Furthering Open Science in Behavior Analysis: An Introduction and Tutorial for Using GitHub in Research

Gilroy, Shawn P.; Kaplan, Brent A.

doi:10.1007/s40614-019-00202-5

Original Research
Published: 24 May 2019

Furthering Open Science in Behavior Analysis: An Introduction and Tutorial for Using GitHub in Research

Perspectives on Behavior Science volume 42, pages 565–581 (2019)Cite this article

595 Accesses
13 Citations
6 Altmetric
Metrics details

Abstract

Open and transparent practices in scholarly research are increasingly encouraged by academic journals and funding agencies. Various elements of behavior analytic research are communicated transparently, though it is not common practice to archive study materials to support future replications. This tutorial presents a review of the Transparent and Open Practices guidelines provided by the Open Science Foundation and provides instructions on how behavior analysts can use GitHub transparency in research across multiple levels. GitHub is presented as a service that can be used to publicly archive various elements of research and is uniquely suited to research that is technical, data driven, and collaborative. The GitHub platform is reviewed, and the steps necessary to create an account, initialize repositories, archive study files, and synchronize changes to remote repositories are described in several examples. Implications of increased calls for transparency and modern statistical methods are discussed with regard to behavior analysis, and archiving platforms such as GitHub are reviewed as one means of supporting transparent research.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Notes

The history of the Wikipedia entry related to “Perspectives on Behavior Science” is available at https://en.wikipedia.org/w/index.php?title=Perspectives_on_Behavior_Science&action=history
Numbers provided from https://github.com/search?q=is:public as of September 1, 2018.
The current location for downloading this program is https://desktop.Github.com
We note here that a “.gitignore” file can be used to determine which files are tracked and which are ignored. Intermediate build objects and other binaries are traditionally not tracked because such objects are unlikely to be useful on other machines and are not tracked for this reason.
We note that GitHub users may push changes to private repositories, though the primary focus of this tutorial is on the public archiving of files. Repositories that are kept private can be made public later (e.g., after submission for publication).
The GitHub repository for the AAC application is available at https://www.github.com/miyamot0/FastTalkerSkiaSharp
The GitHub repository for the novel behavioral economic calculation is available at https://www.github.com/miyamot0/PmaxEvaluation
We note here that Gilroy et al. (2019) validated a novel calculation of unit elasticity for models of operant demand.
Given nature of this particular example, it is likely that users of this level of proficiency would more likely perform this operation via the command line using “git clone https://github.com/[username]/beezdemand.git.”

References

Branch, M. N. (2014). Malignant side effects of null-hypothesis significance testing. Theory & Psychology, 24(2), 256–277. https://doi.org/10.1177/0959354314525282.
Article Google Scholar
Branch, M. N. (2018). The reproducibility crisis: Might the methods used frequently in behavior-analysis research help? Perspectives on Behavior Science. https://doi.org/10.1007/s40614-018-0158-5.
Bullock, C. E., Fisher, W. W., & Hagopian, L. P. (2017). Description and validation of a computerized behavioral data program: BDataPro. The Behavior Analyst, 40(1), 275–285. https://doi.org/10.1007/s40614-016-0079-0.
Article Google Scholar
Corbet, J., & Kroah-Hartman, G. (2017). 2017 Linux Kernel development report. Linux Foundation. Retrieved from https://www.linuxfoundation.org/2017-linux-kernel-report-landing-page/.
Fisher, W. W., & Lerman, D. C. (2014). It has been said that, There are three degrees of falsehoods: Lies, damn lies, and statistics. Journal of School Psychology, 52(2), 243–248. https://doi.org/10.1016/j.jsp.2014.01.001.
Article PubMed Google Scholar
Gelman, A., & Loken, E. (2013). The garden of forking paths: Why multiple comparisons can be a problem, even when there is no “fishing expedition” or “p-hacking” and the research hypothesis was posited ahead of time. Department of Statistics, Columbia University.
Gilroy, S. P. (2016). FastTalker: Cross-platform AAC application. GitHub Repository. Retrieved from https://github.com/miyamot0/FastTalkerSkiaSharp.
Gilroy, S. P., Franck, C. T., & Hantula, D. A. (2017). The discounting model selector: Statistical software for delay discounting applications. Journal of the Experimental Analysis of Behavior, 107(3), 388–401. https://doi.org/10.1002/jeab.257.
Article PubMed Google Scholar
Gilroy, S. P., & Hantula, D. A. (2018). Discounting model selection with area-based measures: A case for numerical integration. Journal of the Experimental Analysis of Behavior, 109(2), 433–449. https://doi.org/10.1002/jeab.318.
Article PubMed Google Scholar
Gilroy, S. P., Kaplan, B. A., Reed, D. D., Hantula, D. A., & Hursh, S. R. (2019). An exact solution for unit elasticity in the exponential model of operant demand. Experimental & Clinical Psychopharmacology. https://doi.org/10.1037/pha0000268.
Gilroy, S. P., Kaplan, B. A., Reed, D. D., Koffarnus, M. N., & Hantula, D. (2018a). The Demand Curve Analyzer: Behavioral economic software for applied researchers. Journal of the Experimental Analysis of Behavior.
Gilroy, S. P., McCleery, J. P., & Leader, G. (2018b). A community-based randomized-controlled trial of speech generating devices and the Picture Exchange Communication System for children diagnosed with autism spectrum disorder. Autism Research. https://doi.org/10.1002/aur.2025.
Grahe, J. (2018). Another step towards scientific transparency: Requiring research materials for publication. Journal of Social Psychology, 158(1), 1–6. https://doi.org/10.1080/00224545.2018.1416272.
Article PubMed Google Scholar
Hanley, G. P. (2017). Editor's note. Journal of Applied Behavior Analysis, 50(1), 3–7. https://doi.org/10.1002/jaba.366.
Article PubMed Google Scholar
Hantula, D. A. (2019). Editorial: Replication and reliability in behavior science and behavior analysis: A call for a conversation. Perspectives on Behavior Science. https://doi.org/10.1007/s40614-019-00194-2.
Horner, R. H., Carr, E. G., Halle, J., McGee, G., Odom, S., & Wolery, M. (2005). The use of single-subject research to identify evidence-based practice in special education. Exceptional Children, 71(2), 165–179. https://doi.org/10.1177/001440290507100203.
Article Google Scholar
Houtkoop, B. L., Chambers, C., Macleod, M., Bishop, D. V. M., Nichols, T. E., & Wagenmakers, E.-J. (2018). Data sharing in psychology: A survey on barriers and preconditions. Advances in Methods & Practices in Psychological Science, 1(1), 70–85. https://doi.org/10.1177/2515245917751886.
Article Google Scholar
John, L. K., Loewenstein, G., & Prelec, D. (2012). Measuring the prevalence of questionable research practices with incentives for truth telling. Psychological Science, 23(5), 524–532. https://doi.org/10.1177/0956797611430953.
Article PubMed Google Scholar
Kaplan, B. A., Gilroy, S. P., Reed, D. D., Koffarnus, M. N., & Hursh, S. R. (2018). The R package beezdemand: Behavioral Economic Easy Demand. Perspectives on Behavior Science. https://doi.org/10.1007/s40614-018-00187-7.
Kazdin, A. E. (2011). Single-case research designs: Methods for clinical and applied settings. Oxford, UK: Oxford University Press.
Google Scholar
Klein, O., Hardwicke, T. E., Aust, F., Breuer, J., Danielsson, H., Hofelich Mohr, A., . . . Frank, M. C. (2018). A practical guide for transparency in psychological science. Collabra: Psychology, 4(1). doi:https://doi.org/10.1525/collabra.158.
Kratochwill, T. R., Hitchcock, J. H., Horner, R. H., Levin, J. R., Odom, S. L., Rindskopf, D. M., & Shadish, W. R. (2012). Single-case intervention research design standards. Remedial & Special Education, 34(1), 26–38. https://doi.org/10.1177/0741932512452794.
Article Google Scholar
Kyonka, E. G. E. (2018). Tutorial: Small-N power analysis. Perspectives on Behavior Science. https://doi.org/10.1007/s40614-018-0167-4.
Laine, H. (2017). Afraid of scooping: Case study on researcher strategies against fear of scooping in the context of open science. Data Science Journal, 16. doi:https://doi.org/10.5334/dsj-2017-029.
Lilienfeld, S. O. (2017). Psychology's replication crisis and the grant culture: Righting the ship. Perspectives on Psychological Science, 12(4), 660–664. https://doi.org/10.1177/1745691616687745.
Article PubMed Google Scholar
Lo, B., & Demets, D. L. (2016). Incentives for clinical trialists to share data. New England Journal of Medicine, 375(12), 1112–1115. https://doi.org/10.1056/NEJMp1608351.
Article PubMed Google Scholar
Nosek, B. A., Alter, G., Banks, G. C., Borsboom, D., Bowman, S. D., Breckler, S. J., et al. (2015). Promoting an open research culture. Science, 348(6242), 1422–1425. https://doi.org/10.1126/science.aab2374.
Article PubMed PubMed Central Google Scholar
Nosek, B. A., Spies, J. R., & Motyl, M. (2012). Scientific utopia: II. Restructuring incentives and practices to promote truth over publishability. Perspectives on Psychological Science, 7(6), 615–631. https://doi.org/10.1177/1745691612459058.
Article PubMed Google Scholar
Nuijten, M. B., Borghuis, J., Veldkamp, C. L. S., Dominguez-Alvarez, L., Van Assen, M. A. L. M., & Wicherts, J. M. (2017). Journal data sharing policies and statistical reporting inconsistencies in psychology. Collabra: Psychology, 3(1). https://doi.org/10.1525/collabra.102.
Nuijten, M. B., Hartgerink, C. H., van Assen, M. A., Epskamp, S., & Wicherts, J. M. (2016). The prevalence of statistical reporting errors in psychology (1985–2013). Behavior Research Methods, 48(4), 1205–1226.
Article Google Scholar
Open Science Collaboration. (2012). An open, large-scale, collaborative effort to estimate the reproducibility of psychological science. Perspectives on Psychological Science, 7(6), 657–660. https://doi.org/10.1177/1745691612462588.
Article Google Scholar
Open Science Collaboration. (2015). Estimating the reproducibility of psychological science. Science, 349(6251), aac4716. https://doi.org/10.1126/science.aac4716.
Article Google Scholar
R Core Team. (2017). R: A language and environment for statistical computing (Version 3.4.1). R Foundation for Statistical Computing.
Shadish, W. R., Zelinsky, N. A., Vevea, J. L., & Kratochwill, T. R. (2016). A survey of publication practices of single-case design researchers when treatments have small or large effects. Journal of Applied Behavior Analysis, 49(3), 656–673. https://doi.org/10.1002/jaba.308.
Article PubMed Google Scholar
Sham, E., & Smith, T. (2014). Publication bias in studies of an applied behavior-analytic intervention: an initial analysis. Journal of Applied Behavior Analysis, 47(3), 663–678. https://doi.org/10.1002/jaba.146.
Article PubMed Google Scholar
Shull, R. L. (1999). Statistical inference in behavior analysis: Discussant’s remarks. The Behavior Analyst, 22(2), 117–121. https://doi.org/10.1007/bf03391989.
Article PubMed PubMed Central Google Scholar
Smith, J. D. (2012). Single-case experimental designs: A systematic review of published research and current standards. Psychological Methods, 17(4). doi:https://doi.org/10.1037/a0029312
Soderberg, C. K. (2018). Using OSF to share data: A step-by-step guide. Advances in Methods & Practices in Psychological Science, 1(1), 115–120. https://doi.org/10.1177/2515245918757689.
Article Google Scholar
Tenopir, C., Allard, S., Douglass, K., Aydinoglu, A. U., Wu, L., Read, E., et al. (2011). Data sharing by scientists: practices and perceptions. PLoS One, 6(6), e21101. https://doi.org/10.1371/journal.pone.0021101.
Article PubMed PubMed Central Google Scholar
Tincani, M., & Travers, J. (2017). Publishing single-case research design studies that do not demonstrate experimental control. Remedial & Special Education, 39(2), 118–128. https://doi.org/10.1177/0741932517697447.
Article Google Scholar
Tincani, M., & Travers, J. (2019). Replication research, publication bias, and applied behavior analysis. Perspectives on Behavior Science. https://doi.org/10.1007/s40614-019-00191-5.
Torvalds, L. (2018). Linux kernel source tree. GitHub Respository. Retrieved from https://github.com/torvalds/linux.
Wasserstein, R. L., & Lazar, N. A. (2016). The ASA's statement on p-values: Context, process, and purpose. The American Statistician, 70(2), 129–133. https://doi.org/10.1080/00031305.2016.1154108.
Article Google Scholar
Wolery, M., & Dunlap, G. (2001). Reporting on studies using single-subject experimental methods. Journal of Early Intervention, 24(2), 5.
Article Google Scholar
Wolery, M., & Ezell, H. K. (1993). Subject descriptions and single-subject research. Journal of Learning Disabilities, 26(10), 642–647. https://doi.org/10.1177/002221949302601001.
Article PubMed Google Scholar
Young, M. E. (2018). A place for statistics in behavior analysis. Behavior Analysis: Research and Practice, 18(2), 193–202. https://doi.org/10.1037/bar0000099.
Article Google Scholar
Zimmermann, Z. J., Watkins, E. E., & Poling, A. (2015). JEAB research over time: Species used, experimental designs, statistical analyses, and sex of subjects. Behav Anal, 38(2), 203–218. https://doi.org/10.1007/s40614-015-0034-5.
Article PubMed PubMed Central Google Scholar

Download references

Author information

Authors and Affiliations

Louisiana State University, 226 Audubon Hall, Baton Rouge, LA, 70802, USA
Shawn P. Gilroy
Fralin Biomedical Research Institute at VTC, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
Brent A. Kaplan

Authors

Shawn P. Gilroy
View author publications
You can also search for this author in PubMed Google Scholar
Brent A. Kaplan
View author publications
You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shawn P. Gilroy.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Gilroy, S.P., Kaplan, B.A. Furthering Open Science in Behavior Analysis: An Introduction and Tutorial for Using GitHub in Research. Perspect Behav Sci 42, 565–581 (2019). https://doi.org/10.1007/s40614-019-00202-5

Download citation

Published: 24 May 2019
Issue Date: September 2019
DOI: https://doi.org/10.1007/s40614-019-00202-5