Writing Reproducible Manuscripts in R & Python

Welcome!

Open Science practices are becoming central to the way research is conducted. In this workshop, you will learn to set up a reproducible workflow to create a publication-ready manuscript that combines data, R or Python code, text, and references.

We will use the Quarto publishing system in conjunction with R or Python to create a publication-ready manuscript that combines data, code, text, and references. More specifically, you will learn how to:

• Create a reproducible project (folder) structure
• Use Markdown syntax effectively for writing text
• Run analyses in code chunks or cells
• Manage references using Zotero and Better BibTex for Zotero
• Render your Quarto project to docx, HTML, and pdf files

This workflow reduces the amount of human error, improves computational reproducibility and makes updating your scientific manuscript more efficient.

By the end of the workshop, you will be sufficiently familiar with the tools and components behind a reproducible manunscript, so you can implement the workflow in your own research projects.

Our workshop material is licensed under a Creative Commons Attribution 4.0 International License. You can view the license on our GitHub repository.

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. “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.

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.