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      Indices of Effect Existence and Significance in the Bayesian Framework

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          Abstract

          Turmoil has engulfed psychological science. Causes and consequences of the reproducibility crisis are in dispute. With the hope of addressing some of its aspects, Bayesian methods are gaining increasing attention in psychological science. Some of their advantages, as opposed to the frequentist framework, are the ability to describe parameters in probabilistic terms and explicitly incorporate prior knowledge about them into the model. These issues are crucial in particular regarding the current debate about statistical significance. Bayesian methods are not necessarily the only remedy against incorrect interpretations or wrong conclusions, but there is an increasing agreement that they are one of the keys to avoid such fallacies. Nevertheless, its flexible nature is its power and weakness, for there is no agreement about what indices of “significance” should be computed or reported. This lack of a consensual index or guidelines, such as the frequentist p-value, further contributes to the unnecessary opacity that many non-familiar readers perceive in Bayesian statistics. Thus, this study describes and compares several Bayesian indices, provide intuitive visual representation of their “behavior” in relationship with common sources of variance such as sample size, magnitude of effects and also frequentist significance. The results contribute to the development of an intuitive understanding of the values that researchers report, allowing to draw sensible recommendations for Bayesian statistics description, critical for the standardization of scientific reporting.

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          Most cited references58

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          The ASA's Statement onp-Values: Context, Process, and Purpose

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            Bayes Factors

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              Stan: A Probabilistic Programming Language

              Stan is a probabilistic programming language for specifying statistical models. A Stan program imperatively defines a log probability function over parameters conditioned on specified data and constants. As of version 2.14.0, Stan provides full Bayesian inference for continuous-variable models through Markov chain Monte Carlo methods such as the No-U-Turn sampler, an adaptive form of Hamiltonian Monte Carlo sampling. Penalized maximum likelihood estimates are calculated using optimization methods such as the limited memory Broyden-Fletcher-Goldfarb-Shanno algorithm. Stan is also a platform for computing log densities and their gradients and Hessians, which can be used in alternative algorithms such as variational Bayes, expectation propagation, and marginal inference using approximate integration. To this end, Stan is set up so that the densities, gradients, and Hessians, along with intermediate quantities of the algorithm such as acceptance probabilities, are easily accessible. Stan can be called from the command line using the cmdstan package, through R using the rstan package, and through Python using the pystan package. All three interfaces support sampling and optimization-based inference with diagnostics and posterior analysis. rstan and pystan also provide access to log probabilities, gradients, Hessians, parameter transforms, and specialized plotting.
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                Author and article information

                Contributors
                Journal
                Front Psychol
                Front Psychol
                Front. Psychol.
                Frontiers in Psychology
                Frontiers Media S.A.
                1664-1078
                10 December 2019
                2019
                : 10
                : 2767
                Affiliations
                [1] 1School of Social Sciences, Nanyang Technological University , Singapore, Singapore
                [2] 2Department of Psychology, Ben-Gurion University of the Negev , Beersheba, Israel
                [3] 3Centre for Research and Development in Learning, Nanyang Technological University , Singapore, Singapore
                [4] 4Lee Kong Chian School of Medicine, Nanyang Technological University , Singapore, Singapore
                [5] 5Department of Medical Sociology, University Medical Center Hamburg-Eppendorf , Hamburg, Germany
                Author notes

                Edited by: Pietro Cipresso, Istituto Auxologico Italiano (IRCCS), Italy

                Reviewed by: Richard S. John, University of Southern California, United States; Jose D. Perezgonzalez, Massey University Business School, New Zealand

                *Correspondence: Dominique Makowski, dmakowski@ 123456ntu.edu.sg ; dom.makowski@ 123456gmail.com
                S. H. Annabel Chen, annabelchen@ 123456ntu.edu.sg

                These authors share senior authorship

                This article was submitted to Quantitative Psychology and Measurement, a section of the journal Frontiers in Psychology

                Article
                10.3389/fpsyg.2019.02767
                6914840
                31920819
                00480a43-b6b5-41a7-a185-ff57800827fb
                Copyright © 2019 Makowski, Ben-Shachar, Chen and Lüdecke.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 18 September 2019
                : 25 November 2019
                Page count
                Figures: 6, Tables: 3, Equations: 1, References: 63, Pages: 14, Words: 0
                Categories
                Psychology
                Original Research

                Clinical Psychology & Psychiatry
                bayesian,significance,nhst,p-value,bayes factors
                Clinical Psychology & Psychiatry
                bayesian, significance, nhst, p-value, bayes factors

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