Quarto

Club Bioinfo, Jouy

Mahendra Mariadassou

MaIAGE

Cédric Midoux

PROSE & MaIAGE

April 13, 2023

Notebooks

RMarkdown & Jupyter Notebook

  • Framework for data science
  • Easiest way to make computational documents
    • An (optional) YAML header surrounded by ---
    • R/Python code chunks surrounded by ```
    • Text mixed with simple text formatting with markdown.
  • Export knit and processed by pandoc to produce a complete report containing all text, code and results.

Analyze. Share. Reproduce.

RMarkdown & Jupyter Notebook

R Markdown: The Definitive Guide

R Markdown: The Definitive Guide

R Markdown Cookbook

R Markdown Cookbook

IPython Cookbook

IPython Cookbook

The R Markdown ecosystem

Quarto: Next generation R Markdown

Quarto unifies and extends the R Markdown ecosystem

Quarto is a new, open-source, scientific and technical publishing system

So what is Quarto ?

Quarto is a command line interface (CLI) that renders plain text formats (.qmd, .rmd, .md) OR mixed formats (.ipynb/Jupyter notebook) into static PDF/Word/HTML reports, books, websites, presentations and more

More than just knitr

Quarto powers Computo

A journal of the French Statistical Society SFdS - ISSN 2824-7795

A journal of the French Statistical Society SFdS - ISSN 2824-7795

Benefits of Quarto

From the R user point of view: Decoupling from R

  • Quarto is multi-core and multi-engine
  • Dedicated CLI
  • Unlike Rmd / Jupyter notebooks, Quarto is not tied to a language1
  • Compatible with your editor (Jupyter Lab, Neovim, VS Code, RStudio, etc), with many visual edition modes available
  • Makes collaboration easier

Quarto highlights

  • Consistent implementation of attractive and handy features across outputs: tabsets, code-folding, syntax highlighting, etc.
  • More accessible defaults as well as better support for accessibility.
  • Guardrails, particularly helpful for new learners: YAML completion, informative syntax errors, etc.
  • Support for other languages like Python, Julia, Observable, and more via Jupyter engine for executable code chunks.

Native support (I)

  • citations: bibliography files (bibtex), bibliography style (csl)
---
title: "My Document"
bibliography: references.bib
csl: nature.csl
---

"On est super à la bourre!" [@Mariadassou2023,@Midoux2023]
  • cross-references for figures (fig-), tables (tbl-), sections (sec-), equations (eq-), (thm-), etc
## Introduction {#sec-introduction}

See @sec-introduction for additional context.

Native support (II)

  • Appendices
    • automatic: references, footnote and (self-)citation
    • manual: acknowledgements, technical proofs, etc
## Acknowledgments {.appendix}

We are grateful to all people who made beautiful slides 
which greatly inspired us.
  • Document License (as Reuse section)
---
license: "CC BY"
---

Extensions

::: incremental - include-code-files : code from source files - fontawesome, academicons, … : Use icons