quarto-niss

Materials for the NISS GSN Quarto workshop (2023-04-07)

Setup notes

• R 4.2.3 (2023-03-15) -- "Shortstop Beagle"
• RStudio 2023.03.0+386 "Cherry Blossom"
• Quarto 1.3.310
• Packages: tidyverse, palmerpenguins, gt

Demo

Documents

• Open the simple Quarto document called index.qmd and edit it using the RStudio Visual Editor.
• Bold palmerpenguins and add link to https://allisonhorst.github.io/palmerpenguins/.
• Add code chunk options:
  • fig-alt
  • echo: false in execute in the YAML
  • code-fold
  • teaching tip: echo: fenced
• Add a figure and a table and cross reference them
• Add a citation: 10.1371/journal.pone.0090081

Slides

• Change format: revealjs
• Add section headings: First level headings Introduction and Analysis, under Analysis a second level heading called Modeling
• Add columns to slides
• Reveal code with echo: true
  • teaching-tip: code-line-numbers
• Change output-location of figure

Websites

• Add another document about.qmd
• Add quarto.yml

project:
  type: website

website:
  title: "Hello Quarto"
  navbar:
    left:
      - index.qmd
      - talk.qmd

• Render
• Add other formats to index.qmd:

format:
  html: default
  pdf: default

• publish quarto

Journal articles

• Go to https://quarto.org/docs/journals/templates.html

• Click on Quarto journals repo

• Create one with JASA template

my-awesome-paper

• Add a citation

First from Zotero Welcome to the tidyverse

Teaching

• Add code-link true to the document yaml

format: html: code-link: true

• Add include = FALSE as a code chunk option and render and review the error, and fix with YAML completion

• Switch to slides

format: revealjs

Don't need to change anything else

• Show the sidebar > Tools for PDF export of slides

• Add chalkboard

format: revealjs: chalkboard: true

• Add multiplex

format: revealjs: chalkboard: true multiplex: true

Show the files generated and which to post

• Add execute: true to document yaml

execute: echo: true

• Show echo: fenced for a code chunk

• Convert to document - Code annotation (1.3 PRERELEASE)

  to scale_color_colorblind() # <1> to theme elements # <2>

  1. Use a color-blind friendly color scale
  2. Adjust theme elements