Boba: Authoring and Visualizing Multiverse Analyses

The multiverse of universes: A tutorial to plan, execute and interpret multiverses analyses using the R package multiverse

Even when guided by strong theories and sound methods, researchers must often choose a singular course of action from multiple viable alternatives. Regardless of the choice, it, along with all other choices made during the research process, individually and collectively affects study results, often in unpredictable ways. The inability to disentangle how much of an observed effect is attributable to the phenomenon of interest, and how much is attributable to what have come to be known as researcher degrees of freedom (RDF), slows theoretical progress and stymies practical implementation. However, if one could examine the results from a particular set of RDF (known as a universe) against a systematically and comprehensively determined background of alternative viable universes (known as a multiverse), then the effects of RDF can be directly examined to provide greater context and clarity to future researchers, and greater confidence in the recommendations to practitioners. This tutorial demonstrates a means to map result variability directly and efficiently, and empirically investigate RDF impact on conclusions via multiverse analysis. Using the R package multiverse, we outline best practices in planning, executing and interpreting of multiverse analyses.

Post-selection Inference in Multiverse Analysis (PIMA): An Inferential Framework Based on the Sign Flipping Score Test

When analyzing data, researchers make some choices that are either arbitrary, based on subjective beliefs about the data-generating process, or for which equally justifiable alternative choices could have been made. This wide range of data-analytic choices can be abused and has been one of the underlying causes of the replication crisis in several fields. Recently, the introduction of multiverse analysis provides researchers with a method to evaluate the stability of the results across reasonable choices that could be made when analyzing data. Multiverse analysis is confined to a descriptive role, lacking a proper and comprehensive inferential procedure. Recently, specification curve analysis adds an inferential procedure to multiverse analysis, but this approach is limited to simple cases related to the linear model, and only allows researchers to infer whether at least one specification rejects the null hypothesis, but not which specifications should be selected. In this paper, we present a Post-selection Inference approach to Multiverse Analysis (PIMA) which is a flexible and general inferential approach that considers for all possible models, i.e., the multiverse of reasonable analyses. The approach allows for a wide range of data specifications (i.e., preprocessing) and any generalized linear model; it allows testing the null hypothesis that a given predictor is not associated with the outcome, by combining information from all reasonable models of multiverse analysis, and provides strong control of the family-wise error rate allowing researchers to claim that the null hypothesis can be rejected for any specification that shows a significant effect. The inferential proposal is based on a conditional resampling procedure. We formally prove that the Type I error rate is controlled, and compute the statistical power of the test through a simulation study. Finally, we apply the PIMA procedure to the analysis of a real dataset on the self-reported hesitancy for the COronaVIrus Disease 2019 (COVID-19) vaccine before and after the 2020 lockdown in Italy. We conclude with practical recommendations to be considered when implementing the proposed procedure.

Reproducibility in Neuroimaging Analysis: Challenges and Solutions

Recent years have marked a renaissance in efforts to increase research reproducibility in psychology, neuroscience, and related fields. Reproducibility is the cornerstone of a solid foundation of fundamental research-one that will support new theories built on valid findings and technological innovation that works. The increased focus on reproducibility has made the barriers to it increasingly apparent, along with the development of new tools and practices to overcome these barriers. Here, we review challenges, solutions, and emerging best practices with a particular emphasis on neuroimaging studies. We distinguish 3 main types of reproducibility, discussing each in turn. Analytical reproducibility is the ability to reproduce findings using the same data and methods. Replicability is the ability to find an effect in new datasets, using the same or similar methods. Finally, robustness to analytical variability refers to the ability to identify a finding consistently across variation in methods. The incorporation of these tools and practices will result in more reproducible, replicable, and robust psychological and brain research and a stronger scientific foundation across fields of inquiry.

The replication crisis has led to positive structural, procedural, and community changes

The emergence of large-scale replication projects yielding successful rates substantially lower than expected caused the behavioural, cognitive, and social sciences to experience a so-called 'replication crisis'. In this Perspective, we reframe this 'crisis' through the lens of a credibility revolution, focusing on positive structural, procedural and community-driven changes. Second, we outline a path to expand ongoing advances and improvements. The credibility revolution has been an impetus to several substantive changes which will have a positive, long-term impact on our research environment.

Multiverse analyses of fear acquisition and extinction retention in posttraumatic stress disorder

Persistent fear is a cardinal feature of posttraumatic stress disorder (PTSD), and deficient fear extinction retention is a proposed illness mechanism and target of exposure-based therapy. However, evidence for deficient fear extinction in PTSD has been mixed using laboratory paradigms, which may relate to underidentified methodological variation across studies. We reviewed the literature to identify parameters that differ across studies of fear extinction retention in PTSD. We then performed Multiverse Analysis in a new sample, to quantify the impact of those methodological parameters on statistical findings. In 25 PTSD patients (15 female) and 36 trauma-exposed non-PTSD controls (TENC) (20 female), we recorded skin conductance response (SCR) during fear acquisition and extinction learning (day 1) and extinction recall (day 2). A first Multiverse Analysis examined the effects of methodological parameters identified by the literature review on comparisons of SCR-based fear extinction retention in PTSD versus TENC. A second Multiverse Analysis examined the effects of those methodological parameters on comparisons of SCR to a danger cue (CS+) versus safety cue (CS-) during fear acquisition. Both the literature review and the Multiverse Analysis yielded inconsistent findings for fear extinction retention in PTSD versus TENC, and most analyses found no statistically significant group difference. By contrast, significantly elevated SCR to CS+ versus CS- was consistently found across all analyses in the literature review and the Multiverse Analysis of new data. We discuss methodological parameters that may most contribute to inconsistent findings of fear extinction retention deficit in PTSD and implications for future clinical research.

Open and reproducible neuroimaging: From study inception to publication

Empirical observations of how labs conduct research indicate that the adoption rate of open practices for transparent, reproducible, and collaborative science remains in its infancy. This is at odds with the overwhelming evidence for the necessity of these practices and their benefits for individual researchers, scientific progress, and society in general. To date, information required for implementing open science practices throughout the different steps of a research project is scattered among many different sources. Even experienced researchers in the topic find it hard to navigate the ecosystem of tools and to make sustainable choices. Here, we provide an integrated overview of community-developed resources that can support collaborative, open, reproducible, replicable, robust and generalizable neuroimaging throughout the entire research cycle from inception to publication and across different neuroimaging modalities. We review tools and practices supporting study inception and planning, data acquisition, research data management, data processing and analysis, and research dissemination. An online version of this resource can be found at https://oreoni.github.io. We believe it will prove helpful for researchers and institutions to make a successful and sustainable move towards open and reproducible science and to eventually take an active role in its future development.

Exposing and overcoming the fixed-effect fallacy through crowd science

By organizing crowds of scientists to independently tackle the same research questions, we can collectively overcome the generalizability crisis. Strategies to draw inferences from a heterogeneous set of research approaches include aggregation, for instance, meta-analyzing the effect sizes obtained by different investigators, and parsing, attempting to identify theoretically meaningful moderators that explain the variability in results.

A Critical Reflection on Visualization Research: Where Do Decision Making Tasks Hide?

It has been widely suggested that a key goal of visualization systems is to assist decision making, but is this true? We conduct a critical investigation on whether the activity of decision making is indeed central to the visualization domain. By approaching decision making as a user task, we explore the degree to which decision tasks are evident in visualization research and user studies. Our analysis suggests that decision tasks are not commonly found in current visualization task taxonomies and that the visualization field has yet to leverage guidance from decision theory domains on how to study such tasks. We further found that the majority of visualizations addressing decision making were not evaluated based on their ability to assist decision tasks. Finally, to help expand the impact of visual analytics in organizational as well as casual decision making activities, we initiate a research agenda on how decision making assistance could be elevated throughout visualization research.

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.