A Bayesian perspective on Biogen's aducanumab trial.

This perspective is a companion to a recent editorial on the use of Bayesian analysis in clinical research. We aim to introduce and highlight the relevance and advantages that Bayesian inference offers to clinical trials using the data on the amyloid antibody aducanumab presented at a Food and Drug Administration hearing in November 2020 as an applied example. We apply Bayesian analysis of model plausibility and effect sizes based on simulated data of the two phase 3 trials of aducanumab in prodromal and mild dementia stages of Alzheimer's disease (AD). Bayesian analysis can quantify evidence in favor of, or against, the presence of an effect (i.e., provide evidence of absence), as well as assess the strength of the effect. This is in contrast to the binary conclusions provided by frequentist tests.

Bayes Factors for Mixed Models: Perspective on Responses.

In van Doorn et al. (2021), we outlined a series of open questions concerning Bayes factors for mixed effects model comparison, with an emphasis on the impact of aggregation, the effect of measurement error, the choice of prior distributions, and the detection of interactions. Seven expert commentaries (partially) addressed these initial questions. Surprisingly perhaps, the experts disagreed (often strongly) on what is best practice-a testament to the intricacy of conducting a mixed effect model comparison. Here, we provide our perspective on these comments and highlight topics that warrant further discussion. In general, we agree with many of the commentaries that in order to take full advantage of Bayesian mixed model comparison, it is important to be aware of the specific assumptions that underlie the to-be-compared models.

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.

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.

Behavioural and neural evidence for self-reinforcing expectancy effects on pain.

Beliefs and expectations often persist despite evidence to the contrary. Here we examine two potential mechanisms underlying such 'self-reinforcing' expectancy effects in the pain domain: modulation of perception and biased learning. In two experiments, cues previously associated with symbolic representations of high or low temperatures preceded painful heat. We examined trial-to-trial dynamics in participants' expected pain, reported pain and brain activity. Subjective and neural pain responses assimilated towards cue-based expectations, and pain responses in turn predicted subsequent expectations, creating a positive dynamic feedback loop. Furthermore, we found evidence for a confirmation bias in learning: higher- and lower-than-expected pain triggered greater expectation updating for high- and low-pain cues, respectively. Individual differences in this bias were reflected in the updating of pain-anticipatory brain activity. Computational modelling provided converging evidence that expectations influence both perception and learning. Together, perceptual assimilation and biased learning promote self-reinforcing expectations, helping to explain why beliefs can be resistant to change.

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.