Organize yourself in RStudio

Jupyter hub at our department’s server

Work in your web browser, URL below.
Use your individual user name and password.

Figure 1: Login to Jupyterlab

Select RStudio

Figure 2: Select RStudio

Files in RStudio

Quarto Editor Options: Visual

many formatting options as buttons
document displays as a rich text, even with images inserted.

Figure 3: Quarto with the visual editor

Quarto Editor Options: Source

Displays strictly plain text
You must format everything manually.

Figure 4: Quarto editor in the source mode

YAML header

File YAML_header_multiformat
Copy-paste it into your new file to get the same formatting you see here.
Keep files atrium.css and atrium.tex in the same folder!!!

---
title: "Organize yourself in RStudio"
echo: true
format:
  revealjs:
    notes: true
    css: atrium.css
  pdf:
    include-in-header: atrium.tex
  html:
    css: atrium.css
---

What makes plain text files real Quarto files is a piece of plain text metadata in the beginning: the YAML header, which you can overwrite.

YAML is not part of R and you will be perfectly fine without it in this course. Here are easy-to-read references to YAML, should you really crave for more:

Quarto has introduced a set of attributes and values in YAML. Here you see some of them. Some attributes explained:

echo: true When you render the document (i.e. typeset the document for printing), also display executable code snippets.
format: revealjs, pdf, html (watch out for the indentation!): you can render it in these three formats. revealjs are dynamic html slides as you see them in this presentation. Each format is specified with more fine-grained attributes. We are not going to delve into this. You can read the Quarto user guide and experiment yourself to become an expert.

CSS file

Format template for HTML pages, not R-specific.
Main purpose of atrium.css: larger font in code snippets
No atrium.css/.tex in YAML header ⟾ Quarto default

My YAML header contains references to styling files for html (atrium.css) and LaTeX (atrium.tex), mainly to make code snippets more legible on slides and to prevent code spilling over the margin in LaTeX (PDF).

Generally, you should do fine without .css and .tex files like this, because the Quarto defaults are reasonable.

Understand note taking with these teaching materials

Render your source .qmd files to PDF, HTML, ~~MS Word~~
https://quarto.org/docs/presentations/revealjs/

Figure 5: The `Render` button produces the document in the format you have specified in the YAML header as `format`.

Figure 6: When your YAML header lists multiple output formats, you have to choose which you want to render.

.qmd is not very pretty for sharing. You should render it for print or web. Available document formats are PDF, HTML, and MS Word. The last one is not going to work here on the cloud because it needs MS Word locally installed and AIC Jupyterlab is a Linux machine.

Another option is rendering it as revealjs slides. revealjs is a Java format based on HTML. It creates dynamic presentations that open in the web browser. It is a different file from the HTML file you get when you render qmd as HTML. In fact, you have to render it live from the source every time you want to run the slide show.

The revealjs slide show enables speaker view, export to pdf, and many other widgets, if you list them in the YAML header. Render one of my source files as a slide show and explore it. And here is the user guide for revealjs Quarto presentations: https://quarto.org/docs/presentations/revealjs/ .

Find Settings, hit e as Export to PDF mode and you will get all slides (without speakers notes). Then find Print in the browser menu and send it to a printer or to PDF to get a PDF file. Anyway, if you want all this accompanying text along, then you are better off rendering this directly as PDF.

Resume broken connection

Figure 7: You can see this after login or being idle. Just launch the server.

Figure 8: When connection gets interrupted, you will see this. Just refresh and relaunch the server.

Control RStudio’s behavior

Figure 9: Saving, Encoding, Working directory, Line wrapping...

Check autosaving options

Figure 10: Some reasonable options for autosaving.

Control character encoding

Figure 11: UTF-8 fits most use cases.

Soft-wrap code

You will be able to see the entire line even if you narrow your browser window.

Figure 12: Control code softwrapping

Control text in `.qmd/.Rmd` documents

Soft-wrap text lines.
Display inserted figures in the editor (before rendering).

Figure 13: For .qmd/.Rmd documents, you have to adjust some options in a separate menu.