Publications

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In progress

Submitted or under revision

van Doorn, J., Ly, A., Marsman, M., & Wagenmakers, E.-J. (2017). Bayesian latent-normal inference for the rank sum test, the signed rank test, and Spearman’s ρ. Manuscript submitted for publication.

Gronau, Q. F., Ly, A., & Wagenmakers, E.-J. (2017). Informed Bayesian t-tests. Manuscript submitted for publication.

In press

van Doorn, J., Ly, A., Marsman, M., & Wagenmakers, E.-J. (in press). Bayesian Estimation of Kendall’s tau Using a Latent Normal Approach. Statistics and Probability Letters.

Ly, A., Etz, A., Marsman, M., & Wagenmakers, E.-J. (in press). Replication Bayes Factors from Evidence Updating. Behavior Research Methods.

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

van Doorn, J., Ly, A., Marsman, M., & Wagenmakers, E.-J. (in press). Bayesian inference for Kendall’s rank correlation coefficient. The American Statistician.

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. (in press). The pipeline project: Pre-publication independent replications of a single laboratory’s research pipeline. Journal of Experimental Social Psychology. Supplement

Published articles

2018

Ly, A., Raj, A., 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., Raj, A., 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.

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.

Book chapters

Ly, A., Boehm, U., Heathcote, A., Turner, B. M. , Forstmann, B., Marsman, M., and Matzke, D. (2017). A flexible and efficient hierarchical Bayesian approach to the exploration of individual differences in cognitive-model-based neuroscience. Computational Models of Brain and Behavior.

Wagenmakers, E.-J., Verhagen, A. J., Ly, A., Matzke, D., Steingroever, H., Rouder, J. N., & Morey, R. D. (2017). The need for Bayesian hypothesis testing in psychological science. In Lilienfeld, S. O., & Waldman, I. (Eds.), Psychological Science Under Scrutiny: Recent Challenges and Proposed Solutions, 123-138, John Wiley and Sons.

PhD dissertation

Ly, A. (2017). Bayes factors for Research Workers. University of Amsterdam.

Additional information:
Blog post explaining the title
Blog post explaining some of the rituals of a PhD defence in the Netherlands
Video of my layman’s talk
Video of the PhD defence

Presentations

Ly, A., Marsman, M., Epskamp, S., Matzke, D., Selker, R., Gronau, Q., Jamil, T., Steingroever, H., Love, J., & Wagenmakers, E.-J. (2015). Replications Bayes Factors Mathematical Psychology Conference 2015, Newport Beach, United States.

Ly, A., Etz, A., Marsman, M., Gronau, Q., Epskamp, S., Matzke, D., Selker, R., Jamil, T., Steingroever, H., Love, J., & Wagenmakers, E.-J. (2016). Replication Bayes factors from JASP output, TeaP 2016, Heidelberg, Germany.

JASP program: Find it here

Binomial data:
– Original data set: binomialOri.csv
– Scenario A data set: binomialRepA.csv
– Scenario B data set: binomialRepB.csv
– Scenario C data set: binomialRepC.csv

Contingency table data:
– Combined data: ContingencyComb.csv
– Original data: ContingencyOri.csv

Posters

Ly, A., Marsman, M., & Wagenmakers, E.-J. (2015). Jeffreys’s Correlation Test Based on Criteria of Bayarri, Berger, Forte, and Garcia-Donato (2012) Presented at the 11th International Workshop on Objective Bayes Methodology, Valencia, Spain

Code: Change .txt to .R

Appendix code of Wagenmakers, E.-J., Verhagen, A. J., & Ly, A. (2016). How to quantify the evidence for the absence of a correlation, see also OSF page

Popular science

– Press release: Pleidooi voor onzekerder statistiek (in Dutch)
– Interview: Volgens deze wiskundige moet de statistiekmethodiek op de schop (in Dutch)
– Radio: Onzekere wetenschap in een ruizige wereld (in Dutch)

One comment to “Publications”
One comment to “Publications”
  1. Pingback: Link to My Thesis and Hopefully a New PhD at JASP - JASP - Free Statistical Software

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