Hello Quarto

OST-HS23: Open Science Tools
authoring and publishing workflows for collaborative scientific writing

Lars Schöbitz

October 17, 2023

Email from GitHub?

While we are getting ready, please check for this email from GitHub and accept the invitation to join the GitHub organisation for the course.

Welcome! 👋

Lars Schöbitz

• Environmental Engineer
  
• Open Science Specialist at Global Health Engineering
• RStudio certified instructor for Data Science with R

Who has a LinkedIn account?

Who already had ORCID iD?

Who already had a GitHub account?

Who already uses a reference management system? (e.g. Mendeley, EndNote, Zotero)

Who has a personal homepage?

Who has published a report, scientific article, or similar?

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 on the provided paper.

02:00

About you

Pick an item

Take notes for 1 minute:

What does the item you have picked have to do with the reason for you being here?

01:00

OST-HS23

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
Zotero
Git
GitHub
Matrix / Element

Why? -> Reproduciblity

Workshop structure

• My turn: Lecture segments + live coding

• Our turn: Live coding + follow along

• Your turn: Exercises

Getting help

• During my turn and our turn segments – raise your hand

• During your turn segments – also feel free to raise your hand for questions but use the yellow sticky to signal: I’m done

Hello Quarto

Meeting you where you are

I’ll assume you

• know do not have R or git experience

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

• want to learn about Quarto

• want to learn about project management with GitHub

I’ll teach you

• Quarto syntax and formats

• Markdown

• GitHub issues, project management, and publishing

• Reference managemen with Zotero

• 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

1. Open github.com in your browser.
2. Navigate to the GitHub organisation for the course ost-hs23.
3. Under Repositories, use search dialogue to search for your GitHub username.
4. Click on the repository with your username (exercises-USERNAME).
5. Click on the green Code button and copy the URL.
6. Open the workspace for the course on Posit Cloud.
7. Under Content, Click New Project > New Project from Git Repository.
8. Paste the URL you copied into the field.
9. Click OK.

05:00

Your turn

• Open hello-penguins.qmd in RStudio and in visual editing mode
• Render the document
• Update your name and re-render
• Inspect components of the document and make one more update and re-render.
• Compare notes with neighbors about updates you’ve made and note any aspects of the document that are not clear after the tour and your first interaction with it.

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.

• Add a title and your name as the author.

• With reference to writing and publishing: Create three sections,

  • one with a task that gave you joy,
  • one with a task you found challenging,
  • and one with a fact you want to learn,

• Add a table of contents.

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

10:00