Hello Quarto

Quarto - authoring and publishing tools for collaborative scientific writing

Lars Schöbitz

April 3, 2024

This class is being recorded. Access to the recording is restricted to course participants on the Moodle platform.

Welcome! 👋

Meet the lecturers

Margaux Götschmann

• MSc. Applied Mathematics ETH
• Data Science internship with openwashdata.org

Lars Schöbitz

• Environmental Engineer 🔨
• Retired researcher 🛏
• RStudio certified instructor
• Data steward at ETHZ

Learning objectives

1. Learn to use the Quarto file format and the RStudio IDE visual editing mode to produce scholarly documents with citations, footnotes, cross-references, figures, and tables.

2. Learn to use Quarto Pub to publish a website and share research with a broader audience.

Your turn

Think about the last time you published a written document:

• Which tasks gave you joy?
• Which tasks were challenging or frustrating?

Take some written notes.

02:00

Quarto

authoring and publishing workflows for collaborative scientific writing

Every student will have a personal, published, free website that links to their (academic) profiles, shows slides, and has the potential to be used as a (scientific) blog.

Quarto
RStudio IDE on Posit Cloud
Quarto Pub

Why? -> Reproduciblity

Course structure

• My turn: Lecture segments + live coding
• Our turn: Live coding + follow along
• Your turn: Exercises in break-out rooms

Getting help

• During my turn and our turn segments: Please keep your microphone on mute. Send message to the Zoom chat and we will try to support you.

• During your turn segments: Due to the large number of participants, it will not be feasible to join individual break-out rooms, but you will always be working in pairs.

Hello Quarto

Meeting you where you are

I’ll assume you

• do not have R experience

• have not worked in an IDE before (e.g. RStudio IDE)

• want to learn about Quarto

I’ll teach you

• Quarto syntax and formats

• Markdown

• Some R along the way!

What is Quarto?

Quarto …

• is a new, open-source, scientific, and technical publishing system
• aims to make the process of creating and collaborating dramatically better

Artwork from “Hello, Quarto” keynote by Julia Lowndes and Mine Çetinkaya-Rundel, presented at RStudio Conference 2022. Illustrated by Allison Horst.

A tour of Quarto

Sit back and enjoy!

Your turn

• Open posit.cloud & login with your details
• Open the workspace for the course: https://posit.cloud/spaces/497061/content/all?sort=name_asc
• Click “Start” next to the exercises project
• Wait until the project has deployed
• Open hello-penguins.qmd in RStudio from the Files tab in the bottom-right window
• Render the document
• Update your name and re-render
• Inspect components of the document and make one more update and re-render.

10:00

From the comfort of your own workspace

Quarto formats

One install, “Batteries included”

• RMarkdown grew into a large ecosystem, with varying syntax.

• Quarto comes “batteries included” straight out of the box

  • HTML reports and websites
  • PDF reports
  • MS Office (Word, Powerpoint)
  • Presentations (Powerpoint, Beamer, revealjs)
  • Books

• Any language, exact same approach and syntax

Many Quarto formats

Feature	R Markdown	Quarto
Basic Formats	html_document pdf_document word_document	html pdf docx
Beamer	beamer_presentation	beamer
PowerPoint	powerpoint_presentation	pptx
HTML Slides	xaringan ioslides revealjs	revealjs
Advanced Layout	tufte distill	Quarto Article Layout

Many Quarto formats

Feature	R Markdown	Quarto
Cross References	html_document2 pdf_document2 word_document2	Quarto Crossrefs
Websites & Blogs	blogdown distill	Quarto Websites Quarto Blogs
Books	bookdown	Quarto Books
Interactivity	Shiny Documents	Quarto Interactive Documents
Journal Articles	rticles	Journal Articles
Dashboards	flexdashboard	Coming soon!

Your turn

In your exercises project in RStudio on Posit Cloud, go to File > New File > Quarto document to create a Quarto document with HTML output. Render the document, which will ask you to give it a name – you can use my-first-document.qmd. Use the visual editor for the next steps.

• In the YAML header at the top of the document, add a title in the title: field and your name to the author: field.

• Create three sections in the document formatted as Heading 2, name these sections

  • Joyful tasks
  • Challenging tasks
  • A fact to learn

• Stretch goal: In the YAML header add a table of contents in the format: field. Tipp: Check quarto.org and use search function with “HTML table of contents”

• Stretch goal: Change the html theme to sketchy. Tipp: Check quarto.org and use search function with “HTML theming”

10:00

Take a break

Please get up and move! Let your emails rest in peace.

10:00

Thanks! 🌻

Slides created via revealjs and Quarto: https://quarto.org/docs/presentations/revealjs/

Access slides as PDF on GitHub

All material is licensed under Creative Commons Attribution Share Alike 4.0 International.