Introductie tot Git en FAIR development flows

Pablo Mosteiro
p.j.mosteiroromero@uu.nl

Methodology & Statistics @ UU University

16 Dec 2025

Introduction

Version Control

Git

Git - Revert

Git - Branch and Merge

Git - Branch, Merge, Revert

GitHub

GitHub - Collaborate

This course on GitHub

Installing GitHub packages in RStudio

install.packages("devtools")
devtools::install_github(repo = "stefvanbuuren/mice")

Command line interface vs. GUI

Linking GitHub and RStudio

Making research reproducible

  • reproducible documents
  • FAIR
  • research compendiums

FAIR

Gold standard?

Peng (2011)

In practice

Research Data Management Support workshop:

Writing Reproducible Manuscripts in R and Python

Steps

  • Think about a good folder structure
    • Split up ‘read-only’, ‘human-generated’, and ‘project-generated’ files
  • Create folder structure (main directory and sub directories)
    • Add a landing page in the form of a README document
    • Make the compendium executable (to automatically generate the results; optional)
    • Make the compendium into a git repository (optional)
  • Add all files needed for reproducing the results of the project
    • Avoid ‘hard coded’ parameters or human intervention in the execution
  • Make the compendium as clean and easy to use as possible
    • Include a citation file and a LICENSE file with info on how it can be used
  • Publish your compendium
    • E.g. on Zenodo (optional, more on this in the last course week)

Adapted from The Turing Way

Next session

Git en GitHub tutorial

  • Deelnemers leren samenwerken aan code middels git en GitHub. De basis voor deze tutorial is de groepsopdracht die in de ochtend is gemaakt.

References and further reading

Baker, M. (2016). 1,500 scientists lift the lid on reproducibility. https://www.nature.com/articles/533452a

Bryan, J., & TAs, T. S. 545. (n.d.-a). Chapter 33 Why and how we automate data analyses + examples | STAT 545. Retrieved October 30, 2023, from https://stat545.com/

Checklist. (n.d.). Retrieved October 31, 2023, from https://guide.esciencecenter.nl/#/best_practices/checklist

Checklist for a Software Management Plan. (n.d.). https://doi.org/10.5281/zenodo.2159713

Drost, N., Spaaks, J. H., Andela, B., Veen, L., Zwaan, J. M., Verhoeven, S., Bos, P., Kuzak, M., Werkhoven, B., Attema, J., Hidding, J., Hees, V., Martinez-Ortiz, C., Spreeuw, H., Borgdorff, J., Leinweber, K., Diblen, F., Oord, G., Goncalves, R., … Bakker, T. (2020). Netherlands eScience Center—Software Development Guide (v0.9.1). Zenodo. https://doi.org/10.5281/ZENODO.4020564

References and further reading

Gentleman, R., & Temple Lang, D. (2007). Statistical Analyses and Reproducible Research. Journal of Computational and Graphical Statistics, 16(1), 1–23. https://doi.org/10.1198/106186007X178663

Ivimey-Cook, E. R., Culina, A., Dimri, S., Grainger, M., Kar, F., Lagisz, M., Moran, N. P., Nakagawa, S., Roche, D. G., Sanchez-Tojar, A., Windecker, S. M., & Pick, J. L. (2025). TADA! Simple guidelines to improve code sharing. https://ecoevorxiv.org/repository/view/9806/

Jiménez, R. C., Kuzak, M., Alhamdoosh, M., Barker, M., Batut, B., Borg, M., Capella-Gutierrez, S., Hong, N. C., Cook, M., Corpas, M., Flannery, M., Garcia, L., Gelpí, J. L., Gladman, S., Goble, C., Ferreiro, M. G., Gonzalez-Beltran, A., Griffin, P. C., Grüning, B., … Crouch, S. (2017). Four simple recommendations to encourage best practices in research software (6:876). F1000Research. https://doi.org/10.12688/f1000research.11407.1

Knuth, D. E. (1984). Literate Programming. The Computer Journal, 27(2), 97–111. https://doi.org/10.1093/comjnl/27.2.97

Marwick, B., Boettiger, C., & Mullen, L. (2018). Packaging Data Analytical Work Reproducibly Using R (and Friends). The American Statistician, 72(1), 80–88. https://doi.org/10.1080/00031305.2017.1375986

Navarro, D. (2025, May 18). When good pseudorandom numbers go bad. Notes from a Data Witch. https://blog.djnavarro.net/posts/2025-05-18_multivariate-normal-sampling-floating-point/

NHANES Questionnaires, Datasets, and Related Documentation. (n.d.). Retrieved October 30, 2023, from https://wwwn.cdc.gov/nchs/nhanes/continuousnhanes/default.aspx?Begi-nYear=2015

References and further reading

Nüst, D., Ostermann, F., Sileryte, R., Hofer, B., Granell, C., Teperek, M., Graser, A., Broman, K., Hettne, K., & Clare, C. (2019). AGILE Reproducible Paper Guidelines. https://doi.org/10.17605/OSF.IO/CB7Z8

Peng, R. D. (2011). Reproducible Research in Computational Science. Science, 334(6060), 1226–1227. https://doi.org/10.1126/science.1213847

Sandve, G. K., Nekrutenko, A., Taylor, J., & Hovig, E. (2013). Ten Simple Rules for Reproducible Computational Research. PLOS Computational Biology, 9(10), e1003285. https://doi.org/10.1371/journal.pcbi.1003285

Sayre, F., & Riegelman, A. (2019). Replicable Services for Reproducible Research: A Model for Academic Libraries | Sayre | College & Research Libraries. https://doi.org/10.5860/crl.80.2.260

Telford, R. J. (2023, September 6). Enough Markdown to Write a Thesis. https://biostats-r.github.io/biostats/quarto/

References and further reading

The Turing Way Community (2022). The Turing Way: A handbook for reproducible, ethical and collaborative research (1.0.2) [Computer software]. Zenodo. https://doi.org/10.5281/ZENODO.3233853

The Turing Way Community & Scriberia. (2023). Illustrations from The Turing Way: Shared under CC-BY 4.0 for reuse. Zenodo. https://doi.org/10.5281/ZENODO.3332807

TIER Protocol 4.0 | Project TIER | Teaching Integrity in Empirical Research. (n.d.). Retrieved October 30, 2023, from https://www.projecttier.org/tier-protocol/protocol-4-0/

Trisovic, A., Lau, M. K., Pasquier, T., & Crosas, M. (2022). A large-scale study on research code quality and execution. Scientific Data, 9(1), Article 1. https://doi.org/10.1038/s41597-022-01143-6

Utrecht University (2023a, September 26). Best Practices for Writing Reproducible Code. https://utrechtuniversity.github.io/workshop-computational-reproducibility/

Utrecht University (2023b, October 24). Writing Reproducible Manuscripts in R & Python. https://utrechtuniversity.github.io/workshop-reproducible-manuscripts/