Task: Reproducible documents with Quarto

Find the solution here after the session ends.

Getting started

In this task, you will create a report on the penguins dataset using Quarto.

In the Files pane, click New File -> Quarto Document. Give it a name like penguin_report.qmd.

Tip

Render your document often to check if everything still works. It’s much easier to find mistakes if you render after every small change. Use the keyboard shortcut Ctrl + Shift + K (Cmd + Shift + K on Mac) to render quickly.

Add text

The file is empty. Write a short introduction about the penguins dataset. Include different markdown formatting like:

A section header (e.g. ## Introduction)
A sentence or two with bold and italic formatting
A bullet list (e.g. listing the three penguin species)
A link to a website of your choice

Render the document to see how the formatted text looks in the output.

Add code chunks

Add a code chunk

You can add a code chunk in two ways:

keyboard shortcut Ctrl + Alt + I (or Cmd + Option + I on Mac)
going to Code -> Insert Code Chunk in the menu

Add a code chunk that loads the tidyverse package.
Add another code chunk that explores the data like head(), summary(), or str().

Now add a new section (e.g. ## Analysis) with a plot, e.g.:

A scatterplot of two variables of your choice from the penguins data (e.g. bill length vs. bill depth, or flipper length vs. body mass)
A boxplot comparing a measurement across species or sex

Render to see the code and output in the document.

Chunk options

Experiment with chunk options to control what shows up in the output:

Hide the setup chunk where you load the tidyverse completely using #| include: false
Hide the code of one of your plots using #| echo: false
What is the difference between the two?
Add #| warning: false to the plot code chunk

Render to check the effect of each option.

Inline code

Write a sentence that includes a value computed by R, for example the number of observations or species. Use inline code like this: `r nrow(penguins)`

Render and check that the number appears in the text.

Add a YAML header

Your document doesn’t have a title or author yet. Add a YAML header at the very top of the file:

---
title: "Penguin Report"
author: "Your Name"
format: html
---

You can also set default chunk options for the whole document by adding execute options to the YAML header. Try adding warning: false and message: false so you don’t need them in every chunk:

---
title: "Penguin Report"
author: "Your Name"
format: html
execute:
  warning: false
  message: false
---

For the fast ones

You can do these in any order, or skip them and just take a break.

Explore YAML document options

YAML options for a specific format

You can add options specific to the HTML format by nesting them under html: in the YAML header. Careful, the indentation has to be correct!

The example below e.g. adds a table of contents to the HTML output and numbers the sections.

---
format:
  html:
    toc: true
    number-sections: true
---

Try adding options under html: in the YAML header. For example:

code-fold: true: hides code behind a clickable button
code-line-numbers: true: adds line numbers to code chunks

Browse the HTML format reference for more options to try.

Explore chunk options

Try adding more options to your code chunks. For example:

#| fig-cap: "Your caption" adds a figure caption
#| fig-align: center centers the figure
#| out-width: "80%" controls the figure width

Browse the code cell reference for more options.

Explore markdown formatting

Try out more markdown features like images, block quotes, footnotes, or tables.

Browse the Markdown basics reference for ideas.

Render to PDF

Change format: html to format: pdf in the YAML header and render. If you get an error about missing LaTeX, you may need to install a lightweight LaTeX distribution first. Run this in the R console:

# install.packages("tinytex") # only run this once
# Install tinytex (also only run this once)
tinytex::install_tinytex()