OPAM 2025: Reproducible Manuscripts in R with Quarto
Welcome!
Science practices are transforming how research is conducted, emphasizing transparency, reproducibility, and collaboration. In this hands-on workshop, you’ll learn how to build a fully reproducible workflow for writing and publishing a scientific manuscript that integrates text, data, and code. We will use the Quarto publishing system (predecessor to Rmarkdown) in combination with R (or optionally Python) to produce publication-ready outputs in multiple formats.
In this workshop, you will learn to:
● Set up a reproducible folder and project structure
● Write using Markdown for clean, structured text
● Run analyses directly within code chunks or cells and reference statistics in-text
● Manage references using Zotero and Better BibTeX, and cite them seamlessly in your manuscript
● Render your Quarto document to Word (.docx), HTML, and PDF
This workshop is ideal for researchers aiming to streamline their scientific writing and adopt Open Science principles.
Materials
You can follow along by opening up a Posit cloud browser (you need an account, but it is free and easy).
My workshop material is licensed under a Creative Commons Attribution 4.0 International License. You can view the license on our GitHub repository.