Acknowledgements

These materials were drafted with the help from the following contributors:

• Neha Moopen
• Dorien Huijser

Our materials have borrowed liberally from Mock (2022b), Mock (2022a), Hartgerink (2017) and the Quarto documentation (Quarto (n.d.b)). See also the references.

Frank, Mike, and Chris Hartgerink. 2017. “RMarkdown for Writing Reproducible Scientific Papers.” https://libscie.github.io/rmarkdown-workshop/handout.html.

Hartgerink, Chris. 2017. “Composing Reproducible Manuscripts Using R Markdown.” eLife. https://elifesciences.org/labs/cad57bcf/composing-reproducible-manuscripts-using-r-markdown; eLife Sciences Publications Limited.

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

Lasser, Jana. 2020. “Creating an Executable Paper Is a Journey Through Open Science.” Communications Physics 3 (1): 1–5. https://doi.org/10.1038/s42005-020-00403-4.

Mock, Tom. 2022a. “Get Started with Quarto - Getting Started with Quarto.” https://jthomasmock.github.io/quarto-2hr-webinar/.

———. 2022b. “Get Started with Quarto - Rstudio::conf 2022 Workshop.” https://rstudio-conf-2022.github.io/get-started-quarto/.

Quarto. n.d.a. “Publish and Share with Quarto :: Cheatsheet.” https://rstudio.github.io/cheatsheets/html/quarto.html. Accessed May 23, 2025.

Quarto. n.d.b. “Quarto - Guide.” Quarto. https://quarto.org/docs/guide/. Accessed November 21, 2023.

The Turing Way Community. n.d. “Research Compendia.” The Turing Way. https://the-turing-way.netlify.app/reproducible-research/compendia. Accessed November 21, 2023.

Tierney, Nicholas. 2025. “Quarto for Scientists.” https://qmd4sci.njtierney.com/.

Van Lissa, Caspar J., Andreas M. Brandmaier, Loek Brinkman, Anna-Lena Lamprecht, Aaron Peikert, Marijn E. Struiksma, and Barbara M. I. Vreede. 2021. “WORCS: A Workflow for Open Reproducible Code in Science.” Data Science 4 (1): 29–49. https://doi.org/10.3233/DS-210031.