A library to run them all?

RSE Conference 2022 | Newcastle Upon Tyne

Carlos Cámara-Menoyo | Cagatay Turkay | James Tripp

Centre for Interdisciplinary Methodologies (University of Warwick) | IT Services (University of Warwick)


  • Introduce Quarto
  • Facilitate you working with Quarto
  • Have a discussion evaluating Quarto


  1. Introductions
  2. Introduction to Quarto
  3. Use cases
    1. Group formation and cases
    2. Working in groups - with break!
  4. Large group Discussion
  5. Farewell


Let’s get to know each other

About us

Carlos Cámara

Carlos Cámara

Research Software Engineer

  • R user
  • Interested in reproducibility, open science, geospatial data, visualisation

Carlos Cámara

Cagatay Turkay



  • Python user
  • Interested in visualisation and data science

Carlos Cámara

James Tripp

Research Software Engineer

  • Python, R and PHP user
  • Interested in research software engineering, data science and digital humanities

About you

Let us know about your prior knowledge about quarto

  1. Experts
  2. Some degree of knowledge
  3. Never used before, but I know what it is
  4. I do not know what it is

About your preferred programming language:

  • R | Python | Julia

About this workshop: Have you had time to read cases’ descriptions?


About us

We are not Quarto experts!

We are not affiliated in any way to Quarto or Posit. We do not have any commercial interest.

We are just quarto users who want to share our progress and engage with other users in a co-creation process with an attitude of healthy skepticism.

About the session

This is not (just) a talk about quarto. Others have done it very well before1. We will be presenting quarto’s main claims and putting them to a test (with your help).

About the slides

These slides have been created with quarto (of course!)


A brief overview to quarto

(that’s why we are here, right?)


  • Agreement on importance of Literate programming (concept) and notebooks (artifacts)
  • Lots of different solutions, mostly language specific

R: Rmarkdown

  • Markdown with configurable code blocks
  • Focus on R (but does support other languages see here)
  • Can compile to other formats:
    • natively
    • bookdown, blogdown, …

Python: Jupyter notebook

  • Single JSON file containing code, text and output
  • Kernels for many programming languages
  • Can compile to other formats:
    • Jupyter book, nbconvert, …

This might be about to change with quarto

What’s quarto?

According to their creators1 (Posit -formerly RStudio)):

  • “Open-source scientific and technical publishing system built on Pandoc” - quarto.org
  • “Code output via integration with Jupyter, Knitr, and Observable” - GitHub Repo

From a technical standpoint (Adapted from Mock, 2022):

Quarto is a command line interface (CLI) that renders mixed-format files (.ipynb/Jupyter notebook) OR plain text files (.qmd, .rmd, .md) into different outputs (reports, books, websites, presentations…) , which can be in different formats (PDF/Word/HTML…) .

How does it work? (Overview)

From a qmd file…

title: "ggplot2 demo"
author: "Norah Jones"
date: "5/22/2021"
    fig-width: 8
    fig-height: 4
    code-fold: true

## Air Quality

@fig-airquality further explores the impact of temperature 
    on ozone level.

#| label: fig-airquality
#| fig-cap: Temperature and ozone level.
#| warning: false
ggplot(airquality, aes(Temp, Ozone)) + 
    geom_point() + 
    geom_smooth(method = "loess"


  • Frontmatter defintions
  • Content
    • Text (Markdown with batteries)
    • Code blocks

… to its output.

In this case, an html document (line 6) with text, code (folded -see line 9) and output.

Does this look familiar to you?

How does it work?

This is what happens behind the scenes for single file documents:

Not comprehensive (i.e. does not include projects, bibliographical references and cross-references -tables, figures, chapters-, add custom css, including files within files…)

How can quarto be called?

From CLI:

quarto --help

  Usage:   quarto 
  Version: 0.9.563


    Quarto CLI


    -h, --help     - Show this help.                            
    -V, --version  - Show the version number for this program.  


    render          [input] [args...]   - Render input file(s) to various document types.   
    preview         [file] [args...]    - Render and preview a document or website project. 
    serve           [input]             - Serve a Shiny interactive document.               
    create-project  [dir]               - Create a project for rendering multiple documents 
    convert         <input>             - Convert documents to alternate representations.   
    pandoc          [args...]           - Run the version of Pandoc embedded within Quarto. 
    run             [script] [args...]  - Run a TypeScript, R, Python, or Lua script.       
    tools           <command> [tool]    - Installation and update of ancillary tools.       
    check           [target]            - Verify correct functioning of Quarto installation.
    help            [command]           - Show this help or the help of a sub-command.  

From your favourite IDE:

A screenshot of a Quarto document rendered inside RStudio

A screenshot of a Quarto document rendered inside JupyterLab

A screenshot of a Quarto document rendered inside VSCode

What can quarto do?

Articles and reports in html, docx, pdf, with complex layouts or based on templates.

Some examples:

  • Tufte-inspired layout (in HTML and PDF)
  • Multi-page document with a template, aimed at being printed (source, PDF)
  • Docx document (source, output)

In ppt, beamer or revealjs

Combine several *.qmd files + _quarto.yml with config (project type, structure, properties).

Project is generated using quarto render instead of quarto preview

What can quarto do? (Interactivity)

Additionally, we can add interactivity1 to the previous outputs:


leaflet() %>%
  addTiles() %>%  # Add default OpenStreetMap map tiles
  addMarkers(lat=54.9734625, lng=-1.6242486, popup="RSECon 2022")

Key features

  • Language agnostic (Works with R, Python, Julia, Observable):
    • Can combine different languages in a single document
    • Same syntax
    • One command line
  • IDE Agnostic (Integrations - see getting started)
    • RStudio
    • Visual Studio Code/VS Codium
    • Jupyter
  • Diverse outputs
    • Formats: pdf, html, epub, docx
    • Media: articles, presentations (like this one!), blogs, websites, books…
  • Sensible defaults
    • Bootstrap

Key features

Most of the “not so great” features derive from being under heavy development:

  • New features to come (to be at par with knitr and to surpass it)
    • No new features added to Rmarkdown1
  • Not as mature as other solutions
  • Weekly releases
    • Different versions, different results

Further references

These references introduce quarto way more extensively than we just did:

Use cases

Your turn, now

Group formation and cases

  1. Choose a case from the (case list) on GitHub

2. Each case has a place in the room. Please go to the place for your corresponding case.

3. Form groups of 4 or 5. Say hi to your new friends

4. Choose Documentors and Spokesperson

Work on your case

  1. Install quarto’s binaries: https://quarto.org/docs/get-started/
  2. Fork this repository
  1. Create a new folder for your case under cases/
  2. Copy the template from cases/template/documentation_template.qmd to your folder, which will be used to document the process
  3. Make any changes needed
  1. Commit any changes
  2. Submit Pull Request to the Workshop’s GitHub repo

Please document the process!

Let the games begin!

See you at 16:00


For the large group discussion


For the large group discussion

Group Feedback

  • Spokesperson from each group
  • What did you do? What were your thoughts?

Group Discussion

Some ideas (but feel free to add yours!):

  • How are you going to use quarto in the future?
  • If not, why not?
  • What’s missing?

What’s next?

If you’ve enjoyed the workshop and want to keep exploring quarto, there are some things that can be done:

  • Tell us how we did (fill in this form)
  • We can continue the discussion on the repos’ discussions section
  • Keep in touch with us!
  • Keep extending the use cases and convert this into a repository for quarto use cases


Carlos Cámara, carlos.camara@warwick.ac.uk, https://carloscamara.es/en

James Tripp, james.tripp@warwick.ac.uk

Cagatay Turkay, cagatay.turkay@warwick.ac.uk