Transitioning from R Markdown to Quarto

A One-Week Workshop for R Markdown Users

Welcome

This is the online version of Transitioning from R Markdown to Quarto: A One-Week Workshop by The rgtlab Curriculum Project, a short workshop for analysts who already write R Markdown and wish to move their work to Quarto.

The book covers everything an experienced R Markdown user needs to become fluent in Quarto over one week: installing Quarto and rendering an existing .Rmd unchanged; the document anatomy that differs from R Markdown, including the #| cell-option syntax and the execution model; output formats, figures, tables, and native cross-references; projects at scale, from websites to books to manuscripts; and reproducible publishing, with a systematic checklist for migrating a real project. It is designed for five consecutive days of work: one hour of lecture content each day, two hours of homework, no examinations.

The organizing principle is that Quarto is a superset of what R Markdown already does, so the transition is a matter of translation and extension rather than of starting over. An analyst who can write an .Rmd today already knows most of what Quarto asks; this book maps the familiar constructs onto their Quarto equivalents and then shows what Quarto adds. Every chapter opens with a concrete authoring problem, develops the Quarto mechanism that addresses it, and returns to the problem to judge what the mechanism did and did not solve.

The workshop is a companion to the rgtlab curriculum sequence:

• R for Biostatistics: A One-Week Boot Camp (https://r-bootcamp.rgtlab.org), the preparatory volume for R.
• Git and GitHub for Biostatistics, the preparatory volume for version control, on which the publishing chapter of this workshop draws.
• Biostatistics Practicum, workflow infrastructure (Git in depth, Docker, renv, Quarto, CDISC) that builds directly on this workshop.
• Reproducible Research for the Health Sciences, the reproducibility volume that extends the freeze, caching, and publishing material introduced here.

A reader who has completed R for Biostatistics and Git and GitHub for Biostatistics arrives at this workshop ready to place a Quarto project under version control and publish it reproducibly by the end of the week.

See the Preface for the design rationale and the Conventions page for visual cues.

License

This book is licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International.

Code samples are licensed under Creative Commons CC0 1.0 Universal, i.e. public domain.