Quarto for Reproducible Medical Manuscripts

Recently I gave a webinar for R/Medicine titled “Quarto for Reproducible Medical Manuscripts”. You can watch the video below or on the R Consortium website at https://www.r-consortium.org/r-medicine-quarto-for-reproducible-medical-manuscripts.¹

Some highlights from the webinar include:

• Step-by-step instructions for getting started with a new manuscript project

• Obtaining multiple formats from one source

• An overview of the rich front matter

• Embedding computations from supplementary notebooks

  • Note that I demoed embedding computations in R from .qmd files however it’s also possible to embed computations from Jupyter notebooks and computations done in Python.

• A live-coding demo of authoring Quarto manuscripts with RStudio and all the bells-and-whistles of the visual editor, including:

  • cross referencing
  • citations
  • inline code

• Ability to actually interact with code from a manuscript with Binder

• And a rich Q&A, thanks to the audience!

The slides (also written in Quarto!) and their source code can be found at the links below:

• Slides: https://mine.quarto.pub/quarto-manuscripts-rmed

• Source code for slides: https://github.com/mine-cetinkaya-rundel/quarto-manuscripts-rmed

In addition, the webinar featured a reproduction of a medical manuscript with Quarto.² Materials from this reproduction can be found at the links below:

• Manuscript homepage: https://mine-cetinkaya-rundel.github.io/indo-rct

  • This is an HTML page but you can also access PDF and MS Word versions of the manuscript by clicking on their respective links.
  • You can also find a link to the Binder instance for this manuscript.³

• Source code for manuscript: https://github.com/mine-cetinkaya-rundel/indo-rct

Ready to get started writing a manuscript with Quarto? Go to https://quarto.org/docs/manuscripts for more info and a step-by-step tutorial. Happy authoring!

Footnotes

1. Huge thanks to the R Consortium for hosting the webinar and making the recording available so quickly!

2. Huge thanks to Peter Higgins who pointed me to this article as well as the R package that contains code from the article (medicaldata) and shared some starter code with me.

3. The Binder instance takes a few minutes to launch, you can leave that running in a tab while you browse the rest of the manuscript in another tab.