Introduction to literate programming with Quarto

Elizabeth Waterfield

08/03/2026

Licence


Creative Commons Attribution 4.0

This work was originally created by Anna Krystalli from RSE-Sheffield under a MIT licence (original repository). It was subsequently adapted by Malika Ihle during her time at Reproducible Research Oxford, with the contributions of Adam Kenny. The overview image is from Dumitru Uzun. The exercice is based on the research of Jen Bright who also kindly provided the gifs used in the exercice. It is now maintained by Malika Ihle and Sarah von Grebmer zu Wolfsthurn at the LMU Open Science Center. This current work by Elizabeth Waterfield, Sarah von Grebmer zu Wolfsthurn and Malika Ihle is licensed under a CC-BY-SA-4.0 Creative Commons Attribution 4.0 International SA License licence. It permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited. If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original.

Contribution statement

Creator: Waterfield, Elizabeth (orcid logo 0009-0006-3725-6730)

Reviewer: von Grebmer zu Wolfsthurn, Sarah (orcid logo 0000-0002-6413-3895)

Acknowledgments: Ihle, Malika (orcid logo 0000-0002-3242-5981)

Prerequisites

Prerequisites

Before completing this submodule, please carefully read about the necessary prerequisites.

Prerequisite Description Where to find it
Basic R skills 3.2. Introduction to R - Part I Module 3.2.
Advanced R skills 3.3. Introduction to R - Part II Module 3.3.
Basic Git skills 3.4. Introduction version control (Git) with RStudio Module 3.4.
Collaboration on GitHub 3.5. Introduction to collaborative coding with GitHub Module 3.5.
Zotero Reference Management Tool Download Link

Setting up Quarto

During this session, we will be using Quarto from RStudio. To set up Quarto, follow these steps:

  1. Open RStudio
  2. Install the most recent version of Quarto here
  3. In RStudio, go to the Terminal tab and install tinytex by typing quarto install tinytex into your terminal
  4. Type quarto --version into the terminal to check with version of Quarto you are using (should be 1.7 or higher)

Important

Make sure to have a recent version of R (Version 4.4.3 or higher) and RStudio (Version 2025.05.1+513 or higher) installed before you install/update Quarto. For installing R and RStudio, see here.

Questions from previous submodule?

Before we start: Survey time!

Click on the following link or scan the QR code to test your prior Quarto knowledge: Quarto Survey

An image of a QR code that leads to a survey.

Starting Survey

Please complete survey labeled “OS-M3-S6-Quarto_starting_survey”.

Discussion of survey results


What do we see in the results?

Where are we at?

Previously:
  • Basic and advanced R skills (data manipulation, plotting, etc.)
  • Introduction to version control using Git
  • Collaborative coding using GitHub
Up next:
  • Combining text, code, and media to create a simple website
  • Publishing the website on GitHub

Quarto and Open Science

Quarto is a tool that can help us connect ideas, data, and people through open and reproducible research.

Covered in this session

  • Key terms and definitions: Understanding core concepts in Quarto
  • Setting up Quarto: Opening a Quarto document in RStudio
  • Authoring: Writing text and structuring content in Quarto
  • Code chunks: Running and displaying code in Quarto
  • Additional authoring features: Inserting images and links in Quarto
  • Citations: Adding citations and bibliography with Zotero in Quarto
  • Publishing: Sharing your Quarto document on GitHub

Learning goals

At the end of this session, you should be able to:

  • Create, edit, and render Quarto documents
  • Use key Quarto features like code chunks, YAML headers, citations, and output formatting
  • Insert citations and generate a bibliography with Zotero directly into the Quarto document
  • Publish and share your work using GitHub Pages

Key terms and definitions

  • .qmd file
  • YAML header
  • Code chunks
  • Quarto markdown text

Key terms and definitions

  • .qmd file: The type of file the Quarto document is saved as.
  • YAML header: The section at the top of the Quarto document that controls settings like the title, output format, and author.
  • Code chunks: The sections of the document that contain code (from R or Python, for example) that are used for showing results such as tables, plots, or calculations.
  • Quarto markdown text: Text written using Markdown syntax to structure and format the content of a document.

Note

The YAML header, code chunks, and markdown text are the components of the .qmd file.

What is Quarto?

An open-source scientific and publishing system that combines text, code and media to produce transparent and reproducible work that can be freely accessed by others.

With Quarto, you can easily:

  • Analyze data, text, or research content
  • Share results and outputs like reports, slides, or websites
  • Reproduce entire workflows

Quarto Website

You can always check out the Quarto Website to learn more.

So, why Quarto?

  1. Readability: Research is more accessible when results, explanations, and code are presented in a way that is easy to read and understand.

Take a look at these 2 examples. Which side is easier to read?

Side A

With **Quarto**, combine into *one single document*:

- text 
- media
- code

For example, easily calculate and display the difference between two sets:

```r
set1 <- c(6.8, 7.0, 6.9)
set2 <- c(7.6, 7.9, 7.8)

mean(set2) - mean(set1)
```

Side B

With Quarto, combine into one single document:

  • text
  • media
  • code

For example, easily calculate and display the difference between two sets:

set1 <- c(6.8, 7.0, 6.9)
set2 <- c(7.6, 7.9, 7.8)

mean(set2) - mean(set1)
[1] 0.8666667

So, why Quarto?

  1. Reproducibility: Research is more reliable when others can clearly see how results were produced and reproduce them from the original code and data.

Current challenges:

  • Research outputs are often separated from the code that generated them
  • Results can become outdated as analyses change
  • It can be difficult to share workflows clearly with others

How Quarto can help:

  • Keeps text, code, and results in a single, executable document
  • Ensures results are regenerated directly from the underlying code
  • Supports transparent and shareable research workflows

“Rendering” in Quarto

What is rendering? The process where Quarto runs the code, combines it with the text, and creates a final output.

  • There are two ways to render in Quarto:

    • Render on Save: Quarto will automatically re-render the document each time you click “Save”
    • Manual Rendering: You have to click on the “Render” each time you want to see the output
A screenshot of a menu bar in an RStudio workspace with red rectangles highlighting the 'Render on Save' checkbox and 'Render' button.

You can find both Render on Save and Manual Rendering at the top of your workspace.

Quarto modes

You can write Quarto documents in Source mode or Visual mode in RStudio.

  • Source mode allows you write directly in plain text/Markdown Syntax, allowing for more control and it’s closer to raw code

  • Visual mode gives a WYSIWYM-style interface which is easier for beginners, but sometimes hides syntax

Note

Choosing modes is part of the authoring process, and it allows you to format the text, add code, and build your document.

Creating a Quarto document

These are the steps to create a Quarto Document in RStudio:

An image of the drop-down menu in RStudio's File tab highlighting the 'New File' option and then the selection of the 'Quarto Document' option.

  • Select “File”
  • Select “New File”
  • Select “Quarto Document”

Setting up a Quarto document

This image shows the setup screen when creating a New Quarto Document for actions such as setting the title, author, and output format.

  • You can set some of the YAML header details here:
    • Put in the title of your document
    • Choose an output format (the default format is HTML)
    • Hit “Create”

Practical exercise 1

Why make a new folder?

Creating a folder on your device helps you stay organized! Keeping all the files (such as Quarto documents and images) in one designated folder makes it easier for you to store and retrieve all materials related to the project or exercise.

Authoring a Quarto document

What is authoring?

  • The process of writing and structuring the Quarto document.
  • Consider it as a formula: Authoring = YAML Header + Markdown

To practice authoring in Quarto, let’s start with setting the YAML header and adding markdown text in Source mode.

Practical exericise 2

---
title: "ChickWeight Analysis"
author: "Your Name"
format:
  html:
    code-fold: false
    toc: true
---

Output format

In future projects, you can replace “html” to render the document to a different format.

Here is a link to a list of the different output formats.

Authoring: Text formatting

Basic Markdown Text Formatting:

  • bullet point: - bullet point
  • Bold: **bold** → bold
  • Italic: *italic* → italic
  • Strikethrough: ~~text~~ → text
  • Inline code: `code` → code

Markdown text shortcuts

Here is a link for the full list of markdown text shortcuts for formatting!

Authoring: Markdown text


Have you ever wondered what affects a chick's weight? 
This document explores the ChickWeight dataset using R.  
The goal is to compare chick weight across different diets and time points.  
Key steps include:

- Loading the dataset  
- Visualizing growth trends  
- Summarizing results


This is an example of markdown text. Let’s use it to continue authoring and building our document.

Practical exercise 3

Authoring: The callout box

Quarto callout boxes can highlight important aspects of your document or provide supplementary information.

Important with Title

This is an example of a callout box to highlight particularly important information using callout-important

Tip with Title

This is an example of a callout box to give important tips using callout-tip

Note with Title

This is an example of a callout box to include additional information or context using callout-note

Warning with Title

This is an example of a callout box to include additional information or context using callout-warning

Authoring: Inserting a callout box

Here is the markdown text for inserting a callout note box:

::: callout-note
## Based on Real Data

The ChickWeight dataset in R is based on real experimental data.
:::

Important elements:

  • Begins and ends with three (!) colons :::
  • Specifies the style of the callout box with “-note”
  • The title of callout box is made by using ##

Practical exercise 4


When rendered, it should look like this:

Based on Real Data

The ChickWeight dataset in R is based on real experimental data.

Code chunks

= Sections of the document where you can write and execute pieces of code

  • There are multiple ways to insert code chunks:

    • Simply click the green Insert Code Chunk button on the toolbar A screenshot of an RStudio toolbar with a red rectangle highlighting the 'Insert a new code chunk' action button which is a green square with a the letter C in its center and a green plus icon to its top-left.

    • You can manually type 3 back ticks ``` then {r} to start a coding chunk, enter your code, then end the chunk with 3 back ticks

    • You can use the keyboard shortcut Ctrl + Alt + I (Windows/Linux) or Cmd + Option + I (Mac) to insert a code chunk then simply enter your code

Inserting code chunks


summary(ChickWeight)


library(ggplot2)
ggplot(ChickWeight, aes(x = Time, y = weight, color = Diet)) +
  geom_line(aes(group = Chick)) +
  labs(title = "Chick Growth Over Time")


These are examples of R code chunks. Let’s use these to insert code chunks in our document.

Practical exercise 5

Adjusting the code chunks

Adjust how the code is portrayed by editing the YAML header:

A screenshot of a summary table displaying the weight, time, and diet information for chicks. Below the table is a line graph with multiple colorful lines. Red rectangles highlight the R code for both the summary table and graph.

  • Currently in our YAML header, we have it set to code-fold: false which means the code is visible and not collapsible.

Code chunks display settings

Here are some other code display settings that we can incorporate into our YAML header:

  • code-fold: true collapses the code so the reader can expand it
  • code-tools: true adds the functions “show code” at the top of the page and “copy” next to the chunks
  • echo: true both the code and the output is visible

Let’s edit the YAML header to make the code chunks collapsible and add code tools.

Practical exercise 6

In the YAML header, under the html section:

What have we learned so far?

Here’s a quick recap of what we have learned in this lesson so far:

✅Create a new Quarto Document in RStudio

✅Edit and render the Quarto Document as a website

✅Use key Quarto features like code chunks, YAML headers, and output formatting

Pre-break quiz

Click on the following link or scan the QR code to review some items covered in this lesson so far: Quarto Survey

An image of a QR code that leads to a survey.

Pre-break quiz

Please complete quiz labeled “OS-M3-S6-Quarto_prebreak_quiz”.

Break! 10 minutes

Post-break survey discussion


What do we see in the results?

Additional authoring features

Quarto offers additional authoring features that make it more versatile and comprehensive. These include:

  • Adding links and hyperlinking text
  • Embedding media, for example images

Commonly used authoring features

If you want to learn more about advanced authoring features, click here for commonly used markdown syntax for additional authoring features.

Inserting images

  • Image by itself with no caption: ![](path/image.png)

An image of 3 yellow chicks sitting in the grass.

  • Image with a caption below it: ![caption](path/image.png)

An image of 3 yellow chicks sitting in the grass.

This is a caption about three yellow chicks in the grass.

Inserting images

You can even add a link to an image so that when you click anywhere on the image, it redirects you to that website.

  • Image with link: [![caption](path/image.png)](link)

An image of 3 yellow chicks sitting in the grass.

Click on the image to access a published study on broiler chicks.

Practical exercise 7


![No chicks were harmed in the making of this website.](images/05_Chick_Pic.png)

Adding citations

An image of Zotero's logo. The letter Z in the color red is placed in the center of a white square with rounded edges. The lower-right corner is lifted to reveal written words underneath and four colored tabs are placed around the square.

What is Zotero? A free reference management tool to collect, organize, cite, and share research sources.

  • You can use Zotero in RStudio to easily insert citations into your Quarto document.

Adding citations with Zotero

To insert a citation:

A screenshot of an RStudio toolbar with red rectangles highlighting the 'Source/Visual' mode options and the 'Insert' function.

  • Switch to the “Visual Editor” mode

  • → Press the “Insert” button in the toolbar and select “Citation”

  • → In the Zotero library, select the citation and click “Insert”

What you will notice:

  • bibliography: references.bib will be added to the YAML header

  • After rendering, a reference list or bibliography will be automatically generated at the end of the document with the citations used.

Adding citations with Zotero

A screenshot of the dropdown menu under 'Insert' with a red rectangle around the 'Zotero/My Library' option.

  • You can select citations straight from the folders in your Zotero library

  • Each citation is assigned a short citation key based on the author and year (for example, “pauwels2015”).

  • Quickly cite in your document’s text using the citation key:

    • For regular citation, type @ followed by the citation key, wrapped in square brackets (for example, [@pauwels2015]).
    • For in-text citation, type @ followed by the citation key, for example @li2016. No square brackets.

Practical exercise 8

Let’s practice adding a citation using Zotero.

Diet affects chick body weight. In this study, low-energy feed made fast-growing chicks lighter, while slower-growing chicks compensated by eating more

Practical exercise 8

An image showing the citation key 'pauwels2015' and a red rectangle highlighting the 'Insert' option.

Practical exercise 9

Now, let’s practice adding in-text citations!

 found that broiler chicks fed a higher nutrient-density diet gained more weight and did so more efficiently.

Practical exercise 9

An image showing the citation key 'li2016' and a red rectangle highlighting the ticked In-text checkbox.

Adding citations with Zotero

In your output, you should now have:

  • A citation
  • An in-text citation
  • A reference list (bibliography)

A screenshot showing two sentences about chick body weight including citations and a bibliography below.

Changing the citation style

You can change the citation style by using Citation Style Language (csl) files directly from the Zotero website. For example, putting “csl: https://www.zotero.org/styles/apa” in your YAML changes the citation style to APA.

Publishing

What is publishing with Quarto?

= the process of sharing the rendered documents or projects online so it can become accessible to others.

  • You can publish to:
    • GitHub Pages
    • A personal website
    • Quarto Pub

List of publishing services

Here is a link for a list of publishing services and more information!

Publishing

When sharing your work, it’s important to follow established rules and standards. This includes:

  • Considering the legal aspects
  • Applying appropriate licenses
  • Proper archiving

List of publishing services

Check out the LMU OSC page on sharing, copyright, best practices and more.

Publishing to GitHub

A great option to share your document is publishing to GitHub.

  • GitHub is a platform for hosting and sharing code and projects online
  • An advantage of GitHub is it allows for version control: the ability to track and manage changes over time
  • A free and widely used way to publish your Quarto document to GitHub is by using GitHub Pages

Publishing to GitHub

GitHub Pages enables you to publish content based on source code managed within a GitHub repository.

3 methods to publish a Quarto document to GitHub Pages:

  1. Rendering your output to the docs directory and checking it into your repository
  2. Using the quarto publish command
  3. Using GitHub Actions to auto-render and publish whenever you push changes

Publishing to GitHub

Let’s publish our document using the first method:

Render to docs

Publishing to GitHub

Work directly from the Terminal in RStudio.

  • For Mac and Linux users, simply open a new Terminal by clicking “Terminal” → then “New Terminal”
  • Windows users can connect to Git Bash with “Terminal” → “Terminal Options...”, set it to open with Git Bash, then open a new terminal.

The 'Terminal Options...' selection is highlighted with a red rectangle under the options in Terminal within RStudio.

A screenshot displaying the 'Git Bash' option being selected from the dropdown menu under 'New terminals open with:'.

Practical exercise 10

project:
  type: website
  output-dir: docs

Here is an example of setting the directory using cd: Screenshot of the Terminal with the 'cd' command setting the directory to 'Quarto'.

Practical exercise 10

echo "project:
  type: website
  output-dir: docs" > _quarto.yml
touch .nojekyll

Why we add .nojekyll

Adding a .nojekyll file to the root of your repository tells GitHub Pages not to do additional processing of your published site using Jekyll

Practical exercise 10

quarto render
git init
git branch -M main

Practical exercise 10

quarto render
git add docs
git commit -m "Publish site to docs/"
git push -u origin main

Practical exercise 10

A screenshot of the settings on a GitHub repository where the action of changing 'None' to 'main' branch is highlighted with red rectangles.

A screenshot of the settings on a GitHub repository where the action of changing '/root' to '/docs' is highlighted with red rectangles.

  • After 1-2 minutes, you will see that your site will be live!

Recap

  • Quarto is a powerful tool that combines text, code, and media to make documents more transparent, reproducible, and accessible.
  • Within a .qmd file:
    • The YAML header controls the document settings, such as how code chunks are displayed.
    • Code chunks run code and show results.
    • Markdown text creates the main content and can be formatted using keyboard shortcuts.
  • Use Quarto directly with Zotero for inserting and managing references.
  • Make your work accessible and reproducible by publishing on platforms, such as GitHub Pages, your own website or Quarto Pub.

Download the Quarto cheatsheet

Relevance and implications

Let’s discuss how useful Quarto can be for open research. Consider the following questions:

  1. How can using Quarto improve transparency and reproducibility in your work?
  2. Do you see advantages in using Quarto compared to traditional tools like Word or PowerPoint?
  3. What challenges might you face in adopting Quarto in your current workflow?

What is the take-home message?

Let’s wrap up by identifying the key takeaway from today’s session together.


Ask yourself: “If you had to explain to a colleague in one sentence why learning Quarto matters for research and teaching, what would you say?”

Assignment

After learning about Quarto in today’s lesson, use this homework assignment to:

  • Practice your Quarto skills
  • Explore what more can be added to your documents
  • Build confidence in editing YAML header, adding code chunks, and customizing the layout

Download the Quarto Activity Sheet

To conclude: Survey/Quiz time!

Let’s end this session with a short quiz on topics covered in this lesson.

Click on the following link or scan the QR code to do one final review of this lesson: Quarto Survey

An image of a QR code that leads to a survey.

Finishing quiz

Please complete survey labeled “OS-M3-S6-Quarto_finishing_quiz”.

Discussion of survey results

References

  • Allaire, J., Teague, C., Scheidegger, C., Xie, Y., Dervieux, C., & Woodhull, G. (2025). Quarto (Version 1.8) [Computer software]. https://doi.org/10.5281/zenodo.5960048

  • Bregendahl, K., Sell, J., & Zimmerman, D. (2002). Effect of low-protein diets on growth performance and body composition of broiler chicks. Poultry Science, 81(8), 1156–1167. https://doi.org/10.1093/ps/81.8.1156

  • Duit, R., & Treagust, D. F. (2003). Conceptual change: A powerful framework for improving science teaching and learning. International Journal of Science Education, 25(6), 671–688. https://doi.org/10.1080/09500690305016

  • Forehand, M. (2010). Bloom’s taxonomy. Emerging perspectives on learning, teaching, and technology, 41(4), 47-56.

  • Li, J., Yuan, J., Miao, Z., Song, Z., Yang, Y., Tian, W., & Guo, Y. (2016). Effect of Dietary Nutrient Density on Small Intestinal Phosphate Transport and Bone Mineralization of Broilers during the Growing Period. PLOS ONE, 11(4), e0153859. https://doi.org/10.1371/journal.pone.0153859

  • Pauwels, J., Coopman, F., Cools, A., Michiels, J., Fremaut, D., De Smet, S., & Janssens, G. P. J. (2015). Selection for Growth Performance in Broiler Chickens Associates with Less Diet Flexibility. PLOS ONE, 10(6), e0127819. https://doi.org/10.1371/journal.pone.0127819

  • Ryba, R., Doubleday, Z. A., Dry, M. J., Semmler, C., & Connell, S. D. (2021). Better Writing in Scientific Publications Builds Reader Confidence and Understanding. Frontiers in Psychology, 12, 714321. https://doi.org/10.3389/fpsyg.2021.714321

  • Tierney, N. (2025). Quarto for scientists. https://qmd4sci.njtierney.com/

Thanks!

See you next class :)

Pedagogical add-on tools for instructors

Additional literature for instructors

CREDiT Contribution Statement - TO DO

Elizabeth Waterfield: Conceptualization, Software, Writing - Original Draft, Visualization. Sarah von Grebmer zu Wolfsthurn: Conceptualisation, Writing - Review & Editing, Project Administration, Validation. Malika Ihle: Conceptualisation, Writing - Review & Editing, Supervision, Project Administration, Validation.