Markdown

• 'low end' text editor system

• make content that can be read on different systems

• mainly easy way to generate html files

• you write in 'plain text' and an interpreter generates an nice edited version

Basic syntax

Extension

extended lijst van commando's

Rmarkdown & Quarto

Two roads with the same destination, but...

How Quarto works...

Quarto info

If you want to learn more about Quarto, a lot of information is available at

https://quarto.org/docs/guide/

AND

there are great extensions!

see: https://quarto.org/docs/extensions/

Installing Quarto

Click on GET STARTED

Installing Quarto

Choose the correct version for your pc

Install the software and restart RStudio

Check the installation

You should see the option to open a new "Quarto document" in RStudio

A first basic hands-on exploration of Quarto

Open a New File

Fill in some basic info

Two different views

Two parts of a Quarto document

Code chunks

All R-code can be written in Code chunks

While constructing your Quarto document you can RUN code chunks

Click the green arrow (top-right corner of code chunk)

As a result you get the output printed in your Quarto document

Code chunks

ATTENTION!: The order of code chunks do matter. If you want to run all the code in the code chunks before a certain code chunk, you can click on the button aside of the green arrow (downward green arrow)

Adding a new code chunk

Code chunk options

• #| include: false $/rightarrow$ code and output (result) are hidden but code is executed

• #| echo: false: only results are printed, code is hidden

• #| message: false hides messages coming from R related to running the code

• #| warning: false hides warnings coming from running the code

• #| error: false hides error messages coming rom running the code

• #| fig.cap = "..." adds a caption for a figure created

More detailed information: https://yihui.org/knitr/options/

Inserting references

You can easily insert citations and references

Inserting references

If you work with Zotero there is an easy integration! (https://www.zotero.org/)

Search references based on DOI

Easy to find and insert citations of R packages installed on your computer

Inserting a callout

To highlight some specific piece of text you can use a callout

It will generate something like this in your final html document:

Inserting a callout

Adding a Tabset

In an html file you can also add Tabsets... They look like this in the resulting html file:

This is a way to save space on the canvas and keep your file tight and neat.

Adding a Tabset

Go to Insert and choose Tabset

Adding a Tabset

Adding a Tabset

In the Quarto document you now have a section to make content for each tab in the Tabset:

Changing your theme

If you don't like the formatting of the rendered html file, there are some other themes that can be used!

See: https://quarto.org/docs/output-formats/html-themes.html

This is something you can tweak in the YAML of the file

For instance, let's choose the formatting according to the journal theme

Changing your theme

Tweaking your theme in the YAML

Some elements of formatting can be easily added in the YAML

See https://quarto.org/docs/output-formats/html-basics.html

Code folding

By default all the code is shown for code chunks that have not set the option #| echo: false

This behaviour can be changed in the YAML by introducing the code-fold: true option