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In progress

Submitted or under revision

In press

Holzmeister, F., Johannesson, M., Camerer, C.F., Chen, Y., Ho, T.-H., Hoogeveen, S., Huber, J., Imai, N., Imai, T., Jin, L., Kirchler, M., Ly, A., Mandl, B., Manfredi, D., Nave, G., Nosek, B.A., Pfeiffer, T., Sarafoglou, A., Schwaiger, R., Wagenmakers, E.-J., Waldén, V., Dreber, A. (in press). Examining the replicability of online experiments selected by a decision market. Nature Human Behaviour

Maier, M., Bartoš, F., Quintana, D. S., Dablander, F., van den Bergh, D., Marsman, M., Ly, A., Wagenmakers, E.-J. (in press). Model-Averaged Bayesian t-Tests. Psychonomic Bulletin & Review

Ly, A. (in press). Is there a grow like criterion that does not lead to point priors? The Journal of the Royal Statistical Society, Series B (Statistical Methodology) . To appear as Alexander Ly’s contribution to the Discussion of Safe Testing by Grünwald, de Heide,and Koolen.

Published articles

2024

Ly, A., Boehm, U., Grünwald, P.D. (2024). Anytime-valid confidence sequences as a resolution to the Bayesian/frequentist interval debate. Bayesian Analysis, 19(3), 970-972. Published as “Contributed comment” on Defining a Credible Interval Is Not Always Possible with “Point-Null” Priors: A Lesser-Known Correlate of the Jeffreys-Lindley Paradox (with Discussion) by Harlan Campbell and Paul Gustafson.

Dablander, F., van den Bergh, D., Wagenmakers, E.-J., Ly, A. (2024). Default Bayes Factors for Testing the (In)equality of Several Population Variances. Bayesian analysis, 19(3), 699-723.

ter Schure, J., Perez-Ortiz, M.F., Ly, A., Grünwald, P.D. (2024). The Safe Logrank Test: Error Control under Continuous Monitoring with Unlimited Horizon. The New England Journal of Statistics in Data Science, 2(2), 190-214.

Pawel, S., Ly, A., & Wagenmakers, E.-J. (2024). Evidential Calibration of Confidence Intervals. The American Statistician., 78(1), 47-57.

Turner, R., Ly, A., Grünwald, P.D. (2024). Generic E-variables for exact sequential k-sample tests that allow for optional stopping. Journal of Statistical Planning and Inference, 230, 106116.

2023

Wagenmakers, E.-J., & Ly, A. (2023). History and nature of the Jeffreys-Lindley paradox. Archive for History of Exact Sciences, 77, 25-72.

Gray, J., Cherry, J. L., Wagenmakers, E.-J., & Ly, A. (2023). The Jeffreys-Lindley paradox: An exchange. Archive for History of Exact Sciences, 77, 443-449.

王允宏, van den Bergh, D., Aust, F., Ly, A., Wagenmakers, E.-J., 胡传鹏 (2023). 贝叶斯方差分析在JASP中的实现 Psychology: Techniques and Application, 11(9), 528-541. (English title: “The implementation of Bayesian ANOVA in JASP: A Practical Primer”)

Heck, D., Boehm, U., Böing-Messing, F., Bürkner, P., Derks, K., Dienes, Z., Fu, Q., Gu, X., Karimova, D., Kiers, H. A. L., Klugkist, I., Kuipers, R. M., Lee, M. D., Leenders, R., Leplaa, H. J., Linde, M., Ly, A., Meijerink-Bosman, M., Moerbeek, M., Mulder, J., Palfi, B., Schönbrodt, F. D., Tendeiro, J. N., van den Bergh, D., van Lissa, C., van RavenZwaaij, D., Vanpaemel, W., Wagenmakers, E.-J., Williams, D. R., Zondervan-Zwijnenburg, M., Hoijtink, H. (2023). A Review of Applications of the Bayes Factor in Psychological Research. Psychological Methods, 28(3), 558-579.

Sarafoglou, A., Haaf, J. M., Ly, A., Gronau, Q. F., Wagenmakers, E.-J., & Marsman, M. (2023). Evaluating multinomial order restrictions with bridge sampling. Psychological Methods, 28(2), 322-338. Supplemental materials.

2022

Ly, A., Wagenmakers, E.-J. (2022). Bayes Factors for Peri-Null Hypotheses. Test, 31, 1121-1142.

Ly, A., & Wagenmakers, E.-J. (2022). Measure-theoretic musings cannot salvage the Full Bayesian Significance Test as a measure of evidence: Rejoinder to Kelter. Computational Brain & Behavior, 5(4), 583-589.

Ly, A., Wagenmakers, E.-J. (2022). A Critical Evaluation of the FBST ev for Bayesian Hypothesis Testing. Computational Brain & Behavior, 5(4), 564-571.

Temp, A. G. M., Ly, A., van Doorn, J., Wagenmakers, E.-J., Tang, Y., Lutz, M. W., & Teipel, S. (2022). A Bayesian perspective on Biogen’s Aducanumab trial. Alzheimer’s & Dementia, 18(11), 2341-2351.

2021

Bartos, F, Gronau, Q. F., Timmers, B., Otte, W. M., Ly, A., & Wagenmakers, E.-J. (2021). Bayesian Model-Averaged Meta-Analysis in Medicine. Statistics in Medicine, 40, 6743-6761.

van den Bergh, D., Clyde, M. A., Gupta, A.R.K.N., de Jong, T., Gronau, Q. F., Marsman, M., Ly, A., Wagenmakers, E.-J. (2021). A Tutorial on Bayesian Multi-Model Linear Regression with BAS and JASP. Behavior Research Methods, 53, 2351-2371. Supplemental materials.

ter Schure, J., Grünwald, P.D. & Ly, A. (2021). Pandemic preparedness in data sharing; lessons learned from collaborating in a live meta-analysis STAtOR, 22, 47-52.

van Doorn, J., van den Bergh, D., Bohm, U., Dablander, F., Derks, K., Draws, T., Evans, N.J., Gronau, Q.F., Hinne, M., Kucharsky, S., Ly., A., Marsman, M., Matzke, D., Gupta, A.R.K.N., Sarafoglou, A., Stefan, A., Voelkel, J.G., & Wagenmakers, E.-J. (2021). The JASP Guidelines for Conducting and Reporting a Bayesian Analysis. Psychonomic Bulletin & Review, 28(3), 813–826. https://doi.org/10.3758/s13423-020-01798-5

Van den Bergh, D., Haaf, J.M., Ly, A., Rouder, J.N., & Wagenmakers, E.-J. (2021). A Cautionary Note on Estimating Effect Size. Advances in Methods and Practices in Psychological Science, 4(1). https://doi.org/10.1177/2515245921992035

Ly, A., van den Bergh, D., Bartos, F., & Wagenmakers, E.-J. (2021). Bayesian inference with JASP. ISBA Bulletin, 28(1), 7–15.

Weigard, A., Brislin, S.J., Cope, L.M., Hardee, J.E., Martz, M.E., Ly, A., Zucker, R.A., Sripada, C., Heitzeg, M.M. (2021). Evidence accumulation and associated error-related brain activity as computationally-informed prospective predictors of substance use in emerging adulthood. Psychopharmacology., 238(9), 2629-2644. Supplement

van Doorn, J., van den Bergh, D., Dablander, F., van Dongen, N., Derks, K., Evans, N. J., Gronau, Q. F., Haaf, J. M., Kunisato, Y., Ly, A., Marsman, M., Sarafoglou, A., Stefan, A., & Wagenmakers, E.-J. (2021). Strong Public Claims May Not Reflect Researchers’ Private Convictions. Significance, 18(1), 44-45. Supplemental materials.

2020

Faulkenberry, T. J., Ly, A., & Wagenmakers, E.-J. (2020). Bayesian inference in numerical cognition: A tutorial using JASP. Journal of Numerical Cognition, 6(2), 231-259. Supplemental materials.

van den Bergh, D., van Doorn, J., Marsman, M., Draws, T., van Kesteren, E., Derks, K., Dablander, F., Gronau, Q. F., Kucharsky, S., Gupta, A. R. K. N., Sarafoglou, A., Voelkel, J. G., Stefan, A., Ly, A., Hinne, M., Matzke, D., Wagenmakers, E.-J. (2020). A Tutorial on Conducting and Interpreting a Bayesian ANOVA in JASP L’Année psychologique, 120, 73–96.

Landy, J. F., Jia, M., Ding, I. L., Viganola, D., Tierney, W., Dreber, A., Johannesson, M., Pfeiffer, T., Ebersole, C. R., Gronau, Q. F., Ly, A., van den Bergh, D., Marsman, M., Derks, K., Wagenmakers, E.–J., Proctor, A., Bartels, D. M., Bauman, C. W., Brady, W. J., Cheung, F., Cimpian, A., Dohle, S., Donnellan, M. B., Hahn, A., Hall, M. P., Jimrenez–Leal, W., Johnson, D. J., Lucas, R. E., Monin, B., Montealegre, A., Mullen, E., Pang, J., Ray, J., Reinero, D. A., Reynolds, J., Sowden, W., Storage, D., Su, R., Tworek, C. M., Van Bavel, J. J., Walco, D., Wills, J., Xu, X., Yam, K. C., Yang, X., Cunningham, W. A., Schweinsberg, M., Urwitz, M., Crowdsourcing Hypothesis Tests Collaboration, T., & Uhlmann, E. L. (2020). Crowdsourcing Hypothesis Tests: Making transparent how design choices shape research results. Psychological Bulletin, 146(5), 451–479. OSF repository. The Bayesian analyses report can found here

van Doorn, J., Ly, A., Marsman, M., & Wagenmakers, E.-J. (2020). Bayesian rank-based hypothesis testing for the rank sum test, the signed rank test, and Spearman’s ρ. Journal of Applied Statistics, 47(16), 2984-3006.

Giolla, E. M., & Ly, A. (2020). What to do with all these Bayes factors: How to make Bayesian reports in deception research more informative. Legal and Criminological Psychology, 25(2), 65-71. See also the reply by McLatchie, Warmelink and Tkacheva.

Ly, A., Stefan, A., van Doorn, J., Dablander, F., van den Bergh, D., Sarafoglou, A., Kucharsky, S., Derks, K., Gronau, Q. F., Gupta, A.R.K.N., Boehm, U., van Kesteren, E.-.J., Hinne, M., Matzke, D., Marsman., M, ., & Wagenmakers, E.-J. (2020). The Bayesian Methodology of Sir Harold Jeffreys as a Practical Alternative to the P-value Hypothesis Test. Computational Brain & Behavior 3, 153-161.

Gronau, Q. F., Ly, A., & Wagenmakers, E.-J. (2020). Informed Bayesian t-tests. The American Statistician, 74(2), 137-143.

Hutton, J. L., Diggle, P. J., Bird, S. M., Hennig, C., Longford, N., Mathur, M. B., Vander Weele, T. J., Ioannidis, J. P. A., Chai, C. P., Dowe, D. L., Ferguson, J., Fitz-Simon, N., Friede, T., Rover, C., Grieve, A. P., Kumar, K., Ly, A., Mansmann, U., Mateu, J., Matthews, R. A. J. & 10 others, Neuenschwander, B., Zwahlen, M., Pericchi, L., Roes, K. C. B., Senn, S., Wagenmakers, E. M., Rice, K., Krakauer, C., Bonnett, T. & Held, L., (2020). Discussion on the meeting on ‘Signs and sizes:understanding and replicating statistical findings. Journal of the Royal Statistical Society. Series A (General), 183, 449–469. Two comments: one with EJ Wagenmakers on Held and one on Rice, Bonnett, and Krakauer.

2019

Ly, A., Etz, A., Marsman, M., & Wagenmakers, E.-J. (2019). Replication Bayes Factors from Evidence Updating. Behavior Research Methods, 51(6), pp 2498-2508.

van Doorn, J., Ly, A., Marsman, M., & Wagenmakers, E.-J. (2019). Bayesian Estimation of Kendall’s tau Using a Latent Normal Approach. Statistics and Probability Letters, 145, 268-272. DOI: http://doi.org/10.1016/j.spl.2018.10.004

Love, J., Selker, R., Marsman, M., Jamil, T., Dropmann, D., Verhagen, A. J., Ly, A., Gronau, Q. F., Šmíra, M., Epskamp, S., Matzke, D., Wild, A., Knight, P., Rouder, J. N., Morey, R. D., Wagenmakers, E.-J. (2019). JASP: graphical statistical software for common statistical designs Journal of Statistical Software, 88(2).

Haaf, J.M., Ly, A., Wagenmakers, E.-J. (2019). Retire significance, but still test hypotheses Nature, 567, 461.

2018

van Doorn, J., Ly, A., Marsman, M., & Wagenmakers, E.-J. (2018). Bayesian inference for Kendall’s rank correlation coefficient. The American Statistician, 72(4), 303-308.

胡传鹏, 孔祥祯, Wagenmakers, E.-J., Ly, A., & 彭凯平 (2018). 贝叶斯因子及其在JASP中的实现 Advances in Psychological Sciences, 26(6), 951-965. (English title: The Bayes factor and its implementation in JASP: A practical primer)

Ly, A., Gupta, A.R.K.N., Etz, A., Marsman, M., Gronau, Q. F., & Wagenmakers, E.-J. (2018). Bayesian Reanalyses from Summary Statistics: A Guide for Academic Consumers. Advances in Methods and Practices in Psychological Science, 1(3), 367-374.

Wagenmakers, E.-J., Love, J., Marsman, M., Jamil, T., Ly, A., Verhagen, A. J., Selker, R., Gronau, Q. F., Dropmann, D., Boutin, B., Meerhoff, F., Knight, P., Gupta, A.R.K.N., van Kesteren, E.-J., van Doorn, J., Smira, M., Epskamp, S., Etz, A., Matzke, D., Rouder, J. N., & Morey, R. D. (2018). Bayesian inference for psychology. Part II: Example applications with JASP. Psychonomic Bulletin & Review, 25(1), 58-76. OSF preprint folder

Wagenmakers, E.-J., Marsman, M., Jamil, T., Ly, A., Verhagen, A. J., Love, J., Selker, R., Gronau, Q. F., Smira, M., Epskamp, S., Matzke, D., Rouder, J. N., Morey, R. D. (2018). Bayesian inference for psychology. Part I: Theoretical advantages and practical ramifications. Psychonomic Bulletin & Review, 25(1), 35-57. OSF preprint folder

Ly, A., Marsman, M., Wagenmakers, E.-J. (2018). Analytic Posteriors for Pearson’s Correlation Coefficient. Statistica Neerlandica, 72(1), 4-13. doi: 10.1111/stan.12111. Supplement: R-Code to sample from the posterior (Change .txt to .R) This code is also implemented in JASP and maintained on my github repository.

2017

Jamil, T., Marsman, M., Ly, A., Morey, R. D., & Wagenmakers, E.-J. (2017). What are the odds? Modern relevance and Bayes factor solutions for MacAlister’s problem from the 1881 Educational Times. Educational and Psychological Measurement, 77(5), 819-830.

Gronau, Q. F., Sarafoglou, A., Matzke, D., Ly, A., Boehm, U., Marsman, M., Leslie, D. S., Forster, J. J., Wagenmakers, E.-J., & Steingroever, H. (2017). A Tutorial on Bridge Sampling. Journal of Mathematical Psychology, 81, 80-97, doi:10.1016/j.jmp.2017.09.005.

Matzke, D., Ly, A., Selker, R., Weeda, W. D., Scheibehenne, B., Lee, M. D., & Wagenmakers, E.-J. (2017). Bayesian inference for correlations in the presence of measurement error and estimation uncertainty. Collabra: Psychology, 3(1), 25. doi: 10.1525/collabra.78

Ly, A., Marsman, M., Verhagen, A. J., Grasman, R. P. P. P., Wagenmakers, E.-J. (2017). A tutorial on Fisher information. Journal of Mathematical Psychology, 80, 40-55, doi:10.1016/j.jmp.2017.05.006. This version includes the appendix.

Keuken, M. C., Ly, A., Boekel, W. E., Wagenmakers, E.-J. , Belay, L., Verhagen, A. J., Brown, S. D., & Forstmann, B. U. (in press). Corrigendum for: A purely confirmatory replication study of structural brain-behavior correlations. Cortex 93, 229-233.

Jamil, T., Ly, A., Morey, R. D., Love, J., Marsman, M., & Wagenmakers, E.-J. (2017). Default “Gunel and Dickey” Bayes factors for contingency tables. Behavior Research Methods, 49, 638-652.

Dutilh, G., Vandekerckhove, J., Ly, A., Matzke, D., Pedroni, A., Frey, R., Rieskamp, J., & Wagenmakers, E.-J. (2017). A test of the diffusion model explanation for the worst performance rule using preregistration and blinding. Attention, Perception, & Psychophysics, 79, 713-725.

2016

Marsman, M., Ly, A., & Wagenmakers, E.-J. (2016). Four requirements for an acceptable research program. Basic and Applied Social Psychology, 38, 308–312.

Ly, A., Verhagen, A. J., & Wagenmakers, E.-J. (2016). An evaluation of alternative methods for testing hypotheses, from the perspective of Harold Jeffreys. Journal of Mathematical Psychology, 72, 43-55. This is reply to Christian Robert’s comment, and to Suyog H. Chandramouli and Richard M. Shiffrin’s comment on our previous paper in which we summarize the ideas of Harold Jeffreys on hypothesis testing.

Ly, A., Verhagen, A. J., & Wagenmakers, E.-J. (2016). Harold Jeffreys’s default Bayes factor hypothesis tests: Explanation, extension, and application in psychology. Journal of Mathematical Psychology, 72, 19-32. This paper attracted two comments by renowned researchers: one by Christian Robert, and one by Suyog H. Chandramouli, Richard M. Shiffrin. Our reply to their comments is also posted on this page.

Schweinsberg, M., Madan, N., Vianello, M., Sommer, S. A., Jordan, J., Tierney, W., Awtrey, E., Zhu, L., Diermeier, D., Heinze, J., Srinivasan, M., Tannenbaum, D., Bivolaru, E., Dana, J., Davis-Stober, C. P., Du Plessis, C. Gronau, Q. F., Hafenbrack, A. C., Liao, E. Y., Ly, A., Marsman, M., Murase, T., Qureshi, I., Schaerer, M., Thornley, N., Tworek, C. M., Wagenmakers, E-J., Wong, L., Anderson, T., Bauman, C. W., Bedwell, W. L., Brescoll, V., Canavan, A., Chandler, J. J., Cheries, E., Cheryan, S., Cheung, F., Cimpian, A., Clark, M., Cordon, D., Cushman, F., Ditto, P. H., Donahue, T., Frick, S. E., Gamez-Djokic, M., Hofstein Grady, R., Graham, J., Gu, J., Hahn, A., Hanson, B. E., Hartwich, N. J., Hein, K., Inbar, Y., Jiang, L., Kellogg, T., Kennedy, D. M., Legate, N., Luoma, T. P., Maibeucher, H., Meindl, P., Miles, J., Mislin, A., Molden, D. C., Motyl, M., Newman, G., Ngo, H. H., Packham, H., Ramsay, P. S., Ray, J. L., Sackett, A. M., Sellier, A-L., Sokolova, T., Sowden, W., Storage, D., Sun, X., Van Bavel, J. J., Washburn, A. N., Wei, C., Wetter, E., Wilson, C., Darroux, S-C., & Uhlmann, E. L. (2016). The pipeline project: Pre-publication independent replications of a single laboratory’s research pipeline. Journal of Experimental Social Psychology, 66, 55-67. Supplement

Wagenmakers, E.-J., Verhagen, A. J., & Ly, A. (2016). How to quantify the evidence for the absence of a correlation. Behavior Research Methods, 48, 413-426. R Code (change .txt to .R), see also the OSF page

Tierney, W., Schweinsberg, M., Jordan, J., Kennedy, D., Qureshi, I., Sommer, S. A., Thornley, N., Madan, N., Vianello, M., Awtrey, E., Zhu, L., Diermeier, D., Heinze, J., Srinivasan, M., Tannenbaum, D., Bivolaru, E., Dana, J., Davis-Stober, C., du Plessis, C., Gronau, Q. F., Hafenbrack, A., Liao, E., Ly, A., Marsman, M., Murase, T., Schaerer, M., Tworek, C., Wagenmakers, E.-J., Wong, L., Anderson, T., Bauman, C., Bedwell, W., Brescoll, V., Canavan, A., Chandler, J., Cheries, E., Cheryan, S., Cheung, F., Cimpian, A., Clark, M., Cordon, D., Cushman, F., Ditto, P., Amell, A., Frick, S., Gamez-Djokic, M., Grady, R., Graham, J., Gu, J., Hahn, A., Hanson, B., Hartwich, N., Hein, K., Inbar, Y., Jiang, L., Kellogg, T., Legate, N., Luoma, T., Maibeucher, H., Meindl, P., Miles, J., Mislin, A., Molden, D., Motyl, M., Newman, G., Ngo, H. H., Packham, H., Ramsay, P. S., Ray, J., Sackett, A., Sellier, A.-L.,Sokolova, T., Sowden, W., Storage, D., Sun, X., van Bavel, J., Washburn, A., Wei, C., Wetter, E., Wilson, C., Darroux, S.-C., & Uhlmann, E. (2016). Data from a pre-publication independent replication initiative examining ten moral judgement effects. Scientific Data, 3, 160082.

2015

Dutilh, G., Vandekerckhove, J., Ly, A., Matzke, D., Pedroni, A., Frey, R., Rieskamp, J., & Wagenmakers, E.-J. (2015). Pre–registration for: A Confirmatory Test of the Diffusion Model Explanation for the Worst Performance Rule

Wagenmakers, E.-J., Beek, T., Rotteveel, M., Gierholz, A., Matzke, D., Steingroever, H., Ly, A., Verhagen, A. J., Selker, R., Sasiadek, A., Gronau, Q. F., Love, J., & Pinto, Y. (2015). Turning the hands of time again: A purely confirmatory replication study and a Bayesian analysis. Frontiers in Psychology: Cognition, 6:494.

Love, J.P., Selker, R., Verhagen, A.J., Marsman, M., Gronau, Q.F., Jamil, T., Smira, M., Epskamp, S., Wild, A., Ly, A., Matzke, M., Morey, R.D., Rouder, J.N. & Wagenmakers, E.-J. (2015). “Software to Sharpen Your Stats” APS Observer, 28, 27-28.

Wagenmakers, E.-J., Verhagen, A. J., Ly, A., Bakker, M., Lee, M. D., Matzke, D., Rouder, J. N. (2015). A power fallacy. Behavior Research Methods, 47, 913-917.