The new R Markdown:
Authoring dynamic scientific documents with 
Content from the webinar slides for easier browsing.
Markup & markdown
Markup languages
- Control the formatting of text documents
- Powerful but the unrendered text is visually cluttered and hard to read
Example: Tex—often with macro package LaTeX—to create pdfs
\documentclass{article}
\title{My title}
\author{My name}
\usepackage{datetime}
\newdate{date}{24}{11}{2022}
\date{\displaydate{date}}
\begin{document}
\maketitle
\section{First section}
Some text in the first section.
\end{document}Example: HTML—often with css/scss files—to create webpages
<!DOCTYPE html>
<html lang="en-US">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width" />
<title>My title</title>
<address class="author">My name</address>
<input type="date" value="2022-11-24" />
</head>
<h1>First section</h1>
<body>
Some text in the first section.
</body>
</html>Markdown
- Removes the visual clutter and makes texts readable prior to rendering
- Created in 2004
- By now quasi-ubiquitous
- Initially created for webpages
- Raw HTML can be inserted when easy syntax falls short
Pandoc’s extended Markdown
Pandoc (free and open-source markup formats converter) supports an extended Markdown syntax with functionality for figures, tables, callout blocks, LaTeX equations, citations…
Remains as readable as basic Markdown, but can be rendered in any format (pdf, books, entire websites, Word documents…)
- Removes the visual clutter and makes texts readable prior to rendering
- Created in 2004
- By now quasi-ubiquitous
- Initially created for webpages
- Raw HTML can be inserted when easy syntax falls short
Previous example using Pandoc’s Markdown:
---
title: My title
author: My name
---
# First section
Some text in the first section.Literate programming
Literate programming is a methodology that combines snippets of code and written text.
First introduced in 1984, this approach to the creation of documents has truly exploded in popularity in recent years thanks to the development of new tools such as R Markdown and, later, Jupyter notebooks
Quarto
How it works
Code blocks are executed by Jupyter (Python or Julia) or knitr (R), then pandoc renders the document into any format
Julia/Python:
From Quarto documentation
R:
From Quarto documentation
Code blocks are executed by Jupyter (Python or Julia) or knitr (R), then pandoc renders the document into any format
Can be used from .qmd text files or directly from RStudio or Jupyter notebooks.
Supported languages
Syntax highlighting in pretty much any language
Executable code blocks in Python, R, Julia, Observable JS
Output formats
- HTML
- PDF
- MS Word
- OpenOffice
- ePub
- Revealjs
- PowerPoint
- Beamer
- GitHub Markdown
- CommonMark
- Hugo
- Docusaurus
- Markua
- MediaWiki
- DokuWiki
- ZimWiki
- Jira Wiki
- XWiki
- JATS
- Jupyter
- ConTeXt
- RTF
- reST
- AsciiDoc
- Org-Mode
- Muse
- GNU
- GroffDocument structure & syntax
Front matter
Written in YAML
Sets the options for the document. Let’s see a few examples.
Can be very basic:
---
title: "My title"
author: "My name"
---Written in YAML
Sets the options for the document. Let’s see a few examples.
Or more sophisticated:
---
title: "Some title"
subtitle: "Some subtitle"
institute: "Simon Fraser University"
---Text
Written in Pandoc’s extended Markdown
Code blocks
Syntax highlighting only:
```{.language}
code
```Syntax highlighting and code execution:
```{language}
code
```Options can be added to individual blocks:
```{language}
#| option: value
code
```Rendering
Two commands:
quarto render file.qmd # Renders the document
quarto preview file.qmd # Displays a live previewSome advantages of Quarto
General considerations
- Extremely well documented
- Solid team behind the work
- Free and open source
- Uses only well established and well tested tools
Webpages/websites
- Fast, easy, and clean
- Sites work on screens of any size out of the box (uses Bootstrap 5)
- Can be customized with CSS/SCSS, but good out of the box
- Code blocks can have a copy button
- Great search functionality
- Site/pages can be hosted anywhere easily
Advantages of code execution
- People can see code outputs without running code
- Forces to test every bit of code
- No need for a complex system linking code scripts with publishing documents
Resources
Official sites
Installation
You can find information in the Quarto documentation or in our previous workshop on Quarto
Basic examples
You can find several examples in our previous workshop on Quarto