RaukR 2026 • Workshop Website

NBIS Summer School • Data Science With R

Environment

To edit, preview, and render documents, you need the following prerequisites:

• Quarto>=1.8.27
• RStudio v2025.09.2 or newer or Positron or VS Code
• You need to install the R packages necessary for your topic/document

Quick start

• Fork/clone the repository
• Install Quarto and required R packages
• Preview: quarto preview
• Render: quarto render
• Commit changes and send a pull request

Adding or Modifying Topics

• Fork/Clone the repository

• If your topic doesn't exist, create a branch from develop branch and add your topic

• Keep the topic name simple, preferably one word

• To add a topic, create

  • slides/topic/index.qmd

  • labs/topic/index.qmd

  • The YAML metadata should minimally look like this:

    ---
    title: "Topic"
    author: "Author"
    description: "This topic covers this and that."
    format: html
    ---
    

• format must be html for reports and revealjs for presentations

• For assets relating to the document (figures, files etc), create an assets folder

  • slides/topic/assets/
  • labs/topic/assets/

💡 The document can be live previewed to view changes. Preview is automatically updated on saving the document. Sometimes, the preview can look a bit wonky, in which case, cancel and rerun.

• To preview, run in terminal

  • quarto preview
  • Saving the file updates the preview

• To render, run in terminal

  • quarto render
  • Rendered files are written to /docs
  • To view in browser, open
    • docs/slides/topic/index.html
    • docs/labs/topic/index.html

:tip: Rendered documents in docs/ are only for local preview and are excluded from git. The HTML files for the website are rendered by GitHub Actions. Make sure to commit the _freeze/ folder. We use freeze to cache chunks so rendering works without the original environment on GitHub Actions.

• Finally commit changes

git add .
git commit -m "Added topic"

• Pull latest changes from the repo or from main branch to your branch
• Optionally, merge your branch to develop branch
• Resolve conflicts as needed
• Push your branch or the develop branch and send a pull request like one of the options below

nbisweden/raukr-2026:main <- nbisweden/raukr-2026:your-branch
nbisweden/raukr-2026:main <- you/raukr-2026:your-branch
nbisweden/raukr-2026:main <- nbisweden/raukr-2026:develop
nbisweden/raukr-2026:main <- you/raukr-2026:develop

Branches

• main - Finalized material for the workshop website
• develop - Work in progress including above and working slides and labs
• <topic> - Individual topic branches for development

Tips & Conventions

• Be selective about packages used. Drop packages and dependencies that are not crucial

• Opt for packages with fewer dependencies

• For compute heavy steps, save intermediates and read them in

• Be mindful of the size of files

  • Store large data files elsewhere (dropbox, google drive etc) and link them
  • If you have images that are more than a few hundred KB in size, scale them down to about 600px-800px and compress them and/or use more efficient formats like webp

• Use simple topic labels and do not make them needlessly complex

• The qmd files must be in the correct location when rendering/previewing else metadata from config is not used.

• Declare all R packages at the beginning of every qmd document

• qmd files must have a format defined, either format: html or format: revealjs

• Make a note of the default execute settings in _quarto.yml. This applies to all documents. You can override this by copying the code below to the yaml part of your document and modifying it.

  execute:
    eval: true
    echo: false
  

• Use level 2 heading (##) as the highest level heading

• Bullet points are defined by -

• Define options in code chunks using #| like #| echo: true

• Adjusting dimension of images ![Caption](path/to/image.jpg){width="50%"}

• Divs are defined using ::: and classes are defined using {.class}

  • Example of a class on a div

  ::: {.callout-note}
  content
  :::
  

• Example of a class on a span [Content]{.class}

• Columns are defined as such

:::: {.columns}
::: {.column width="50%"}
Contents
:::
::: {.column width="50%"}
Contents
:::
::::

• Remember to spell-check your document

  • Language used is en-us

• To view a demo report, click here

Reveal.js (Slides)

These are slide specific info. Comparisons here are to xaringan used previously for RaukR.

• Slides are defined by H2 title (##) rather than ---
• Manual increment is defined by . . . rather than --
• Horizontal rule is defined by --- rather than ***
• Presenter notes are defined by :::{.notes} content ::: rather than ???
• For small notes in the bottom of the slide, you can use

::: {.aside}
Contents
:::

• To view a demo presentation, click here

Quarto extensions

Quarto extensions in use:

# Fontawesome icons
quarto add quarto-ext/fontawesome
# Accordion layout
quarto add royfrancis/quarto-accordion
# Top logos in revealjs slides
quarto add royfrancis/quarto-reveal-logo

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2026 • NBIS • SciLifeLab