Reporting with
Quarto

Carlos Matos // ISPUP // November 2023

What is ?


  • Unified authoring framework for data science
    • Seamlessly combine code, results and prose
  • Fully reproducible
  • Supports several output formats (e.g. HTML, PDF, Word, Presentations, …)
    • Write in one language (Markdown), output to several
  • Command line tool
    • But don’t worry, you won’t have to deal with the command line
  • Create websites, blogs, articles, presentations, books, dashboards (in the next version!)

Why Quarto?

  • Communication to decision makers
    • Focus on conclusions, not the code behind
  • Collaboration with other data scientists
    • Interested in conclusions but also the code
  • Environment to work in
    • Modern day notebook
  • Native support for multiple languages
    • (R, python, Observable, …)
  • You can choose between a source and visual editor

Anatomy of a Quarto document

It contains three important types of content:

  1. An (optional) YAML header surrounded by ---.
  2. Chunks of R code surrounded by ```.
  3. Text mixed with simple text formatting like # heading and _italics_.
    • Regular text
    • Inline code
    • Figures
    • Tables
    • Citations
    • Cross-references
    • LaTeX Equations
    • …

Quarto basics

Quarto citations

  • Create a references.bib file in your main project folder
  • Add bibliography: references.bib to the YAML header of your .qmd file
  • Add citations in bibtext format to references.bib
    • To see an example use citation(“tidyverse”) in RStudio
  • (Optionally) define a citation style with csl: [path_to_file.csl]
    • csl files can be found here: https://github.com/citation-style-language/styles
    • You can refer directly to the online file (e.g. https://raw.githubusercontent.com/citation-style-language/styles/master/american-medical-association.csl)

Quarto extensions

Exercises

  1. Create a new Quarto document using File > New File > Quarto Document.
  2. Read the instructions.
  3. Practice running the chunks individually.
  4. Then render the document by clicking the appropriate button.
  5. Verify that you can modify the code, re-run it, and see modified output.
  6. Add a hyperlink to the course website, re-run it, and see the modified output
    • https://c-matos.github.io/Intro-R4Heads/
  7. Change the output type (html, pdf, docx) and render again (may need some package installation)

Exercises

  • Replicate the document “06-quarto.pdf”, using Quarto.
  • Create similar documents in docx and html formats

Carlos Matos // ISPUP::R4HEADS(2023)