Introduction to Quarto

Part of the course: “Version Control of Code & Data”

Slides | Source

License: CC BY 4.0 DOI

May 13, 2024


Last week: Branches

Last week: Branches

This week: Quarto

Goals of this session

💡 Learn the basics of the Markdown syntax

💡 Work on a new quarto branch in your recipes repo

💡 Create a neat recipe file using Quarto

💡 When you are done, merge the changes into your main branch

Outlook: Your Quarto file can later be turned into a website!


Introduction to Quarto

What is Quarto?

“Publishing system” by Posit 1

  • Based on RMarkdown
  • Able to execute code
  • Supports multiple programming languages
  • Integrated in RStudio


Figure 1: A schematic representing the multi-language input (e.g. Python, R, Observable, Julia) and multi-format output (e.g. PDF, html, Word documents, and more) versatility of Quarto. Artwork from “Hello, Quarto” keynote by Julia Lowndes and Mine Çetinkaya-Rundel. Illustrated by Allison Horst (Source).

Getting started with Quarto

How can you work with Quarto?

You can use one of the following editors:

  • RStudio
  • Jupyter
  • Neovim
  • VS Code
  • Text editor

Creating a Quarto file in RStudio

  1. Download and install the newest version of RStudio
  2. Open RStudio
  3. Create a new .qmd file: “File” > “New file” > “Quarto Document”

Rendering Quarto files

Output formats

  • HTML (standard)
  • PDF (requires LaTeX)
  • Word (requires MS Word)


  • reveal.js (HTML)
  • Powerpoint (requires MS Powerpoint)

How to render Quarto files

1. Preview

quarto preview
  • The document will be rendered and a web browser with a “live preview” opened
  • Position this browser so that you can see it as you edit and save the document
  • Every time you save the preview will be automatically updated

2. Render

quarto render
  • Render a document (or group of documents) without previewing them
  • You can also use the Render button in RStudio and enable Render on Save

Your turn

Task 1

  1. Create a new quarto branch in your recipes repository and switch to it

Task 2

  1. Create a new empty Quarto file called recipes.qmd in RStudio and save it in your recipes repository
  2. Write a short introduction note to your recipes repository
  3. Switch between Quarto’s visual and source mode
  4. Render the file to HTML
  5. Stage and commit your new file

Basics of Markdown


  • Easy to use
  • “Markup” language
  • Content and formatting are integrated, not separated
  • Alternative to “What You See Is What You Get” (WYSIWYG) editors like MS Word
  • Used by text editors, GitHub (e.g., READMEs), and more
  • Integrated in RStudio as “RMarkdown”

Example: HedgeDoc

Text Formatting

Input Output
*italics* and **bold**

italics and bold

superscript^2^ / subscript~2~

superscript2 / subscript2



`verbatim code`

verbatim code


Input Output
# Header 1

Header 1

## Header 2

Header 2

### Header 3

Header 3

#### Header 4

Header 4

##### Header 5
Header 5
###### Header 6
Header 6


Input Output
* unordered list
  + sub-item 1
  + sub-item 2
  • unordered list
    • sub-item 1
    • sub-item 2
1. ordered list
2. item 2
    1. sub-item 1
  1. ordered list
  2. item 2
    1. sub-item 1
1. ordered list
1. item 2
1. item 3
1. item 4
  1. ordered list
  2. item 2
  3. item 3
  4. item 4


Input Output
| Right | Left | Default | Center |
|   12  |  12  |    12   |    12  |
|  123  |  123 |   123   |   123  |
|    1  |    1 |     1   |     1  |
Right Left Default Center
12 12 12 12
123 123 123 123
1 1 1 1

💡 Tip: Use a Markdown table generator


Markdown Syntax Output
inline math: $E = mc^{2}$
display math:

$$E = mc^{2}$$
E = mc^{2}


Input Output
> Blockquote


Task 3

  1. Add a recipe to the recipes.qmd file (quickly copy-paste from the web)
  2. Format the text by applying at least three types of Markdown syntax
  3. Stage and commit your changes

The YAML header


  • Document settings: YAML sets up document settings like title, author, and output format.
  • Customization: Use YAML for themes and styling.
  • Specify themes: for example, “default” or “morph”


title: "Document title"
author: "Your Name"
theme: vapor
format: pdf

The YAML header of these slides:

title: "Introduction to Quarto"
subtitle: |
  Part of the course: “Version Control of Code & Data”
  [Slides]( |
  License: CC BY 4.0
theme: default
date: today

Task 4

  1. Add a YAML header to your Quarto file
  2. Include your name, a title, an output format (e.g., HTML) and a theme
  3. Stage and commit your changes

When you are done and your Quarto file is rendering properly:

  1. Merge your quarto branch into your main branch

More features

Code chunks

  • Executable code: Quarto files support code execution during rendering
  • Code chunks can be interactive
  • Customizable options: Specify various options for code chunks
  • You can also use inline code
  • R code enclosed by: ```{r} code ```



x <- c(1, 2, 3, 4, 5)
y <- c(2, 4, 1, 3, 5)
plot(x, y, main = "Scatter Plot Example", xlab = "X-Axis", ylab = "Y-Axis")


Inline code


Number of observations: `r 8*20`


Number of observations: 160


  • You can name and references objects like figures, tables etc.
  • For example: Section 6.4 (@sec-citations)
Type Label Prefix
Figures fig-
Tables tbl-
Equations eq-
Sections sec-
Code listing lst-
Theorem thm-


  • Citations can be added via Insert > Citation
  • Citations can also be added directly with @
  • References are stored in BibTeX files in your project
Markdown Format Output (author-date format)
Blip blop bloop [see @chacon2014, pp. 33-35;
also @ggseg, chap. 1]
Blip blop bloop [see Chacon and Straub (2014), pp. 33-35; also , chap. 1]
Blip blop bloop [@chacon2014, pp. 33-35,
38-39 and passim]
Blip blop bloop (Chacon and Straub 2014, 33–35, 38–39 and passim)
Blip blop bloop [@chacon2014].
Blip blop bloop (Chacon and Straub 2014).
They say blah [-@chacon2014]
Lennart says blah (2014)
@chacon2014 says bloop.
Chacon and Straub (2014) says bloop.

Quarto in action

Usescases for researchers

  • Reproducible papers
  • Data analysis & visualization
  • Dynamic documents
  • Presentation slides
  • Automated reports

Git integration

Using Git with .qmd files


  • Plain Text Files: .qmd files are plain text, ensuring compatibility with git diff
  • Branching and Merging: Use Git’s branching and merging capabilities to manage complex document edits.
  • Conflict Resolution: Resolve conflicts efficiently when collaborating on .qmd files
  • RStudio Integration: RStudio offers a graphical user interface (GUI) for Git integration

GitHub Actions

  • Workflow Automation Can automate various tasks, including document generation.
  • Trigger Events: Specify events, such as pushes or pull requests, to trigger document generation automatically.
  • Can allow you to easily update website built with Quarto (hosted with GitHub pages)

Further reading


Chacon, Scott, and Ben Straub. 2014. Pro Git. Apress.

Tasks until next session

  1. Ensure you have a Git repository named recipes set up on your computer
  2. Inside the repository have a recipes.qmd file and (optionally) a .gitignore file
  3. Inside the recipes.qmd file, share at least one recipe.

If you’ve done this, you’re all set!



  1. (the company formerly known as RStudio)