47  Quarto Markdown Reference

This appendix provides a comprehensive quick reference for Quarto Markdown syntax and features used throughout this book.

47.1 Introduction to Quarto

Quarto is an open-source scientific and technical publishing system built on Pandoc. It allows you to:

  • Combine narrative text with executable code (R, Python, Julia, Observable)
  • Create reproducible documents in multiple formats (HTML, PDF, Word, EPUB)
  • Use consistent syntax across different programming languages
  • Generate professional scientific documents with cross-references, citations, and equations

Quarto documents use the .qmd file extension and combine Markdown for text, code chunks for analysis, and YAML for configuration.

47.2 Basic Markdown Syntax

Headers

Syntax Result Usage
# Header 1 Largest heading Chapter/section title
## Header 2 Second level Major section
### Header 3 Third level Subsection
#### Header 4 Fourth level Sub-subsection
##### Header 5 Fifth level Rarely used
###### Header 6 Smallest heading Rarely used

Headers can include section labels for cross-referencing:

## Methods {#sec-methods}

Text Formatting

Syntax Result Description
*italic* or _italic_ italic Emphasized text
**bold** or __bold__ bold Strong emphasis
***bold italic*** bold italic Both bold and italic
~~strikethrough~~ strikethrough Deleted text
superscript^2^ superscript2 Superscript
subscript~2~ subscript2 Subscript
`code` code Inline code

Lists

Unordered Lists:

- Item 1
- Item 2
  - Nested item 2a
  - Nested item 2b
- Item 3

Ordered Lists:

1. First item
2. Second item
   a. Nested item
   b. Another nested item
3. Third item

Task Lists:

- [ ] Incomplete task
- [x] Completed task

Blockquotes

> This is a blockquote.
> It can span multiple lines.
>
> And multiple paragraphs.

Result: > This is a blockquote. > It can span multiple lines.

Code

Inline Code:

Use the `mean()` function to calculate averages.

Code Blocks:

```
Plain code block without syntax highlighting
```

```r
# R code with syntax highlighting
x <- c(1, 2, 3, 4, 5)
mean(x)
```

```python
# Python code with syntax highlighting
import numpy as np
x = np.array([1, 2, 3, 4, 5])
np.mean(x)
```

47.3 Quarto-Specific Features

YAML Header

Every Quarto document begins with a YAML header enclosed in ---:

---
title: "My Analysis"
author: "Your Name"
date: "2024-01-15"
format:
  html:
    toc: true
    code-fold: true
    theme: cosmo
  pdf:
    documentclass: article
    geometry: margin=1in
execute:
  echo: true
  warning: false
  message: false
bibliography: references.bib
---

Common YAML Options:

Option Description Example
title Document title "My Report"
author Author name(s) "Jane Doe"
date Document date today or "2024-01-15"
format Output format(s) html, pdf, docx
toc Table of contents true or false
number-sections Number sections true or false
bibliography Bibliography file references.bib
execute Global execution options See below

Code Chunk Options

Code chunks in Quarto use #| (hashpipe) notation for options:


::: {.cell}
::: {.cell-output-display}
![Relationship between variables](A5-quarto-reference_files/figure-html/fig-scatter-1.png){#fig-scatter width=576}
:::
:::

Common Chunk Options:

Option Description Values
label Unique chunk identifier fig-name, tbl-name
echo Show code true, false
eval Execute code true, false
include Include output true, false
warning Show warnings true, false
message Show messages true, false
error Show errors true, false
fig-cap Figure caption "Caption text"
fig-width Figure width (inches) 6, 8, etc.
fig-height Figure height (inches) 4, 6, etc.
tbl-cap Table caption "Caption text"
output Control output true, false, asis

Cross-References

Quarto provides automatic numbering and cross-referencing:

Figures:


::: {.cell}

```{.r .cell-code}
hist(rnorm(100))
```

::: {.cell-output-display}
![Distribution of sample data](A5-quarto-reference_files/figure-html/fig-histogram-1.png){#fig-histogram width=672}
:::
:::


See @fig-histogram for the distribution.

Tables:


::: {#tbl-summary .cell tbl-cap='Summary statistics'}

```{.r .cell-code}
knitr::kable(summary(mtcars))
```

::: {.cell-output-display}


|   |     mpg      |     cyl      |     disp     |      hp      |     drat     |      wt      |     qsec     |      vs       |      am       |     gear     |     carb     |
|:--|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:--------------|:--------------|:-------------|:-------------|
|   |Min.   :10.40 |Min.   :4.000 |Min.   : 71.1 |Min.   : 52.0 |Min.   :2.760 |Min.   :1.513 |Min.   :14.50 |Min.   :0.0000 |Min.   :0.0000 |Min.   :3.000 |Min.   :1.000 |
|   |1st Qu.:15.43 |1st Qu.:4.000 |1st Qu.:120.8 |1st Qu.: 96.5 |1st Qu.:3.080 |1st Qu.:2.581 |1st Qu.:16.89 |1st Qu.:0.0000 |1st Qu.:0.0000 |1st Qu.:3.000 |1st Qu.:2.000 |
|   |Median :19.20 |Median :6.000 |Median :196.3 |Median :123.0 |Median :3.695 |Median :3.325 |Median :17.71 |Median :0.0000 |Median :0.0000 |Median :4.000 |Median :2.000 |
|   |Mean   :20.09 |Mean   :6.188 |Mean   :230.7 |Mean   :146.7 |Mean   :3.597 |Mean   :3.217 |Mean   :17.85 |Mean   :0.4375 |Mean   :0.4062 |Mean   :3.688 |Mean   :2.812 |
|   |3rd Qu.:22.80 |3rd Qu.:8.000 |3rd Qu.:326.0 |3rd Qu.:180.0 |3rd Qu.:3.920 |3rd Qu.:3.610 |3rd Qu.:18.90 |3rd Qu.:1.0000 |3rd Qu.:1.0000 |3rd Qu.:4.000 |3rd Qu.:4.000 |
|   |Max.   :33.90 |Max.   :8.000 |Max.   :472.0 |Max.   :335.0 |Max.   :4.930 |Max.   :5.424 |Max.   :22.90 |Max.   :1.0000 |Max.   :1.0000 |Max.   :5.000 |Max.   :8.000 |


:::
:::


Results are shown in @tbl-summary.

Sections:

## Methods {#sec-methods}

As described in @sec-methods, we used...

Equations:

$$
E = mc^2
$$ {#eq-einstein}

According to @eq-einstein, energy equals...

Cross-Reference Prefixes:

Type Prefix Example
Figure fig- @fig-scatter
Table tbl- @tbl-results
Section sec- @sec-intro
Equation eq- @eq-model
Theorem thm- @thm-central-limit
Lemma lem- @lem-property
Proof prp- @prp-main

Citations

Reference bibliography entries using @key:

According to @fisher1925 and @student1908, the t-test...

Multiple citations [@fisher1925; @student1908].

Citation with page number [@fisher1925, p. 42].

Citation with prefix [see @fisher1925, p. 42].

Bibliography File (BibTeX):

@article{fisher1925,
  author = {Fisher, R. A.},
  title = {Statistical Methods for Research Workers},
  journal = {Oliver and Boyd},
  year = {1925}
}

Callout Blocks

Callout blocks highlight important information:

Note:

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

Tip:

:::{.callout-tip}
## Pro Tip
This is a helpful tip for users.
:::

Warning:

:::{.callout-warning}
Be careful with this approach!
:::

Important:

:::{.callout-important}
This is crucial information.
:::

Caution:

:::{.callout-caution}
Proceed with caution.
:::

Callout Types:

Type Icon Color Usage
note Info Blue General information
tip Lightbulb Green Helpful suggestions
warning Warning Orange Potential issues
important Exclamation Red Critical information
caution Fire Red Dangerous operations

Collapsible Callouts:

:::{.callout-note collapse="true"}
## Expandable Note
This content is hidden by default.
:::

Tabsets

Organize content into tabs:

::: {.panel-tabset}

## R Code

::: {.cell}

```{.r .cell-code}
mean(c(1, 2, 3, 4, 5))
[1] 3

:::

47.4 Base R Alternative

Code 
sum(c(1, 2, 3, 4, 5)) / length(c(1, 2, 3, 4, 5))
[1] 3

:::


### Equations {#sec-equations}

**Inline Math:**
```markdown
The mean is calculated as $\bar{x} = \frac{1}{n}\sum_{i=1}^{n}x_i$.

Display Math:

$$
\sigma^2 = \frac{1}{n-1}\sum_{i=1}^{n}(x_i - \bar{x})^2
$$

Numbered Equations:

$$
f(x) = \frac{1}{\sigma\sqrt{2\pi}} e^{-\frac{(x-\mu)^2}{2\sigma^2}}
$$ {#eq-normal}

The normal distribution (@eq-normal) is...

Aligned Equations:

$$
\begin{aligned}
\bar{x} &= \frac{1}{n}\sum_{i=1}^{n}x_i \\
&= \frac{x_1 + x_2 + \cdots + x_n}{n}
\end{aligned}
$$ {#eq-mean}

47.5 Figures and Tables

Figure Syntax

Basic Figure:


::: {.cell}

```{.r .cell-code}
plot(mtcars$mpg, mtcars$hp,
     xlab = "Miles per Gallon",
     ylab = "Horsepower")
```

::: {.cell-output-display}
![Scatter plot of mpg vs hp](A5-quarto-reference_files/figure-html/fig-plot-1.png){#fig-plot width=672}
:::
:::

Multiple Figures (Subfigures):


::: {#fig-multiple .cell layout-ncol="2"}

```{.r .cell-code}
hist(rnorm(1000))
hist(rexp(1000))
```

::: {.cell-output-display}
![Normal distribution](A5-quarto-reference_files/figure-html/fig-multiple-1.png){#fig-multiple-1 width=672}
:::

::: {.cell-output-display}
![Exponential distribution](A5-quarto-reference_files/figure-html/fig-multiple-2.png){#fig-multiple-2 width=672}
:::

Comparison of distributions
:::


See @fig-multiple-1 and @fig-multiple-2.

Markdown Images with Labels:

![Experimental setup](images/setup.png){#fig-setup}

The apparatus shown in @fig-setup was used...

Figure Size and Alignment

Option Description Example
fig-width Width in inches fig-width: 6
fig-height Height in inches fig-height: 4
fig-align Alignment left, center, right
out-width Output width (%) out-width: "80%"
fig-dpi Resolution fig-dpi: 300

Example:


::: {.cell layout-align="center"}

```{.r .cell-code}
plot(pressure)
```

::: {.cell-output-display}
![](A5-quarto-reference_files/figure-html/unnamed-chunk-3-1.png){fig-align='center' width=90%}
:::
:::

Table Syntax

Markdown Tables (Pipe Tables):

| Column 1 | Column 2 | Column 3 |
|:---------|:--------:|---------:|
| Left     | Center   | Right    |
| aligned  | aligned  | aligned  |
| text     | text     | text     |

Table Alignment: - :--- = Left aligned - :--: = Center aligned - ---: = Right aligned

Grid Tables:

+----------+----------+----------+
| Column 1 | Column 2 | Column 3 |
+==========+==========+==========+
| Row 1    | Data     | Values   |
+----------+----------+----------+
| Row 2    | More     | Content  |
+----------+----------+----------+

Code-Generated Tables:


::: {#tbl-mtcars .cell tbl-cap='Summary of mtcars dataset'}

```{.r .cell-code}
knitr::kable(head(mtcars[, 1:4]))
```

::: {.cell-output-display}


|                  |  mpg| cyl| disp|  hp|
|:-----------------|----:|---:|----:|---:|
|Mazda RX4         | 21.0|   6|  160| 110|
|Mazda RX4 Wag     | 21.0|   6|  160| 110|
|Datsun 710        | 22.8|   4|  108|  93|
|Hornet 4 Drive    | 21.4|   6|  258| 110|
|Hornet Sportabout | 18.7|   8|  360| 175|
|Valiant           | 18.1|   6|  225| 105|


:::
:::

Caption and Label:

: Summary statistics for experimental groups {#tbl-summary}

| Group | Mean | SD   | N  |
|:------|-----:|-----:|---:|
| A     | 5.2  | 1.1  | 20 |
| B     | 6.8  | 1.4  | 20 |

47.6 Document Output Options

HTML Output

format:
  html:
    toc: true
    toc-depth: 3
    toc-location: left
    number-sections: true
    code-fold: true
    code-tools: true
    code-copy: true
    theme: cosmo
    highlight-style: github
    embed-resources: false
    fig-width: 7
    fig-height: 5

Common HTML Options:

Option Description Values
toc Table of contents true, false
toc-depth TOC depth 1, 2, 3, etc.
toc-location TOC position left, right, body
code-fold Foldable code true, false, show
code-tools Code tools menu true, false
theme Visual theme default, cosmo, flatly, etc.
embed-resources Self-contained true, false

PDF Output

format:
  pdf:
    documentclass: article
    geometry:
      - margin=1in
      - letterpaper
    number-sections: true
    colorlinks: true
    toc: true
    toc-depth: 2
    keep-tex: false

Common PDF Options:

Option Description Values
documentclass LaTeX class article, report, book
geometry Page layout margin=1in, etc.
fontsize Text size 10pt, 11pt, 12pt
colorlinks Colored links true, false
keep-tex Keep .tex file true, false

Word Output

format:
  docx:
    toc: true
    number-sections: true
    highlight-style: github
    reference-doc: custom-template.docx

Multiple Formats

format:
  html:
    toc: true
    theme: cosmo
  pdf:
    documentclass: article
  docx:
    toc: true

Render specific format:

quarto render document.qmd --to html
quarto render document.qmd --to pdf

47.7 Common Quarto Commands

Basic Commands

Command Description
quarto preview file.qmd Live preview in browser
quarto render file.qmd Render to default format
quarto render file.qmd --to html Render to HTML
quarto render file.qmd --to pdf Render to PDF
quarto render file.qmd --to docx Render to Word
quarto render Render entire project
quarto publish Publish document online

Project Commands

Command Description
quarto create project Create new project
quarto preview Preview project
quarto render Render all project files
quarto check Check installation
quarto tools install Install required tools

Preview Options

# Preview on specific port
quarto preview document.qmd --port 8080

# Preview without opening browser
quarto preview document.qmd --no-browser

# Preview specific format
quarto preview document.qmd --to pdf

Render Options

# Render with parameters
quarto render document.qmd -P alpha:0.05 -P n:100

# Render to specific output file
quarto render document.qmd --output report.html

# Render all formats
quarto render document.qmd --to all

# Execute code even if frozen
quarto render document.qmd --execute

47.8 Keyboard Shortcuts

When using Quarto in RStudio or VS Code:

Shortcut Action Platform
Cmd/Ctrl + Shift + K Render document All
Cmd/Ctrl + Shift + Enter Run current chunk All
Cmd/Ctrl + Alt + I Insert code chunk RStudio
Cmd/Ctrl + Alt + P Run all chunks above RStudio

47.9 Quick Reference Summary

Document Structure:

---
title: "Title"
format: html
---

# Section

Text with **bold** and *italic*.


::: {.cell}

```{.r .cell-code}
code here
Error in parse(text = input): <text>:1:6: unexpected symbol
1: code here
         ^

:::

See ?fig-name and ?sec-other.


**Essential Syntax:**
- Headers: `#`, `##`, `###`
- Bold: `**text**`
- Italic: `*text*`
- Code: `` `code` ``
- Link: `[text](url)`
- Image: `![caption](file.png)`
- Equation: `$math$` or `$$display$$`
- Citation: `@reference`
- Cross-ref: `@fig-name`, `@tbl-name`, `@sec-name`

**Key Features:**
- Use YAML for configuration
- Use `#|` for chunk options
- Label figures/tables/sections with `{#prefix-name}`
- Reference with `@prefix-name`
- Use callouts for important info
- Organize with tabsets and divs




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[Statistics for the Biosciences and Bioengineering]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyLXRpdGxl"}
[Statistics for the Biosciences and Bioengineering]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1uYXZiYXItdGl0bGU="}
[<span class='chapter-number'>48</span>  <span class='chapter-title'>LaTeX Command Reference</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1uZXh0"}
[<span class='chapter-number'>46</span>  <span class='chapter-title'>R Command Reference</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1wcmV2"}
[<span class='chapter-number'>1</span>  <span class='chapter-title'>Why This Book?</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9pbmRleC5odG1sPHNwYW4tY2xhc3M9J2NoYXB0ZXItbnVtYmVyJz4xPC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPldoeS1UaGlzLUJvb2s/PC9zcGFuPg=="}
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[<span class='chapter-number'>6</span>  <span class='chapter-title'>Markdown and LaTeX</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8wNS1tYXJrZG93bi1sYXRleC5odG1sPHNwYW4tY2xhc3M9J2NoYXB0ZXItbnVtYmVyJz42PC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPk1hcmtkb3duLWFuZC1MYVRlWDwvc3Bhbj4="}
[Data Exploration]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOnF1YXJ0by1zaWRlYmFyLXNlY3Rpb24tMg=="}
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[<span class='chapter-number'>12</span>  <span class='chapter-title'>Discrete Probability Distributions</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8xMS1kaXNjcmV0ZS1kaXN0cmlidXRpb25zLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjEyPC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPkRpc2NyZXRlLVByb2JhYmlsaXR5LURpc3RyaWJ1dGlvbnM8L3NwYW4+"}
[<span class='chapter-number'>13</span>  <span class='chapter-title'>Continuous Probability Distributions</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8xMi1jb250aW51b3VzLWRpc3RyaWJ1dGlvbnMuaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+MTM8L3NwYW4+LS08c3Bhbi1jbGFzcz0nY2hhcHRlci10aXRsZSc+Q29udGludW91cy1Qcm9iYWJpbGl0eS1EaXN0cmlidXRpb25zPC9zcGFuPg=="}
[<span class='chapter-number'>14</span>  <span class='chapter-title'>Sampling and Parameter Estimation</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8xMy1zYW1wbGluZy1lc3RpbWF0aW9uLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjE0PC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPlNhbXBsaW5nLWFuZC1QYXJhbWV0ZXItRXN0aW1hdGlvbjwvc3Bhbj4="}
[Statistical Inference]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOnF1YXJ0by1zaWRlYmFyLXNlY3Rpb24tNA=="}
[<span class='chapter-number'>15</span>  <span class='chapter-title'>Experimental Design Principles</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8xNC1leHBlcmltZW50YWwtZGVzaWduLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjE1PC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPkV4cGVyaW1lbnRhbC1EZXNpZ24tUHJpbmNpcGxlczwvc3Bhbj4="}
[<span class='chapter-number'>16</span>  <span class='chapter-title'>Hypothesis Testing</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8xNS1oeXBvdGhlc2lzLXRlc3RpbmcuaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+MTY8L3NwYW4+LS08c3Bhbi1jbGFzcz0nY2hhcHRlci10aXRsZSc+SHlwb3RoZXNpcy1UZXN0aW5nPC9zcGFuPg=="}
[<span class='chapter-number'>17</span>  <span class='chapter-title'>T-Tests</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8xNi10LXRlc3RzLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjE3PC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPlQtVGVzdHM8L3NwYW4+"}
[<span class='chapter-number'>18</span>  <span class='chapter-title'>Nonparametric Tests</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8xNy1ub25wYXJhbWV0cmljLXRlc3RzLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjE4PC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPk5vbnBhcmFtZXRyaWMtVGVzdHM8L3NwYW4+"}
[<span class='chapter-number'>19</span>  <span class='chapter-title'>Resampling Methods</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8xOC1ib290c3RyYXBwaW5nLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjE5PC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPlJlc2FtcGxpbmctTWV0aG9kczwvc3Bhbj4="}
[Linear Models]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOnF1YXJ0by1zaWRlYmFyLXNlY3Rpb24tNQ=="}
[<span class='chapter-number'>20</span>  <span class='chapter-title'>What are Models?</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8xOS13aGF0LWFyZS1tb2RlbHMuaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+MjA8L3NwYW4+LS08c3Bhbi1jbGFzcz0nY2hhcHRlci10aXRsZSc+V2hhdC1hcmUtTW9kZWxzPzwvc3Bhbj4="}
[<span class='chapter-number'>21</span>  <span class='chapter-title'>Correlation</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8yMC1jb3JyZWxhdGlvbi5odG1sPHNwYW4tY2xhc3M9J2NoYXB0ZXItbnVtYmVyJz4yMTwvc3Bhbj4tLTxzcGFuLWNsYXNzPSdjaGFwdGVyLXRpdGxlJz5Db3JyZWxhdGlvbjwvc3Bhbj4="}
[<span class='chapter-number'>22</span>  <span class='chapter-title'>Simple Linear Regression</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8yMS1zaW1wbGUtbGluZWFyLXJlZ3Jlc3Npb24uaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+MjI8L3NwYW4+LS08c3Bhbi1jbGFzcz0nY2hhcHRlci10aXRsZSc+U2ltcGxlLUxpbmVhci1SZWdyZXNzaW9uPC9zcGFuPg=="}
[<span class='chapter-number'>23</span>  <span class='chapter-title'>Residual Analysis</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8yMi1yZXNpZHVhbC1hbmFseXNpcy5odG1sPHNwYW4tY2xhc3M9J2NoYXB0ZXItbnVtYmVyJz4yMzwvc3Bhbj4tLTxzcGFuLWNsYXNzPSdjaGFwdGVyLXRpdGxlJz5SZXNpZHVhbC1BbmFseXNpczwvc3Bhbj4="}
[<span class='chapter-number'>24</span>  <span class='chapter-title'>Statistical Power</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8yMy1zdGF0aXN0aWNhbC1wb3dlci5odG1sPHNwYW4tY2xhc3M9J2NoYXB0ZXItbnVtYmVyJz4yNDwvc3Bhbj4tLTxzcGFuLWNsYXNzPSdjaGFwdGVyLXRpdGxlJz5TdGF0aXN0aWNhbC1Qb3dlcjwvc3Bhbj4="}
[<span class='chapter-number'>25</span>  <span class='chapter-title'>Multiple Regression</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8yNC1tdWx0aXBsZS1yZWdyZXNzaW9uLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjI1PC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPk11bHRpcGxlLVJlZ3Jlc3Npb248L3NwYW4+"}
[<span class='chapter-number'>26</span>  <span class='chapter-title'>Single Factor ANOVA</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8yNS1zaW5nbGUtZmFjdG9yLWFub3ZhLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjI2PC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPlNpbmdsZS1GYWN0b3ItQU5PVkE8L3NwYW4+"}
[<span class='chapter-number'>27</span>  <span class='chapter-title'>Multi-Factor ANOVA</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8yNi1tdWx0aWZhY3Rvci1hbm92YS5odG1sPHNwYW4tY2xhc3M9J2NoYXB0ZXItbnVtYmVyJz4yNzwvc3Bhbj4tLTxzcGFuLWNsYXNzPSdjaGFwdGVyLXRpdGxlJz5NdWx0aS1GYWN0b3ItQU5PVkE8L3NwYW4+"}
[<span class='chapter-number'>28</span>  <span class='chapter-title'>Generalized Linear Models</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8yNy1nbG0uaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+Mjg8L3NwYW4+LS08c3Bhbi1jbGFzcz0nY2hhcHRlci10aXRsZSc+R2VuZXJhbGl6ZWQtTGluZWFyLU1vZGVsczwvc3Bhbj4="}
[Statistical Learning]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOnF1YXJ0by1zaWRlYmFyLXNlY3Rpb24tNg=="}
[<span class='chapter-number'>29</span>  <span class='chapter-title'>Introduction to Statistical Learning</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8yOC1pbnRyby1zdGF0aXN0aWNhbC1sZWFybmluZy5odG1sPHNwYW4tY2xhc3M9J2NoYXB0ZXItbnVtYmVyJz4yOTwvc3Bhbj4tLTxzcGFuLWNsYXNzPSdjaGFwdGVyLXRpdGxlJz5JbnRyb2R1Y3Rpb24tdG8tU3RhdGlzdGljYWwtTGVhcm5pbmc8L3NwYW4+"}
[<span class='chapter-number'>30</span>  <span class='chapter-title'>Model Validation and the Bias-Variance Tradeoff</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8yOS1tb2RlbC12YWxpZGF0aW9uLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjMwPC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPk1vZGVsLVZhbGlkYXRpb24tYW5kLXRoZS1CaWFzLVZhcmlhbmNlLVRyYWRlb2ZmPC9zcGFuPg=="}
[<span class='chapter-number'>31</span>  <span class='chapter-title'>Regularization Methods</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8zMC1yZWd1bGFyaXphdGlvbi5odG1sPHNwYW4tY2xhc3M9J2NoYXB0ZXItbnVtYmVyJz4zMTwvc3Bhbj4tLTxzcGFuLWNsYXNzPSdjaGFwdGVyLXRpdGxlJz5SZWd1bGFyaXphdGlvbi1NZXRob2RzPC9zcGFuPg=="}
[<span class='chapter-number'>32</span>  <span class='chapter-title'>Smoothing and Non-Parametric Regression</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8zMS1zbW9vdGhpbmcuaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+MzI8L3NwYW4+LS08c3Bhbi1jbGFzcz0nY2hhcHRlci10aXRsZSc+U21vb3RoaW5nLWFuZC1Ob24tUGFyYW1ldHJpYy1SZWdyZXNzaW9uPC9zcGFuPg=="}
[<span class='chapter-number'>33</span>  <span class='chapter-title'>Classification and Performance Metrics</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8zMi1jbGFzc2lmaWNhdGlvbi1tZXRob2RzLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjMzPC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPkNsYXNzaWZpY2F0aW9uLWFuZC1QZXJmb3JtYW5jZS1NZXRyaWNzPC9zcGFuPg=="}
[<span class='chapter-number'>34</span>  <span class='chapter-title'>Decision Trees and Random Forests</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8zMy10cmVlcy1mb3Jlc3RzLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjM0PC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPkRlY2lzaW9uLVRyZWVzLWFuZC1SYW5kb20tRm9yZXN0czwvc3Bhbj4="}
[<span class='chapter-number'>35</span>  <span class='chapter-title'>Support Vector Machines</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8zNC1zdm0uaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+MzU8L3NwYW4+LS08c3Bhbi1jbGFzcz0nY2hhcHRlci10aXRsZSc+U3VwcG9ydC1WZWN0b3ItTWFjaGluZXM8L3NwYW4+"}
[<span class='chapter-number'>36</span>  <span class='chapter-title'>Clustering</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8zNS1jbHVzdGVyaW5nLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjM2PC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPkNsdXN0ZXJpbmc8L3NwYW4+"}
[<span class='chapter-number'>37</span>  <span class='chapter-title'>Dimensionality Reduction and Multivariate Methods</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8zNi1kaW1lbnNpb25hbGl0eS1yZWR1Y3Rpb24uaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+Mzc8L3NwYW4+LS08c3Bhbi1jbGFzcz0nY2hhcHRlci10aXRsZSc+RGltZW5zaW9uYWxpdHktUmVkdWN0aW9uLWFuZC1NdWx0aXZhcmlhdGUtTWV0aG9kczwvc3Bhbj4="}
[<span class='chapter-number'>38</span>  <span class='chapter-title'>Non-Linear Dimensionality Reduction: t-SNE and UMAP</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8zNy10c25lLXVtYXAuaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+Mzg8L3NwYW4+LS08c3Bhbi1jbGFzcz0nY2hhcHRlci10aXRsZSc+Tm9uLUxpbmVhci1EaW1lbnNpb25hbGl0eS1SZWR1Y3Rpb246LXQtU05FLWFuZC1VTUFQPC9zcGFuPg=="}
[<span class='chapter-number'>39</span>  <span class='chapter-title'>Bayesian Statistics</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8zOC1iYXllc2lhbi1zdGF0aXN0aWNzLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjM5PC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPkJheWVzaWFuLVN0YXRpc3RpY3M8L3NwYW4+"}
[<span class='chapter-number'>40</span>  <span class='chapter-title'>Introduction to Deep Learning</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy8zOS1kZWVwLWxlYXJuaW5nLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjQwPC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPkludHJvZHVjdGlvbi10by1EZWVwLUxlYXJuaW5nPC9zcGFuPg=="}
[<span class='chapter-number'>41</span>  <span class='chapter-title'>High Performance Computing</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy80MC1oaWdoLXBlcmZvcm1hbmNlLWNvbXB1dGluZy5odG1sPHNwYW4tY2xhc3M9J2NoYXB0ZXItbnVtYmVyJz40MTwvc3Bhbj4tLTxzcGFuLWNsYXNzPSdjaGFwdGVyLXRpdGxlJz5IaWdoLVBlcmZvcm1hbmNlLUNvbXB1dGluZzwvc3Bhbj4="}
[Scientific Communication]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOnF1YXJ0by1zaWRlYmFyLXNlY3Rpb24tNw=="}
[<span class='chapter-number'>42</span>  <span class='chapter-title'>Presenting Statistical Results</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy80MS1wcmVzZW50aW5nLXJlc3VsdHMuaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+NDI8L3NwYW4+LS08c3Bhbi1jbGFzcz0nY2hhcHRlci10aXRsZSc+UHJlc2VudGluZy1TdGF0aXN0aWNhbC1SZXN1bHRzPC9zcGFuPg=="}
[Historical Context]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOnF1YXJ0by1zaWRlYmFyLXNlY3Rpb24tOA=="}
[<span class='chapter-number'>43</span>  <span class='chapter-title'>The Eugenics History of Statistics</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy9BMS1ldWdlbmljcy1oaXN0b3J5Lmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjQzPC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPlRoZS1FdWdlbmljcy1IaXN0b3J5LW9mLVN0YXRpc3RpY3M8L3NwYW4+"}
[Appendices]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOnF1YXJ0by1zaWRlYmFyLXNlY3Rpb24tOQ=="}
[<span class='chapter-number'>44</span>  <span class='chapter-title'>Keyboard Shortcuts Reference</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy9BMi1rZXlib2FyZC1zaG9ydGN1dHMuaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+NDQ8L3NwYW4+LS08c3Bhbi1jbGFzcz0nY2hhcHRlci10aXRsZSc+S2V5Ym9hcmQtU2hvcnRjdXRzLVJlZmVyZW5jZTwvc3Bhbj4="}
[<span class='chapter-number'>45</span>  <span class='chapter-title'>Unix Command Reference</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy9BMy11bml4LXJlZmVyZW5jZS5odG1sPHNwYW4tY2xhc3M9J2NoYXB0ZXItbnVtYmVyJz40NTwvc3Bhbj4tLTxzcGFuLWNsYXNzPSdjaGFwdGVyLXRpdGxlJz5Vbml4LUNvbW1hbmQtUmVmZXJlbmNlPC9zcGFuPg=="}
[<span class='chapter-number'>46</span>  <span class='chapter-title'>R Command Reference</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy9BNC1yLXJlZmVyZW5jZS5odG1sPHNwYW4tY2xhc3M9J2NoYXB0ZXItbnVtYmVyJz40Njwvc3Bhbj4tLTxzcGFuLWNsYXNzPSdjaGFwdGVyLXRpdGxlJz5SLUNvbW1hbmQtUmVmZXJlbmNlPC9zcGFuPg=="}
[<span class='chapter-number'>47</span>  <span class='chapter-title'>Quarto Markdown Reference</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy9BNS1xdWFydG8tcmVmZXJlbmNlLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjQ3PC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPlF1YXJ0by1NYXJrZG93bi1SZWZlcmVuY2U8L3NwYW4+"}
[<span class='chapter-number'>48</span>  <span class='chapter-title'>LaTeX Command Reference</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy9BNi1sYXRleC1yZWZlcmVuY2UuaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+NDg8L3NwYW4+LS08c3Bhbi1jbGFzcz0nY2hhcHRlci10aXRsZSc+TGFUZVgtQ29tbWFuZC1SZWZlcmVuY2U8L3NwYW4+"}
[<span class='chapter-number'>49</span>  <span class='chapter-title'>Greek Letters in Mathematics and Statistics</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy9BNy1ncmVlay1sZXR0ZXJzLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjQ5PC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPkdyZWVrLUxldHRlcnMtaW4tTWF0aGVtYXRpY3MtYW5kLVN0YXRpc3RpY3M8L3NwYW4+"}
[<span class='chapter-number'>50</span>  <span class='chapter-title'>Common Probability Distributions</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy9BOC1wcm9iYWJpbGl0eS1kaXN0cmlidXRpb25zLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjUwPC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPkNvbW1vbi1Qcm9iYWJpbGl0eS1EaXN0cmlidXRpb25zPC9zcGFuPg=="}
[<span class='chapter-number'>51</span>  <span class='chapter-title'>Sampling Distributions in Hypothesis Testing</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy9BOS1zYW1wbGluZy1kaXN0cmlidXRpb25zLmh0bWw8c3Bhbi1jbGFzcz0nY2hhcHRlci1udW1iZXInPjUxPC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPlNhbXBsaW5nLURpc3RyaWJ1dGlvbnMtaW4tSHlwb3RoZXNpcy1UZXN0aW5nPC9zcGFuPg=="}
[<span class='chapter-number'>52</span>  <span class='chapter-title'>Matrix Algebra Fundamentals</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jaGFwdGVycy9BMTAtbWF0cml4LWFsZ2VicmEuaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+NTI8L3NwYW4+LS08c3Bhbi1jbGFzcz0nY2hhcHRlci10aXRsZSc+TWF0cml4LUFsZ2VicmEtRnVuZGFtZW50YWxzPC9zcGFuPg=="}
[References]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWludC1zaWRlYmFyOi9yZWZlcmVuY2VzLmh0bWxSZWZlcmVuY2Vz"}
[Appendices]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWJyZWFkY3J1bWJzLUFwcGVuZGljZXM="}
[<span class='chapter-number'>47</span>  <span class='chapter-title'>Quarto Markdown Reference</span>]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLWJyZWFkY3J1bWJzLTxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+NDc8L3NwYW4+LS08c3Bhbi1jbGFzcz0nY2hhcHRlci10aXRsZSc+UXVhcnRvLU1hcmtkb3duLVJlZmVyZW5jZTwvc3Bhbj4="}

:::{.hidden .quarto-markdown-envelope-contents render-id="Zm9vdGVyLWxlZnQ="}
Statistics for Biosciences and Bioengineering
:::


:::{.hidden .quarto-markdown-envelope-contents render-id="Zm9vdGVyLXJpZ2h0"}
Built with [Quarto](https://quarto.org/)
:::

:::



:::{#quarto-meta-markdown .hidden}
[[[47]{.chapter-number}  [Quarto Markdown Reference]{.chapter-title}]{#sec-quarto-reference .quarto-section-identifier} – Statistics for the Biosciences and Bioengineering]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLW1ldGF0aXRsZQ=="}
[[[47]{.chapter-number}  [Quarto Markdown Reference]{.chapter-title}]{#sec-quarto-reference .quarto-section-identifier} – Statistics for the Biosciences and Bioengineering]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLXR3aXR0ZXJjYXJkdGl0bGU="}
[[[47]{.chapter-number}  [Quarto Markdown Reference]{.chapter-title}]{#sec-quarto-reference .quarto-section-identifier} – Statistics for the Biosciences and Bioengineering]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLW9nY2FyZHRpdGxl"}
[Statistics for the Biosciences and Bioengineering]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLW1ldGFzaXRlbmFtZQ=="}
[]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLXR3aXR0ZXJjYXJkZGVzYw=="}
[]{.hidden .quarto-markdown-envelope-contents render-id="cXVhcnRvLW9nY2FyZGRkZXNj"}
:::




<!-- -->

::: {.quarto-embedded-source-code}
```````````````````{.markdown shortcodes="false"}
# Quarto Markdown Reference {#sec-quarto-reference}

This appendix provides a comprehensive quick reference for Quarto Markdown syntax and features used throughout this book.

## Introduction to Quarto {#sec-quarto-intro}

Quarto is an open-source scientific and technical publishing system built on Pandoc. It allows you to:

- Combine narrative text with executable code (R, Python, Julia, Observable)
- Create reproducible documents in multiple formats (HTML, PDF, Word, EPUB)
- Use consistent syntax across different programming languages
- Generate professional scientific documents with cross-references, citations, and equations

Quarto documents use the `.qmd` file extension and combine Markdown for text, code chunks for analysis, and YAML for configuration.

## Basic Markdown Syntax {#sec-markdown-basics}

### Headers {#sec-markdown-headers}

| Syntax | Result | Usage |
|:-------|:-------|:------|
| `# Header 1` | Largest heading | Chapter/section title |
| `## Header 2` | Second level | Major section |
| `### Header 3` | Third level | Subsection |
| `#### Header 4` | Fourth level | Sub-subsection |
| `##### Header 5` | Fifth level | Rarely used |
| `###### Header 6` | Smallest heading | Rarely used |

Headers can include section labels for cross-referencing:
```markdown
## Methods {#sec-methods}

Text Formatting

Syntax Result Description
*italic* or _italic_ italic Emphasized text
**bold** or __bold__ bold Strong emphasis
***bold italic*** bold italic Both bold and italic
~~strikethrough~~ strikethrough Deleted text
superscript^2^ superscript2 Superscript
subscript~2~ subscript2 Subscript
`code` code Inline code

Lists

Unordered Lists:

- Item 1
- Item 2
  - Nested item 2a
  - Nested item 2b
- Item 3

Ordered Lists:

1. First item
2. Second item
   a. Nested item
   b. Another nested item
3. Third item

Task Lists:

- [ ] Incomplete task
- [x] Completed task

Blockquotes

> This is a blockquote.
> It can span multiple lines.
>
> And multiple paragraphs.

Result: > This is a blockquote. > It can span multiple lines.

Code

Inline Code:

Use the `mean()` function to calculate averages.

Code Blocks:

```
Plain code block without syntax highlighting
```

```r
# R code with syntax highlighting
x <- c(1, 2, 3, 4, 5)
mean(x)
```

```python
# Python code with syntax highlighting
import numpy as np
x = np.array([1, 2, 3, 4, 5])
np.mean(x)
```

47.10 Quarto-Specific Features

YAML Header

Every Quarto document begins with a YAML header enclosed in ---:

---
title: "My Analysis"
author: "Your Name"
date: "2024-01-15"
format:
  html:
    toc: true
    code-fold: true
    theme: cosmo
  pdf:
    documentclass: article
    geometry: margin=1in
execute:
  echo: true
  warning: false
  message: false
bibliography: references.bib
---

Common YAML Options:

Option Description Example
title Document title "My Report"
author Author name(s) "Jane Doe"
date Document date today or "2024-01-15"
format Output format(s) html, pdf, docx
toc Table of contents true or false
number-sections Number sections true or false
bibliography Bibliography file references.bib
execute Global execution options See below

Code Chunk Options

Code chunks in Quarto use #| (hashpipe) notation for options:

quarto-executable-code-5450563D

```r
#| label: fig-scatter
#| fig-cap: "Relationship between variables"
#| echo: false
#| warning: false
#| fig-width: 6
#| fig-height: 4

plot(mtcars$mpg, mtcars$hp)
```

Common Chunk Options:

Option Description Values
label Unique chunk identifier fig-name, tbl-name
echo Show code true, false
eval Execute code true, false
include Include output true, false
warning Show warnings true, false
message Show messages true, false
error Show errors true, false
fig-cap Figure caption "Caption text"
fig-width Figure width (inches) 6, 8, etc.
fig-height Figure height (inches) 4, 6, etc.
tbl-cap Table caption "Caption text"
output Control output true, false, asis

Cross-References

Quarto provides automatic numbering and cross-referencing:

Figures:

quarto-executable-code-5450563D

```r
#| label: fig-histogram
#| fig-cap: "Distribution of sample data"

hist(rnorm(100))
```

See @fig-histogram for the distribution.

Tables:

quarto-executable-code-5450563D

```r
#| label: tbl-summary
#| tbl-cap: "Summary statistics"

knitr::kable(summary(mtcars))
```

Results are shown in @tbl-summary.

Sections:

## Methods {#sec-methods}

As described in @sec-methods, we used...

Equations:

$$
E = mc^2
$$ {#eq-einstein}

According to @eq-einstein, energy equals...

Cross-Reference Prefixes:

Type Prefix Example
Figure fig- @fig-scatter
Table tbl- @tbl-results
Section sec- @sec-intro
Equation eq- @eq-model
Theorem thm- @thm-central-limit
Lemma lem- @lem-property
Proof prp- @prp-main

Citations

Reference bibliography entries using @key:

According to @fisher1925 and @student1908, the t-test...

Multiple citations [@fisher1925; @student1908].

Citation with page number [@fisher1925, p. 42].

Citation with prefix [see @fisher1925, p. 42].

Bibliography File (BibTeX):

@article{fisher1925,
  author = {Fisher, R. A.},
  title = {Statistical Methods for Research Workers},
  journal = {Oliver and Boyd},
  year = {1925}
}

Callout Blocks

Callout blocks highlight important information:

Note:

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

Tip:

:::{.callout-tip}
## Pro Tip
This is a helpful tip for users.
:::

Warning:

:::{.callout-warning}
Be careful with this approach!
:::

Important:

:::{.callout-important}
This is crucial information.
:::

Caution:

:::{.callout-caution}
Proceed with caution.
:::

Callout Types:

Type Icon Color Usage
note Info Blue General information
tip Lightbulb Green Helpful suggestions
warning Warning Orange Potential issues
important Exclamation Red Critical information
caution Fire Red Dangerous operations

Collapsible Callouts:

:::{.callout-note collapse="true"}
## Expandable Note
This content is hidden by default.
:::

Tabsets

Organize content into tabs:

::: {.panel-tabset}

## R Code
quarto-executable-code-5450563D

```r
mean(c(1, 2, 3, 4, 5))

47.11 Base R Alternative

quarto-executable-code-5450563D

sum(c(1, 2, 3, 4, 5)) / length(c(1, 2, 3, 4, 5))

:::


### Equations {#sec-equations}

**Inline Math:**
```markdown
The mean is calculated as $\bar{x} = \frac{1}{n}\sum_{i=1}^{n}x_i$.

Display Math:

$$
\sigma^2 = \frac{1}{n-1}\sum_{i=1}^{n}(x_i - \bar{x})^2
$$

Numbered Equations:

$$
f(x) = \frac{1}{\sigma\sqrt{2\pi}} e^{-\frac{(x-\mu)^2}{2\sigma^2}}
$$ {#eq-normal}

The normal distribution (@eq-normal) is...

Aligned Equations:

$$
\begin{aligned}
\bar{x} &= \frac{1}{n}\sum_{i=1}^{n}x_i \\
&= \frac{x_1 + x_2 + \cdots + x_n}{n}
\end{aligned}
$$ {#eq-mean}

47.12 Figures and Tables

Figure Syntax

Basic Figure:

quarto-executable-code-5450563D

```r
#| label: fig-plot
#| fig-cap: "Scatter plot of mpg vs hp"

plot(mtcars$mpg, mtcars$hp,
     xlab = "Miles per Gallon",
     ylab = "Horsepower")
```

Multiple Figures (Subfigures):

quarto-executable-code-5450563D

```r
#| label: fig-multiple
#| fig-cap: "Comparison of distributions"
#| fig-subcap:
#|   - "Normal distribution"
#|   - "Exponential distribution"
#| layout-ncol: 2

hist(rnorm(1000))
hist(rexp(1000))
```

See @fig-multiple-1 and @fig-multiple-2.

Markdown Images with Labels:

![Experimental setup](images/setup.png){#fig-setup}

The apparatus shown in @fig-setup was used...

Figure Size and Alignment

Option Description Example
fig-width Width in inches fig-width: 6
fig-height Height in inches fig-height: 4
fig-align Alignment left, center, right
out-width Output width (%) out-width: "80%"
fig-dpi Resolution fig-dpi: 300

Example:

quarto-executable-code-5450563D

```r
#| fig-width: 8
#| fig-height: 5
#| fig-align: center
#| out-width: "90%"

plot(pressure)
```

Table Syntax

Markdown Tables (Pipe Tables):

| Column 1 | Column 2 | Column 3 |
|:---------|:--------:|---------:|
| Left     | Center   | Right    |
| aligned  | aligned  | aligned  |
| text     | text     | text     |

Table Alignment: - :--- = Left aligned - :--: = Center aligned - ---: = Right aligned

Grid Tables:

+----------+----------+----------+
| Column 1 | Column 2 | Column 3 |
+==========+==========+==========+
| Row 1    | Data     | Values   |
+----------+----------+----------+
| Row 2    | More     | Content  |
+----------+----------+----------+

Code-Generated Tables:

quarto-executable-code-5450563D

```r
#| label: tbl-mtcars
#| tbl-cap: "Summary of mtcars dataset"

knitr::kable(head(mtcars[, 1:4]))
```

Caption and Label:

: Summary statistics for experimental groups {#tbl-summary}

| Group | Mean | SD   | N  |
|:------|-----:|-----:|---:|
| A     | 5.2  | 1.1  | 20 |
| B     | 6.8  | 1.4  | 20 |

47.13 Document Output Options

HTML Output

format:
  html:
    toc: true
    toc-depth: 3
    toc-location: left
    number-sections: true
    code-fold: true
    code-tools: true
    code-copy: true
    theme: cosmo
    highlight-style: github
    embed-resources: false
    fig-width: 7
    fig-height: 5

Common HTML Options:

Option Description Values
toc Table of contents true, false
toc-depth TOC depth 1, 2, 3, etc.
toc-location TOC position left, right, body
code-fold Foldable code true, false, show
code-tools Code tools menu true, false
theme Visual theme default, cosmo, flatly, etc.
embed-resources Self-contained true, false

PDF Output

format:
  pdf:
    documentclass: article
    geometry:
      - margin=1in
      - letterpaper
    number-sections: true
    colorlinks: true
    toc: true
    toc-depth: 2
    keep-tex: false

Common PDF Options:

Option Description Values
documentclass LaTeX class article, report, book
geometry Page layout margin=1in, etc.
fontsize Text size 10pt, 11pt, 12pt
colorlinks Colored links true, false
keep-tex Keep .tex file true, false

Word Output

format:
  docx:
    toc: true
    number-sections: true
    highlight-style: github
    reference-doc: custom-template.docx

Multiple Formats

format:
  html:
    toc: true
    theme: cosmo
  pdf:
    documentclass: article
  docx:
    toc: true

Render specific format:

quarto render document.qmd --to html
quarto render document.qmd --to pdf

47.14 Common Quarto Commands

Basic Commands

Command Description
quarto preview file.qmd Live preview in browser
quarto render file.qmd Render to default format
quarto render file.qmd --to html Render to HTML
quarto render file.qmd --to pdf Render to PDF
quarto render file.qmd --to docx Render to Word
quarto render Render entire project
quarto publish Publish document online

Project Commands

Command Description
quarto create project Create new project
quarto preview Preview project
quarto render Render all project files
quarto check Check installation
quarto tools install Install required tools

Preview Options

# Preview on specific port
quarto preview document.qmd --port 8080

# Preview without opening browser
quarto preview document.qmd --no-browser

# Preview specific format
quarto preview document.qmd --to pdf

Render Options

# Render with parameters
quarto render document.qmd -P alpha:0.05 -P n:100

# Render to specific output file
quarto render document.qmd --output report.html

# Render all formats
quarto render document.qmd --to all

# Execute code even if frozen
quarto render document.qmd --execute

47.15 Keyboard Shortcuts

When using Quarto in RStudio or VS Code:

Shortcut Action Platform
Cmd/Ctrl + Shift + K Render document All
Cmd/Ctrl + Shift + Enter Run current chunk All
Cmd/Ctrl + Alt + I Insert code chunk RStudio
Cmd/Ctrl + Alt + P Run all chunks above RStudio

47.16 Quick Reference Summary

Document Structure:

---
title: "Title"
format: html
---

# Section

Text with **bold** and *italic*.

quarto-executable-code-5450563D

```r
#| label: fig-name
#| fig-cap: "Caption"
code here

See ?fig-name and ?sec-other.


**Essential Syntax:**
- Headers: `#`, `##`, `###`
- Bold: `**text**`
- Italic: `*text*`
- Code: `` `code` ``
- Link: `[text](url)`
- Image: `![caption](file.png)`
- Equation: `$math$` or `$$display$$`
- Citation: `@reference`
- Cross-ref: `@fig-name`, `@tbl-name`, `@sec-name`

**Key Features:**
- Use YAML for configuration
- Use `#|` for chunk options
- Label figures/tables/sections with `{#prefix-name}`
- Reference with `@prefix-name`
- Use callouts for important info
- Organize with tabsets and divs

:::