Children (ALSPAC) as a case example. Methods. We emailed a Web-based survey to researchers who had previously applied for access to ALSPAC's transgenerational observational dataset. Results. We received 103 responses, for a 9% response rate. The results suggest that-at least among our sample of respondents-ECAWs hold the potential to serve their intended purpose and appear relatively acceptable. For example, only 10% of respondents disagreed that ALSPAC should run a study on ECAWs (versus 55% who agreed). However, as many as 26% of respondents agreed that they would be less willing to use ALSPAC data if they were required to use an ECAW (versus 45% who disagreed). Conclusion. Our data and findings provide information for organizations and individuals interested in implementing ECAWs and related interventions. Preregistration. https://osf.io/g2fw5 Deviations from the preregistration are outlined in electronic supplementary material A.

Multibridge: an R package to evaluate informed hypotheses in binomial and multinomial models.

The multibridge R package allows a Bayesian evaluation of informed hypotheses [Formula: see text] applied to frequency data from an independent binomial or multinomial distribution. multibridge uses bridge sampling to efficiently compute Bayes factors for the following hypotheses concerning the latent category proportions 𝜃: (a) hypotheses that postulate equality constraints (e.g., 𝜃1 = 𝜃2 = 𝜃3); (b) hypotheses that postulate inequality constraints (e.g., 𝜃1 < 𝜃2 < 𝜃3 or 𝜃1 > 𝜃2 > 𝜃3); (c) hypotheses that postulate combinations of inequality constraints and equality constraints (e.g., 𝜃1 < 𝜃2 = 𝜃3); and (d) hypotheses that postulate combinations of (a)-(c) (e.g., 𝜃1 < (𝜃2 = 𝜃3),𝜃4). Any informed hypothesis [Formula: see text] may be compared against the encompassing hypothesis [Formula: see text] that all category proportions vary freely, or against the null hypothesis [Formula: see text] that all category proportions are equal. multibridge facilitates the fast and accurate comparison of large models with many constraints and models for which relatively little posterior mass falls in the restricted parameter space. This paper describes the underlying methodology and illustrates the use of multibridge through fully reproducible examples.

Evaluating multinomial order restrictions with bridge sampling.

Hypotheses concerning the distribution of multinomial proportions typically entail exact equality constraints that can be evaluated using standard tests. Whenever researchers formulate inequality constrained hypotheses, however, they must rely on sampling-based methods that are relatively inefficient and computationally expensive. To address this problem we developed a bridge sampling routine that allows an efficient evaluation of multinomial inequality constraints. An empirical application showcases that bridge sampling outperforms current Bayesian methods, especially when relatively little posterior mass falls in the restricted parameter space. The method is extended to mixtures between equality and inequality constrained hypotheses. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

A survey on how preregistration affects the research workflow: better science but more work.

The preregistration of research protocols and analysis plans is a main reform innovation to counteract confirmation bias in the social and behavioural sciences. While theoretical reasons to preregister are frequently discussed in the literature, the individually experienced advantages and disadvantages of this method remain largely unexplored. The goal of this exploratory study was to identify the perceived benefits and challenges of preregistration from the researcher's perspective. To this end, we surveyed 355 researchers, 299 of whom had used preregistration in their own work. The researchers indicated the experienced or expected effects of preregistration on their workflow. The results show that experiences and expectations are mostly positive. Researchers in our sample believe that implementing preregistration improves or is likely to improve the quality of their projects. Criticism of preregistration is primarily related to the increase in work-related stress and the overall duration of the project. While the benefits outweighed the challenges for the majority of researchers with preregistration experience, this was not the case for the majority of researchers without preregistration experience. The experienced advantages and disadvantages identified in our survey could inform future efforts to improve preregistration and thus help the methodology gain greater acceptance in the scientific community.

Seven steps toward more transparency in statistical practice.

We argue that statistical practice in the social and behavioural sciences benefits from transparency, a fair acknowledgement of uncertainty and openness to alternative interpretations. Here, to promote such a practice, we recommend seven concrete statistical procedures: (1) visualizing data; (2) quantifying inferential uncertainty; (3) assessing data preprocessing choices; (4) reporting multiple models; (5) involving multiple analysts; (6) interpreting results modestly; and (7) sharing data and code. We discuss their benefits and limitations, and provide guidelines for adoption. Each of the seven procedures finds inspiration in Merton's ethos of science as reflected in the norms of communalism, universalism, disinterestedness and organized scepticism. We believe that these ethical considerations-as well as their statistical consequences-establish common ground among data analysts, despite continuing disagreements about the foundations of statistical inference.

Consensus-based guidance for conducting and reporting multi-analyst studies.

Any large dataset can be analyzed in a number of ways, and it is possible that the use of different analysis strategies will lead to different results and conclusions. One way to assess whether the results obtained depend on the analysis strategy chosen is to employ multiple analysts and leave each of them free to follow their own approach. Here, we present consensus-based guidance for conducting and reporting such multi-analyst studies, and we discuss how broader adoption of the multi-analyst approach has the potential to strengthen the robustness of results and conclusions obtained from analyses of datasets in basic and applied research.

The JASP guidelines for conducting and reporting a Bayesian analysis.

Despite the increasing popularity of Bayesian inference in empirical research, few practical guidelines provide detailed recommendations for how to apply Bayesian procedures and interpret the results. Here we offer specific guidelines for four different stages of Bayesian statistical reasoning in a research setting: planning the analysis, executing the analysis, interpreting the results, and reporting the results. The guidelines for each stage are illustrated with a running example. Although the guidelines are geared towards analyses performed with the open-source statistical software JASP, most guidelines extend to Bayesian inference in general.

Author Correction: A consensus-based transparency checklist.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The Creativity-Verification Cycle in Psychological Science: New Methods to Combat Old Idols.

Over the years, researchers in psychological science have documented and investigated a host of powerful cognitive fallacies, including hindsight bias and confirmation bias. Researchers themselves may not be immune to these fallacies and may unwittingly adjust their statistical analysis to produce an outcome that is more pleasant or better in line with prior expectations. To shield researchers from the impact of cognitive fallacies, several methodologists are now advocating preregistration-that is, the creation of a detailed analysis plan before data collection or data analysis. One may argue, however, that preregistration is out of touch with academic reality, hampering creativity and impeding scientific progress. We provide a historical overview to show that the interplay between creativity and verification has shaped theories of scientific inquiry throughout the centuries; in the currently dominant theory, creativity and verification operate in succession and enhance one another's effectiveness. From this perspective, the use of preregistration to safeguard the verification stage will help rather than hinder the generation of fruitful new ideas.

Bayesian inference for psychology. Part II: Example applications with JASP.

Bayesian hypothesis testing presents an attractive alternative to p value hypothesis testing. Part I of this series outlined several advantages of Bayesian hypothesis testing, including the ability to quantify evidence and the ability to monitor and update this evidence as data come in, without the need to know the intention with which the data were collected. Despite these and other practical advantages, Bayesian hypothesis tests are still reported relatively rarely. An important impediment to the widespread adoption of Bayesian tests is arguably the lack of user-friendly software for the run-of-the-mill statistical problems that confront psychologists for the analysis of almost every experiment: the t-test, ANOVA, correlation, regression, and contingency tables. In Part II of this series we introduce JASP ( http://www.jasp-stats.org ), an open-source, cross-platform, user-friendly graphical software package that allows users to carry out Bayesian hypothesis tests for standard statistical problems. JASP is based in part on the Bayesian analyses implemented in Morey and Rouder's BayesFactor package for R. Armed with JASP, the practical advantages of Bayesian hypothesis testing are only a mouse click away.

A tutorial on bridge sampling.

The marginal likelihood plays an important role in many areas of Bayesian statistics such as parameter estimation, model comparison, and model averaging. In most applications, however, the marginal likelihood is not analytically tractable and must be approximated using numerical methods. Here we provide a tutorial on bridge sampling (Bennett, 1976; Meng & Wong, 1996), a reliable and relatively straightforward sampling method that allows researchers to obtain the marginal likelihood for models of varying complexity. First, we introduce bridge sampling and three related sampling methods using the beta-binomial model as a running example. We then apply bridge sampling to estimate the marginal likelihood for the Expectancy Valence (EV) model-a popular model for reinforcement learning. Our results indicate that bridge sampling provides accurate estimates for both a single participant and a hierarchical version of the EV model. We conclude that bridge sampling is an attractive method for mathematical psychologists who typically aim to approximate the marginal likelihood for a limited set of possibly high-dimensional models.

Study Protocol on Cognitive Performance in Bulgaria, Croatia, and the Netherlands: The Normacog Brief Battery.

The Normacog Brief Battery (NBB) provides a comprehensive overview of an individual's cognitive functioning within a short amount of time. It was originally developed for the Spanish population in Spain. However, there is a considerable need for brief batteries in clinical neuropsychological assessment, especially in eastern European countries. Cultural background and other individual characteristics-such as age, level of education, and sex-are shown to influence both cognition and patients' performance on neuropsychological tests. Therefore, it is important to develop understanding of how and why culture impacts on cognitive testing and determine which sociodemographic variables affect cognitive performance. The current study aims to translate, adapt, and standardize the NBB in Bulgaria, Croatia, and the Netherlands, and to analyze the effect of sex, age, and education level on cognitive performance between these three countries. This brief battery assesses eleven cognitive domains, including those most currently relevant in cognition such as premorbid intelligence, attention, executive function, processing speed, and memory. The translation and adaptation of the battery for different cultures will be done using the back-translation process. After exclusion criteria, the current study will include a total sample of 300 participants (≥18 years old). The samples of 100 participants per country will be balanced through the consideration of their age and level of education. Effects of the sociodemographic variables (age, level of education, and sex) on cognitive performance are expected. Furthermore, this relationship is expected to differ across countries. A multivariate hierarchical linear regression will be used and exploratory analysis will be carried out to investigate further effects. The results will be particularly valuable for future research and assessment in cognitive performance. The growing demand for accurate and fast neuropsychological assessment shows the importance of creating a universal brief assessment tool for wider cross-cultural application.