4.4 Quarto

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

Quarto Tutorial: https://jmjung.quarto.pub/m02-advanced-literate-programming/#learning-outcomes

Run Quarto in VS Code: https://quarto.org/docs/tools/vscode/index.html

Quarto is based on Pandoc and uses its variation of markdown as its underlying document syntax. See the full documentation of Pandoc’s Markdown for more in-depth documentation.

Cell Execution

Quarto Command Keyboard Shortcut
Run Current Cell ⇧ + ⌘ + Enter
Run Current Cell and Jump to Next Cell ⇧ + Enter
Run Selected Line(s) ⌘ + Enter
Run All Cells ⌥ + ⌘ + R

Host Quarto on GitHub Pages.

To get started, change your project configuration _quarto.yml to use docs as the output-dir.

project:
  type: book
  output-dir: docs

Then, add a .nojekyll file to the root of your repository that tells GitHub Pages not to do additional processing of your published site using Jekyll (the GitHub default site generation tool):

touch .nojekyll
  • Note that .nojekyll’s location is different than that of bookdown, which is at /docs folder.

4.4.0.1 Only re-render changed files

You can add the following to your _quarto.yml file to only re-render changed files:

execute: 
  freeze: auto

When freeze: auto is enabled, Quarto checks for modifications in the source files of your computational documents. If no changes are detected, Quarto will utilize the cached results from previous computations, skipping the re-execution of code chunks.

This significantly speeds up rendering times, especially for large projects with many computational documents. ✅

There are drawbacks: some files may not be updated in time.

  • Use freeze: false to force re-rendering of all files when you are able to submit your changes.
  • Use freeze: auto when you are editing actively and want to see your changes in time.

Strengths of Quarto:

  • hoverable citations and cross-references, easy to read
  • easy subplots

Weaknesses of Quarto:

  • slow compared to Bookdown

    Workaround:

    • Use quarto preview in terminal to enable live preview
    • Set freeze: auto in _quarto.yml to only re-render changed files.

  • Issues when you want to compile one single page within a package. Changes are not reflected in time unless you render the whole website.

    Workaround: Need to exclude from project index, and need file header yaml to import mathjax settings and themes.

    Bookdown is reliable. Don’t need yaml in single Rmd, website theme will apply automatically.

  • Not support rstudioapi functions. E.g., the following is often used to set working directory to the folder where the current script is located.

    But it does NOT work in Quarto.

    # set working dir, return error in Quarto
dir_folder <- dirname(rstudioapi::getSourceEditorContext()$path)
setwd(dir_folder)

4.4.1 Book Structure

book:
  chapters:
    - index.qmd
    - preface.qmd
    - part: dice.qmd
      chapters: 
        - basics.qmd
        - packages.qmd
    - part: cards.qmd
      chapters:
        - objects.qmd
        - notation.qmd
        - modifying.qmd
        - environments.qmd
    - references.qmd
  appendices:
    - tools.qmd
    - resources.qmd

  • The index.qmd file is required (because Quarto books also produce a website in HTML format). This page should include the preface, acknowledgements, etc.

  • The remainder of chapters includes one or more book chapters.

    You can divide your book into parts using part within the book chapters.

    Note that the markdown files dice.qmd and cards.qmd contain the part title (as a level one heading) as well as some introductory content for the part.

    If you just need a part title then you can alternatively use this syntax:

    book:
  chapters:
    - index.qmd
    - preface.qmd
    - part: "Dice"
      chapters: 
        - basics.qmd
        - packages.qmd

  • The references.qmd file will include the generated bibliography (see References below for details).

4.4.2 Code chunks

Both R markdown and Quarto can use the following ways to specify chunk options:

Use tag=value in the chunk header ```{r}.

```{r my-label, fig.cap = caption}

# R code
```

Alternatively, you can write chunk options in the body of a code chunk after #|, e.g.,

```{r}
#| label: fig-my-label
#| fig-cap: caption 

# R code
```

tag: value is the YAML syntax.

Options format:

  • space after #| and colon :
  • Logical values in YAML can be any of: true/false, yes/no, and on/off.
    • They all equivalent to TRUE/FALSE (uppercase) in Rmd.
    • Note that TRUE/FALSE need to be in uppercase in Rmd.

Note that Quarto accepts Rmd’s way of specifying chunk options. The difference is that Quarto’s label for figures must start with fig-, while Rmd accepts any labels.

```{r label = "fig-my-label", fig.cap = caption}

# R code
```

❗️ Note that NOT all Rmd chunk options are supported in Quarto. See Quarto Chunk Options for all available options.

Quarto chunk options available for customizing output include:

Option Description
eval Evaluate the code chunk (if false, just echos the code into the output).
echo Include the source code in output
output\(^{[1]}\) Include the results of executing the code in the output (true, false, or asis to indicate that the output is raw markdown and should not have any of Quarto’s standard enclosing markdown).
warning Include warnings in the output.
error Include errors in the output (note that this implies that errors executing code will not halt processing of the document).
include Catch all for preventing any output (code or results) from being included (e.g. include: falsesuppresses all output from the code block).
renderings Specify rendering names for the plot or table outputs of the cell, e.g. [light, dark]

\(^{[1]}\) output is similar to results in Rmd. You cannot use results='hide' in Quarto, use output: false instead.

4.4.3 Knitr Options

If you are using the Knitr cell execution engine, you can specify default document-level Knitr chunk options in YAML. For example:

---
title:"My Document"
format: html
knitr:
  opts_chunk:
    collapse: true
    comment: "#>"
    R.options:
      knitr.graphics.auto_pdf:true
---

You can additionally specify global Knitr options using opts_knit.

The R.options chunk option is a convenient way to define R options that are set temporarily via options() before the code chunk execution, and immediately restored afterwards.

In the example above, we establish default Knitr chunk options for a single document. You can also add shared knitr options to a project-wide _quarto.yml file or a project-directory scoped _metadata.yml file.

ref: https://quarto.org/docs/computations/execution-options.html#knitr-options

4.4.4 PDF Options

Use the pdf format to create PDF output. For example:

---
title: "Lab 1: Solutions"
format: 
  pdf:
    include-in-header: ../latex/preamble.tex
    fontsize: 12pt
    pdf-engine: xelatex
---

See HERE for all available options.

See Metadata variables for yaml options that Pandoc recognizes.

Title & Author

PDF Options Functions
title Document title
date Document date
author Author or authors of the document
abstract Summary of document

Format Options

PDF Options Functions
pdf-engine Specify the PDF engine to use.
Options include pdflatex, xelatex, and lualatex. The default is xelatex.

Includes

PDF Options Functions
include-in-header Include contents at the end of the header.
Specify your pdf template here.

Subkeys for include-in-header

  • file: path to a file to include at the end of the header.

  • text: |: include raw latex content in the YAML header.

    | indicates that the content is in multiple lines.

  • If you omit file: or text:, Quarto assumes file: by default.

Use example

format:
  pdf:
    include-in-header:
      - text: |
          \usepackage{eplain}
          \usepackage{easy-todo}
      - file: packages.tex
      - macros.tex            # assume file by default
  • Note that you need the dash - before text: and file: to indicate a list of items.

Any packages specified using includes that you don’t already have installed locally will be installed by Quarto during the rendering of the document.

header-includes: | is a pandoc variable for including raw LaTeX code in the document header.

header-includes: |
  \RedeclareSectionCommand[
    beforeskip=-10pt plus -2pt minus -1pt,
    afterskip=1sp plus -1sp minus 1sp,
    font=\normalfont\itshape]{paragraph}
  \RedeclareSectionCommand[
    beforeskip=-10pt plus -2pt minus -1pt,
    afterskip=1sp plus -1sp minus 1sp,
    font=\normalfont\scshape,
    indent=0pt]{subparagraph}

Format & Typesettings

PDF Options Functions
toc-depth: 3 Specify the number of section levels to include in the table of contents. The default is 3
number-sections: false Number section headings rendered output.
By default, sections are not numbered.
number-depth By default, all headings in your document create a numbered section.

Tables

PDF Options Functions
df-print Method used to print tables in Knitr engine documents.
- default: Use the default S3 method for the data frame.
- kable: Default method. Markdown table using the knitr::kable() function.
- tibble: Plain text table using the tibble package.
- paged: HTML table with paging for row and column overflow.

Engine Binding

PDF Options Functions
keep-tex: false Whether to keep the intermediate tex file used during render. Defaults to false.
Helpful when you want to debug or share tex files with others.

Q: How to print dollar sign in pdf output?
A: qmd supports $ directly. No need to escape. If it fails, try \$ or \\$.

After rendering, the following info will appear in the console:

pandoc 
  to: latex
  output-file: lab1_solutions.tex
  standalone: true
  pdf-engine: xelatex
  variables:
    graphics: true
    tables: true
  default-image-extension: pdf
  
metadata
  documentclass: scrartcl
  classoption:
    - DIV=11
    - numbers=noendperiod
  papersize: letter
  header-includes:
    - \KOMAoption{captions}{tableheading}
  block-headings: true
  title: 'Lab 1: Solutions'
  fontsize: 12pt

Note that documentclass: scrartcl is the KOMA-Script article class.

It has good looking default settings, and is highly customizable.

4.4.4.1 Title Margin

One issue is it might have too wide margins around the title.

To reduce the margin above the title, add the following line to your preamble.tex file:

% reduce title top margin
\usepackage{xpatch}
\makeatletter
\xpatchcmd{\@maketitle}{\vskip2em}{
    % Insert here the space you want between the top margin and the title.
    \vspace{-2em} % Example of smaller margin. 
}{}{}
\makeatother

To reduce the margin below the title, in individual qmd file, add the following line after the YAML header:

  • fenced divs

    ::: {=latex}
\vspace{-6em}
:::

  • code chunks

    ```{=latex} 
\vspace{-6em}
```

For pdf output, it is possible to write LaTeX code directly in Markdown document using fenced divs or code chunks with {=latex}.

  • Don’t forget the equal sign before latex.

ref: R Markdown Cookbook: Section 6.11 Write raw LaTeX code

4.4.4.2 Templates

See HERE for an overview of how to set template for tex files.

  • pakage setup
  • article typsetting

Starter template for qmd file.

  • yaml header
  • structure of your qmd

4.4.4.3 Add Appendices

\newpage

# Appendices {.unnumbered}

\appendix
\renewcommand{\thesubsection}{\Alph{subsection}}
\setcounter{table}{0}
\renewcommand{\thetable}{\thesection\arabic{table}}
\setcounter{figure}{0}
\renewcommand{\thefigure}{\thesection\arabic{figure}}

## Optimal Portfolio R Code
  • # Appendices {.unnumbered} creates a title for the appendices section without a section number.
  • Use \appendix to reset the section counter to 0 and \renewcommand{\thesubsection}{\Alph{subsection}} to change the section numbering to letters (A, B, C, …).
  • Similarly, reset the table and figure counters and change their numbering to include the section letter “A”, “B”, … as a prefix.
  • Finally, use ## Optimal Portfolio R Code to create an appendix section for your first appendix. The # Appendices will be level one heading, and ## Optimal Portfolio R Code will be level two heading under the appendices section.

4.4.5 HTML Theming

One simple theme

title: "My Document"
format:
  html: 
    theme: cosmo
    fontsize: 1.1em
    linestretch: 1.7

Enable dark and light modes

format:
  html:
    include-in-header: themes/mathjax.html
    respect-user-color-scheme: true
    theme:
      dark: [cosmo, themes/cosmo-dark.scss]
      light: [cosmo, themes/cosmo-light.scss]

respect-user-color-scheme: true honors the user’s operating system or browser preference for light or dark mode.

Otherwise, the order of light and dark elements in the theme or brand will determine the default appearance for your html output. For example, since the dark option appears first in the first example, a reader will see the light appearance by default, if respect-user-color-scheme is not enabled.

As of Quarto 1.7, respect-user-color-scheme requires JavaScript support: users with JavaScript disabled will see the author-preferred (first) brand or theme.

Custom Themes

Your custom.scss file might look something like this:

/*-- scss:defaults --*/
$h2-font-size:          1.6rem !default;
$headings-font-weight:  500 !default;

/*-- scss:rules --*/
h1, h2, h3, h4, h5, h6 {
  text-shadow: -1px -1px 0 rgba(0, 0, 0, .3);
}

Note that the variables section is denoted by

  • /*-- scss:defaults --*/: the defaults section (where Sass variables go)

    Used to define global variables that can be used throughout the theme.

  • /*-- scss:rules --*/: the rules section (where normal CSS rules go)

    Used to define more fine grained behavior of the theme, such as specific styles for headings, paragraphs, and other elements.

Theme Options

You can do extensive customization of themes using Sass variables. Bootstrap defines over 1,400 Sass variables that control fonts, colors, padding, borders, and much more.

The Sass Variables can be specified within SCSS files. These variables should always be prefixed with a $ and are specified within theme files rather than within YAML options

Commonly used Sass variables:

Category Variable Description
Colors $body-bg The page background color.
$body-color The page text color.
$link-color The link color.
$input-bg The background color for HTML inputs.
$popover-bg The background color for popovers (for example, when a citation preview is shown).

You can see all of the variables here:

https://github.com/twbs/bootstrap/blob/main/scss/_variables.scss

Note that when you make changes to your local .scss, the changes will be implemented in-time. That is, you don’t need to re-build your website to see the effects.

Ref:

4.4.6 Render Quarto

Rendering the whole website is slow. When you are editing a new section/page, you may want to edit as a standalone webpage and when you are finished, you add the qmd file to the _quarto.yml file index.

Difference btw a standalone webpage from a component of a qmd project

  • Standalone webpage: include yaml at the header of the file.

    Fast compile and rendering. ✅

  • A component of qmd project: added to the file index, no yaml needed, format will automatically apply.

    Slow, need to render the whole qmd project in order to see your change.

In terminal

This will provide live preview of the document in your web browser. Newest changes will be reflected while you edit the document. ✅

  • Render a Quarto document to HTML using the command line:

    $quarto render 0304-Quarto.Rmd --to html

  • Quarto Preview: display output in the external web browser.

    $ quarto preview 0304-Quarto.Rmd # all formats
$ quarto preview 0304-Quarto.Rmd --to html # specific format
    • Note that quarto render can be used to Rmd files too.
    • Run quarto preview help to see its complete syntax.

  • You can also render a Quarto project using:

    $quarto render --to html

quarto preview [file] [args] first provide file name, then additional arguments.

Supported arguments:

  • --port Suggested port to listen on (defaults to random value between 3000 and 8000).

  • --host Hostname to bind to (defaults to 127.0.0.1)

  • --no-browser Use internal viewer, do not open external browser.

  • --no-watch-inputs flag specifically prevents Quarto from automatically re-rendering the output when changes are detected in your input source files (e.g., .qmd files). This means that if you edit and save your .qmd file, the preview in your browser will not automatically update.

    To see changes in the preview when using this flag, you would need to manually stop the quarto preview process and restart it, or explicitly trigger a re-render using quarto render.

    Even when using this flag, Quarto will still print the message “Watching file for changes.” This means that Quarto is still watching CSS files and _quarto.yml for changes, but not the main input files.

quarto preview [file] --port 7200 Previewing website using a specific port. This is useful when your want to preview multiple documents simultaneously.

The default “internal” viewer in VS Code opens only one document at a time. Can use Simple Browser Multi Extension to open multiple internal browsers in VS Code.

Steps:

  1. Install Simple Browser Multi Extension.

  2. Use command quarto preview 0304-Quarto.Rmd --port 7200 in terminal to start live preivew. This will open the preview in your external web browser.

    If you don’t want automatic re-rendering when you save the file, add --no-watch-inputs flag.

  3. In VS Code, use command palette Simple Browser Multi: Show and enter the url in Step 2 to open the preview in the internal browser.

In VS Code

By default Quarto does not automatically render .qmd or .ipynb files when you save them. This is because rendering might be very time consuming (e.g. it could include long running computations) and it’s good to have the option to save periodically without doing a full render.

You have to refresh to see your updates when using VS Code command palette quarto preview.

You can render a Quarto document in VS Code using the command palette:

  • Quarto: Render Document to render the document.
  • Quarto: Render Project to render the entire project.
  • Quarto: Preview to preview the default document in a web browser. If you want to preview a different format, use the Quarto: Preview Format command:

This will show a preview of the project in the internal browser.

However, you can configure the Quarto extension to automatically render whenever you save. In settings, set quarto.renderOnSave to true.

You might also want to control this behavior on a per-document or per-project basis. If you include the editor: render-on-save option in your document or project YAML it will supersede whatever your VS Code setting is. For example:

---
editor:
  render-on-save:true  
---

Q: Quarto Preview pane not refreshing and updating changes.
A: The issue seems to come from the --no-watch-inputs option to the preview command, preventing the live update. ↩︎

Use the following command in terminal to enable live preview:

quarto preview "path-to-file/file-name.qmd"

Copy and paste the url to the internal browser in VS Code. The command supports live preview. When you make changes to your qmd file and save, the preview will be updated in time.

In R

quarto::quarto_render(input = NULL, output_format = "html") can be used to render a Quarto document or project in R.

  • If input is not specified, it will render the current Quarto project. If input is specified, it will render the specified Quarto document.

  • If output_format is not specified, it will render the document to HTML. You can specify other formats such as PDF or Word.

    • output_format = "all" will render all formats specified in the _quarto.yml file.
# Render a Quarto document to HTML
quarto::quarto_render("0304-Quarto.Rmd", output_format = "html")
# Render a Quarto project to HTML
quarto::quarto_render(output_format = "html")
# Render a Quarto document to PDF
quarto::quarto_render("0304-Quarto.Rmd", output_format = "pdf")
# Render a Quarto project to PDF
quarto::quarto_render(output_format = "pdf")

Alternatively, you can use the Render button in RStudio. The Render button will render the first format listed in the document YAML. If no format is specified, then it will render to HTML.

4.4.7 Cross References

  1. Add labels

    Two options:

    • Code cell: add option label: prefix-LABEL
    • Markdown: add attribute #prefix-LABEL
      • Note that the prefix should be connected to the label with a hyphen -.
      • Note that the hash sign # is required.

  2. Add references: @prefix-LABEL, e.g.

    You can see in @fig-scatterplot, that...
Element ID How to cite
Figure #fig-xxx @fig-xxx
Table #tbl-xxx @tbl-xxx
Equation #eq-xxx @eq-xxx
Section #sec-xxx @sec-xxx

Cross-reference to a figure:

```{r #fig-scatter, fig.cap="Scatter plots example"} 
  # scatter plot example
  plot(1:10)
```
Scatter plots example

Figure 4.1: Scatter plots example

See Figure 4.1 (@fig-scatter) for the scatter plots.

You can customize the prefix of the reference (Figure x) using crossref/*-prefix options in YAML.

---
crossref:
  fig-prefix: "Fig"   # (default is "Figure")
---

Cross-references to Equations

$$
y_i = \beta_{i}'x + u_i.
$$ {#eq-cross_sectional_hetero}

  • @eq-cross_sectional_hetero gives Equation 1. There are no parentheses around the number.

    With the Equation prefx, but no parentheses around labels.

  • ([-@eq-cross_sectional_hetero]) gives only the tag (1), note that you need to add the parentheses yourself.

  • An alternative way is to use \eqref{eq-cross_sectional_hetero} from amsmath package, which gives (1) with parentheses automatically. You need to add the prefix Eq. yourself. ↩︎

You can customize the appearance of inline references by either changing the syntax of the inline reference or by setting options.

Here are the various ways to compose a cross-reference and their resulting output:

Type Syntax Output
Default @fig-elephant Figure 1
Capitalized @Fig-elephant Figure 1
Custom Prefix [Fig @fig-elephant] Fig 1
No Prefix [-@fig-elephant] 1

Note that the capitalized syntax makes no difference for the default output, but would indeed capitalize the first letter if the default prefix had been changed via an option to use lower case (e.g. “fig.”).

Change the prefix in inline reference using *-prefix options. You can also specify whether references should be hyper-linked using the ref-hyperlink option.

---
title: "My Document"
crossref:
  fig-prefix: figure   # (default is "Figure")
  tbl-prefix: table    # (default is "Table")
  ref-hyperlink: false # (default is true)
---

4.4.8 Equations

4.4.8.1 Individual qmd file

Load MathJax Config

For individual qmd files, load mathjax.html in YAML

---
title: "Model specifications"
author: "GDP and climate"
date: "2025-05-13"
format: 
  html:
    toc: true
    self-contained: true
    html-math-method: mathjax
    include-in-header: mathjax.html
    from: markdown+tex_math_single_backslash
---

  • from can be a top-level option (same level as title) or a third-level option under format/html in YAML.

    • It specifies formats to read from.
    • Extensions can be individually enabled or disabled by appending +EXTENSION or -EXTENSION to the format name (e.g. markdown+emoji).
    • See Quarto Extensions for available extensions.

  • from: markdown+tex_math_single_backslash tells Quarto/Pandoc to read the input as Pandoc Markdown with the tex_math_single_backslash extension enabled.

In mathjax.html, define the MathJax configuration, e.g., user-defined macros.

<script>
MathJax = { 
    tex: { 
        tags: 'ams',  // should be 'ams', 'none', or 'all' 
        macros: {  // define TeX macro
            RR: "{\\bf R}",
            bold: ["{\\bf #1}", 1]
        },
    },
};
</script>

tags: 'ams' allows equation numbering.

4.4.8.2 Quarto project

In _quarto.yml,

format:
  html:
    include-in-header: 
      - file: themes/mathjax.html       # MathJax for LaTeX custom macro support
      - file: themes/common-header.html # load js scripts and external css (e.g., font-awesome) for all pages
    from: markdown+tex_math_single_backslash

Note that from is under html, rather than at the top level of YAML.

4.4.8.3 Cross-referencing Equations

Equations need to be labeled to be numbered and cross-referenced.

  • Note that labels must begin with #eq-xxx. Don’t forget the hyphen - between eq and xxx.
  • Put the label after the $$ and inside curly braces {}.
  • References to equations are made using @eq-xxx.
Quarto way to label an equation:
$$
y_i = \beta_{i}'x + u_i.
$$ {#eq-cross_sectional_hetero}

  • Difference with bookdown.

    bookdown, on the other hand, use (\#eq:label) (must use colon) after the equation but inside the $$.

4.4.8.4 Math delimiters

Use $ delimiters for inline math and $$ delimiters for display math.

Note that for inline math, NO spaces are allowed between the dollar signs and the math content. Otherwise, it will NOT be recognized as math.

Examples:

  • Inline math: $E = mc^2$

  • Block math:

    $$
a^2 + b^2 = c^2
$$

or you can put the dollar signs on the same line as the equation:
$$a^2 + b^2 = c^2$$

Issue: Cannot use \( and \[ for math delimiters.
Fix: Add from: markdown+tex_math_single_backslash to YAML frontmatter. Source

---
title: "Quarto Playground"
from: markdown+tex_math_single_backslash
format:
  html:
    html-math-method: mathjax
---

Inline math example: \( E = mc^2 \)

Block math example:

\[
a^2 + b^2 = c^2
\]

form: Format to read from. Extensions can be individually enabled or disabled by appending +EXTENSION or -EXTENSION to the format name (e.g. markdown+emoji).

Extension: tex_math_single_backslash

Causes anything between \( and \) to be interpreted as inline TeX math, and anything between \[ and \] to be interpreted as display TeX math. Note: a drawback of this extension is that it precludes escaping ( and [.

Refer to Docs of Quarto and Pandoc:

Q: How to get rid of the qmd dependence file?
A: Use

format: 
  html:
    self-contained: true

4.4.9 Extensions

Quarto Extensions

4.4.9.1 Color Text

Create a filter to apply blue text color to fenced div.

  • Created a minimal local color-text filter:
    • Added _quiz/_extensions/color-text/color-text.lua
    • It supports the .blue class for both blocks and inline spans:
      • HTML: adds style="color: blue;"
      • PDF: wraps with LaTeX xcolor; automatically injects \usepackage{xcolor}
  • Updated the qmd file YAML to reference this local filter:
    • filters:
      • _extensions/color-text/color-text.lua
  • You can use fenced divs and inline spans with .blue.

Use example

  1. In the yaml header of your qmd file, add the following line to reference the local filter:

    ---
title: "Quiz: Linear Regression and Hypothesis Testing (p2)"
from: markdown+tex_math_single_backslash
params:
  # solution: false
  solution: true
filters:
  - _extensions/color-text/color-text.lua
format:
  pdf:
    include-in-header: ../latex/preamble.tex
    fontsize: 12pt
---

  2. Use the .blue class in your markdown content:

    ::: {.content-visible when-meta="params.solution"}
::: {.blue}
**Solutions**
(a) The 95% confidence interval for $\beta_1$ is given by
  $$
  \hat{\beta}_1 \pm t_{0.975, n-2} \cdot SE(\hat{\beta}_1)
  $$
  Degrees of freedom: $df = n-2 = 50-2 = 48$
(b)
:::
:::

4.4.9.2 Emoji

In the yaml, add the emoji extension to the from option in document metadata.

---
title: "My Document"
from: markdown+emoji
---

For markdown formats that support text representations of emojis 😁 (e.g. :grinning:), the text version will be written. For other formats the literal emoji character will be written. Currently, the gfm and hugo (with enableEmoji = true in the site config) formats both support text representation of emojis.

Note: This does NOT work for quarto pdf. Use twemoji approach instead. See below.

twemoji

How to add more emoji later:

  1. Open twemoji_manifest.json and append new code points to the emoji object

    • Example: "1f44d": ["👍", ":thumbsup:"]

    How to find the code points of an emoji:

    node -e 'const s=process.argv[1]; const codes=[...s].map(ch=>ch.codePointAt(0).toString(16)); console.log(codes.join("-"))' '⚠️'
# Prints: 26a0-fe0f  → Twemoji file: assets/72x72/26a0-fe0f.png (often 26a0.png also exists)

  2. Run the fetcher again:

    Within the project directory:

    $./emoji/fetch_twemoji.sh

    From anywhere:

    $'/Users/menghan/Documents/language/norsk/norskprøver/B2/exam notes/emoji/fetch_twemoji.sh'
Exists: 1f4a1.png
Exists: 1f4c8.png
Exists: 1f4dd.png
Exists: 1f539.png
Exists: 1f600.png
Exists: 1f604.png
Exists: 1f680.png
Exists: 26a0.png
Downloading: 2705.png
Done. Files saved in ~/Documents/language/norsk/norskprøver/B2/exam notes/emoji. Map to filter names as needed (already matching).

    The script downloads only missing PNGs. If you add more codes to twemoji_manifest.json, just run it again.

    To refresh files, delete specific PNGs (or all) in emoji and rerun.

  3. Add to unicode_map in emoji.lua to point to the same filename.

    • Example: ["⚠️"] = "26a0.png",

    This ensures when you use the emoji directly, it maps to the correct image file.

  4. Optionally add a shortcode mapping in emoji.lua’s emoji_map to point to the same filename.

    • Example: [":warning:"] = "26a0.png",

    This allows you to use the shortcode :warning: in addition to the direct emoji.

🎯 Usage Examples

You can now use emojis in your QMD files in two ways:

  • Direct Unicode: Great job! 👍 This is amazing! 🎉
  • Shortcodes: Great job! :thumbsup: This is amazing! :tada:

ref:

4.4.10 Divs and Spans

Quarito Guide: Divs and Spans

You can add classes, attributes, and other identifiers to regions of content using Divs and Spans.

  • classes: .class
  • identifiers: #id
  • key-value attributes: key="value"

Note that:

  • They are separated by spaces, do NOT use commas.

    This is different from bookdown, which uses commas.

  • Order: identifiers, classes, and then key-value attributes.

  • Logical attributes: true/false, yes/no, and on/off are all equivalent to TRUE/FALSE in R.

    It is optional to enclose in quotes.

4.4.10.1 Block Attributes

Apply attributes to a block of content, such as a paragraph, list, or code block.

Div example:

::: {.border} 
This content can be styled with a border 
:::

Once rendered to HTML, Quarto will translate the markdown into:

<div class="border">   
  <p>This content can be styled with a border</p> 
</div>

Note that:

  • The Div should be separated by blank lines from preceding and following blocks.

  • Fenced divs can be nested.

    For example

    ::::: {#special .sidebar}

::: {.warning}
Here is a warning.
:::

More content.
:::::

    will be rendered to

    <div id="special" class="sidebar">
  <div class="warning">
    <p>Here is a warning.</p>
  </div>
  <p>More content.</p>
</div>

More examples

  • Headings with attributes

    ## Data Analysis {.highlight #analysis}

    renders to:

    <h2 id="analysis" class="highlight">Data Analysis</h2>

  • List with attributes

    - Item 1
- Item 2
{.fancy-list}

    renders to:

    <ul class="fancy-list">
  <li>Item 1</li>
  <li>Item 2</li>
</ul>

  • Paragrphs with attributes

    This is a paragraph with a yellow background.
{.yellow-bg}

    renders to:

    <p class="yellow-bg">This is a paragraph with a yellow background.</p>

4.4.10.2 Inline Attributes

Apply attributes to inline text, such as selected words within a paragraph.

A bracketed sequence of inlines [text here] (as one would use to begin a link) will be treated as a <span> with attributes if it is followed immediately by attributes {attributes here}.

Syntax for inline attributes:

[This is *some text*]{.class key="val"}

Once rendered to HTML, Quarto will translate the markdown into

<span class="class" data-key="val">
  This is <em>some text</em>
</span>

Note that:

  • No space between ] and {.

  • Ordering of attributes matter.

    #id comes first then .class then key="val".

    Any of these can be omitted, but must follow that order if they are provided.

    Valid example:

    [This is good]{#id .class key1="val1" key2="val2"}

    Invalid example:

    [This does *not* work!]{.class key="val" #id}

Use example:

This is a [highlighted word]{.red} in the text.

renders to:

This is a <span class="red">highlighted word</span> in the text.

4.4.11 Theorems

::: {#thm-line}
The equation of any straight line, called a linear equation, can be written as:

$$
y = mx + b
$$
:::

See @thm-line.

In Quarto, #thm-line is a combined command us .theorem #thm-line in bookdown. In bookdown, the label can be anything, does not have to begin with #thm-. But in Quarto, #thm-line is restrictive, it indicates the thm environment and followed by the label of the theorem line.

Theorem 4.1 The equation of any straight line, called a linear equation, can be written as:

\[ y = mx + b \]

See Theorem 4.1.

To add a name to Theorem, use name="...".

::: {#thm-topo name="Topology Space"}
A topological space $(X, \Tcal)$ is a set $X$ and a collection $\Tcal \subset \Pcal(X)$ of subsets of $X,$ called open sets, such that ...
:::

See Theorem @thm-topo.

Theorem 4.2 (Topology Space) A topological space \((X, \Tcal)\) is a set \(X\) and a collection \(\Tcal \subset \Pcal(X)\) of subsets of \(X,\) called open sets, such that …

See Theorem 4.2.

Change the label prefix:

---
crossref:
  cnj-title: "Assumption"
  cnj-prefix: "Assumption"
---
  • cnj-title: The title prefix used for conjecture captions.
  • cnj-prefix: The prefix used for an inline reference to a conjecture.

4.4.12 Tables

Tables in Latex

Tables in raw LaTeX can be included in Quarto documents using fenced divs or code chunks with {=latex}.

  • Use fenced div to add labels #tbl-xxx for cross-referencing. Note the # is mandatory. Without it, the table cross reference will show as ?? in the output.
    • You can ignore the fenced divs if you don’t need cross-reference.
  • Refer to the table using @tbl-xxx.
::: {#tbl-1}

```{=latex} 
% Or whatever actual you want, includegraphics, whatever. 
% (_not_ \begin{table}, just the content of it)
\begin{tabular}{l c r}
\hline
Header 1 & Header 2 & Header 3 \\
\hline
Row 1 Col 1 & Row 1 Col 2 & Row 1 Col 3 \\
Row 2 Col 1 & Row 2 Col 2 & Row 2 Col 3 \\
\hline
\end{tabular}
```

This is a table caption.

:::

For cross-reference: See @tbl-1.

Alternatively, use LaTeX syntax entirely as follows.

The regression results are summarized in Table \ref{tbl-regression-results}.

```{=latex} 
\begin{table}
\centering
\caption{Regression Results: CAPM vs. Fama-French 3-Factor Model}
\label{tbl-regression-results}
\begin{tabular}{l c r}
\hline
Header 1 & Header 2 & Header 3 \\
\hline
Row 1 Col 1 & Row 1 Col 2 & Row 1 Col 3 \\
Row 2 Col 1 & Row 2 Col 2 & Row 2 Col 3 \\
\hline
\end{tabular}
\end{table}
```

Q: How to use [H] to force table placement in qmd?
A: Add the following to the preamble file:

\usepackage{float} % for [H] placement specifier

% Make all tables use [H] placement by default
\makeatletter
\renewenvironment{table}[1][H]{%
  \@float{table}[#1]%
}{%
  \end@float
}
\makeatother

ref: https://github.com/quarto-dev/quarto-cli/discussions/6734#discussioncomment-6919437

Tables in Markdown

You can create tables using standard Markdown syntax.

| Col1 | Col2 | Col3 |
| ---- | ---- | ---- |
| A    | B    | C    |
| E    | F    | G    |
| A    | G    | G    |

: My Caption {#tbl-letters .striped .hover}

See @tbl-letters for the table.

  • Captions are added using Pandoc table syntax: :␣Caption text.

  • Table labels and attributes can be added within curly braces {} after the caption.

    If your table does not have a caption, you can still add attributes by placing them directly after :␣

  • You can also explicitly specify columns widths using the tbl-colwidths attribute or document-level option. If you have a table with two columns, and want to set 1st col to 25% and 2nd col to 75% of the table width, you can do:

    | fruit  | price  |
|--------|--------|
| apple  | 2.05   |
| pear   | 1.37   |
| orange | 3.09   |

: Fruit prices {tbl-colwidths="[25, 75]"}

ref: https://quarto.org/docs/authoring/tables.html#markdown-tables

4.4.13 Raw Content

Raw content can be included directly without Quarto parsing it using Pandoc’s raw attribute. A raw block starts with ```{= followed by a format and closing }, e.g. here’s a raw HTML block:

```{=html}
<iframe src="https://quarto.org/" width="500" height="400"></iframe>
```

For PDF output use a raw LaTeX block:

```{=latex}
\renewcommand*{\labelitemi}{\textgreater}
```

4.4.14 Lists

Basic lists

1. ordered list
2. item 2
   i) sub-item 1
      A. sub-sub-item 1

Will be rendered as:

  1. ordered list
  2. item 2
    1. sub-item 1 A. sub-sub-item 1

Quarto uses Pandoc’s Markdown, which supports a variety of ordered list types, including:

  • numbers: 1. 2. 3.
  • letters: a. b. c. or A. B. C.
  • roman numerals: i. ii. iii. or I. II. III.

These list markers / labels need to be followed by a period and a space. Optionally, list markers may be enclosed in parentheses or followed by a single right-parentheses or period.

Special list marker @ can be used for sequentially numbered examples. The benefit of using @ is that when the list is broken up by other content, the numbering will continue correctly.

(@)  My first example will be numbered (1).
(@)  My second example will be numbered (2).

Explanation of examples. ← This breaks list structure.

(@)  My third example will be numbered (3).

Q: How to start numbering at a number other than 1?
A: Simply explicitly restart the list at the number you want.

1. item 1
1. item 2

Code block


3. item 3
1. item 4

will be rendered as:

  1. item 1
  2. item 2
Code block
  1. item 3
  2. item 4

ref: https://stackoverflow.com/a/78497776

4.4.15 Callouts

There are five different types of callouts available.

  • note (blue)
  • tip (green)
  • important (red)
  • warning (amber 比 caution 更亮眼 vivid )
  • caution (orange)

The color and icon will be different depending upon the type that you select.

::: {.callout-note}
Note that there are five types of callouts, including:
`note`, `warning`, `important`, `tip`, and `caution`.
:::

::: {.callout-tip}
## Tip with Title

This is an example of a callout with a title.
:::

::: {.callout-caution collapse="true"}
## Expand To Learn About Collapse

This is an example of a 'folded' caution callout that can be expanded by the user. You can use `collapse="true"` to collapse it by default or `collapse="false"` to make a collapsible callout that is expanded by default.
:::

Here are what the various types look like in HTML output:

  • Callout heading can be defined using

    • title = "Heading" in the callout header, or

    • ## Heading in the callout body

      It can be any level of heading.

  • icon = false to disable the icon in the callout.
  • To cross-reference a callout, add an ID attribute that starts with the appropriate callout prefix, e.g., #nte-xxx. You can then reference the callout using the usual @nte-xxx syntax.
  • appearance = "default" | "simple" | "minimal"

    • default: to use the default appearance with a background color and border.

    • simple: to remove the background color, but keep the border and icon.

    • minimal: A minimal treatment that applies borders to the callout, but doesn’t include a header background color or icon.

      appearance="minimal" is equivalent to appearance = "simple" icon = false in the callout header.

You can style callouts using CSS. For example, the change font size and alignment of text, you can use the following CSS:

::: {.callout-important appearance="minimal"}
## Research Question

<center style="font-size: 1.5em; font-weight: bold;">
Does expenditure per student affect student performance \
in elementary school education?
</center>
:::

4.4.15.1 Nested Callouts

You can nest callouts within other callouts. For example:

::: {.callout-warning}
## Warning with Nested Callout
This is an example of a warning callout that contains a nested note callout.

::: {.callout-note}
This is a nested note callout.
:::

:::

Note that you need to put a blank line before and after the nested callout to ensure proper rendering.

4.4.15.2 Cross-reference Callouts

To cross-reference a callout, add an ID attribute that starts with the appropriate callout prefix (see Table blow). You can then reference the callout using the usual @ syntax. For example, here we add the ID #tip-example to the callout, and then refer back to it:

::: {#tip-example .callout-tip}
## Cross-Referencing a Tip
Add an ID starting with `#tip-` to reference a tip.
:::
See @tip-example...

  • Note that the ID attribute must come first, before the class attribute.

    This follows the general rule for Divs and Spans that IDs must come before classes.

The prefixes for each type of callout are:

Prefixes for callout cross-references

Callout Type Prefix
note #nte-
— —
tip #tip-
warning #wrn-
important #imp-
caution #cau-

Cross-referencing callouts is currently only supported for HTML, PDF and MS Word.

4.4.16 Conditional Content

In some cases you may want to create content that only displays for a given output format (or only displays when not rendering to a format). You can accomplish this by creating divs, spans and code blocks with the .content-visible and .content-hidden classes.

E.g., you have a home assignment file and you want to have two versions of it: one for questions only, and the other for questions and solutions.

You can set a metadata variable in yaml, e.g., solutions: true or solutions: false.

---
title: "Quiz: Linear Regression and Hypothesis Testing (p1)"
from: markdown+tex_math_single_backslash
solution: false
# solution: true
format:
  pdf:
    include-in-header: ../latex/preamble.tex
    fontsize: 12pt
---

Then, in the body of your document, you can use the following syntax to conditionally include or exclude content based on the value of the solutions variable.

::: {.content-visible when-meta="solutions"}
This content will only be visible if `solutions` is set to `true`.

Put your solutions here.
:::

Expected behavior:

  • If solutions: true, the content will be displayed.
  • If solutions: false, the content will be hidden.

You can use multiple levels of metadata keys separated by periods. For example,

::: {.content-hidden unless-meta="path.to.metadata"}

This content will be hidden unless there exists a metadata entry like such:

```yml
path:
  to:
    metadata: true
```

:::

You need to use unless-meta="path.to.metadata" to refer to your user defined metadata key.

4.4.16.1 Set up multiple profiles

You can also set up multiple profiles in _quarto.yml, so you can just run quarto render --profile with-solutions / --profile no-solutions in terminal to render the document with or without solutions.

project:
  type: book
  output-dir: docs

profiles:
  with-solutions:
    metadata:
      solutions: true
  
  no-solutions:
    metadata:
      solutions: false

You can then render the document with solutions using --profile argument:

quarto render --profile with-solutions

Default profile

To define a default profile, add a default option to the profile key. For example, to make the with-solutions profile the default, you can use the following configuration:

profile:
  default: with-solutions

Then, you can simply run quarto render without specifying a profile, and it will use the with-solutions profile by default.

4.4.16.2 Conditional Code Blocks

Q: Conditional contents NOT working for code blocks.

A: It’s because .content-visible runs after code execution. knitr executes the chunk and emits output even if the wrapper later hides the surrounding Markdown. Control the chunk itself with the meta flag.

Solution: Use params in rmarkdown.

  1. In the YAML header, define a parameter solution with a default value of false.

    ---
title: "Home Assignment"
from: markdown+tex_math_single_backslash
params:
  solution: false
  # solution: true
---
    • solution: false means do not show solutions by default.
    • solution: true means show solutions.

  2. Using a code chunk to get the value of the parameter. Put it at the beginning of the document as part of a global setup.

    ```{r echo=FALSE} 
.solution <- params$solution
```

  3. For following code chunks, you can use eval=.solution, include=.solution to control whether to evaluate and include the chunk based on the value of .solution.

    ```{r eval=.solution, include=.solution} 
# R code for solution
summary(cars)
```
    • When .solution is TRUE, the chunk will be evaluated and included in the output.
      • If you still want to evaluate but not include in the output, use include=.solution only
    • when .solution is FALSE, the chunk will not be evaluated or included in the output.

  4. For regular text, use fenced divs with .content-visible and when-meta="solution" to conditionally include or exclude content based on the value of the solution parameter.

    ::: {.content-visible when-meta="params.solution"}
This content will only be visible if `solution` is set to `true`.

Put your solutions here.
:::
    • Use the attributes unless-meta and when-meta, and use periods . to separate metadata keys.
    • solution is a second-level key under params, so you need to use params.solution to refer to it.

Use scenarios:

  • When preparing the assignment, you can set solution: true to see the solutions while editing.
  • After you finish editing, set solution: false to hide the solutions before submission.

When you want to render the document with solutions, you can set the parameter solution to true in the YAML header or use command line arguments.

ref:

References: