Quarto Document Skill

Usage: Load this file into Claude Code (via CLAUDE.md pointer) or paste into an LLM session for comprehensive Quarto assistance. Covers execution control, journal formatting, cross-references, citations, PDF/HTML configuration, and CLI commands.

Comprehensive reference for creating, rendering, and formatting Quarto documents. Emphasizes practical workflows: Jupyter-first rendering, journal formatting, and execution control.

1) Document Types and When to Use Each

Source Format	Best For	Execution Default on `quarto render`
`.qmd`	Text-heavy docs, articles, websites, books	Executes code
`.ipynb`	Data analysis, exploration, Jupyter-first workflows	Does NOT execute (uses saved outputs)

Key insight: .ipynb files rendered with quarto render notebook.ipynb preserve pre-computed outputs by default. No special configuration needed for the “run in Jupyter, render on command line” workflow.

2) Execution Control (Critical for Jupyter Workflows)

The Problem

You run code interactively in Jupyter, then want to render to HTML/PDF without re-executing. The solution depends on your source format.

For `.ipynb` Files (Simplest Path)

# This preserves all outputs already in the notebook -- no re-execution
quarto render notebook.ipynb
quarto render notebook.ipynb --to html
quarto render notebook.ipynb --to pdf

To force re-execution (when you DO want it):

quarto render notebook.ipynb --execute

Or in the notebook’s Raw cell YAML:

---
execute:
  enabled: true
---

For `.qmd` Files (Must Opt Out of Execution)

.qmd files execute by default. Three ways to prevent it:

Option A: `execute: enabled: false` (Document-Level)

---
title: "My Analysis"
execute:
  enabled: false
---

All code is echoed but not run. Use when code is illustrative or outputs are not needed.

Option B: `freeze` (Project-Level, Recommended for Multi-Doc Projects)

Set in _quarto.yml:

# _quarto.yml
execute:
  freeze: auto    # re-render only when source file changes

Or:

execute:
  freeze: true    # NEVER re-render during project render

How it works: 1. First render executes code and stores results in _freeze/ directory 2. Subsequent quarto render (project-level) uses frozen results 3. To update: render the specific file directly (quarto render file.qmd)

Important constraints: - freeze only applies during project-level renders (quarto render from project root) - Rendering a single file (quarto render myfile.qmd) always executes regardless of freeze - Commit _freeze/ to version control so collaborators can render without the compute environment

Setting	Re-executes when source changes?	Re-executes on single-file render?
`freeze: true`	No	Yes
`freeze: auto`	Yes (project render)	Yes

Option C: `cache` (Cell-Level Caching)

---
execute:
  cache: true
---

Requires: pip install jupyter-cache

Jupyter: caches at whole-notebook level – any code cell change re-executes ALL cells
Knitr (R): caches at individual cell level
Markdown-only changes do NOT invalidate cache

CLI overrides:

quarto render doc.qmd --cache           # force caching on
quarto render doc.qmd --no-cache        # force caching off
quarto render doc.qmd --cache-refresh   # invalidate and re-execute all

Recommended Workflow: Jupyter-First Analysis

1. Work in Jupyter (.ipynb) -- run cells, iterate, explore
2. Save notebook (outputs embedded in .ipynb)
3. Render:  quarto render notebook.ipynb --to html
4. Outputs preserved, no re-execution, fast render

If using .qmd in a project:

1. Set freeze: auto in _quarto.yml
2. Render once: quarto render analysis.qmd  (executes code)
3. Results stored in _freeze/
4. Project renders skip re-execution unless source changes
5. Commit _freeze/ to git

Cell-Level Execution Options

Control individual code cells with #| comments:

#| eval: false       # Don't run this cell
#| echo: false       # Hide source code
#| output: false     # Hide results
#| warning: false    # Suppress warnings
#| error: true       # Show errors without halting render
#| include: false    # Suppress ALL output (code + results)

Document-level defaults:

---
execute:
  eval: true
  echo: false
  warning: false
  error: false
---

Intermediate File Preservation (Debugging)

---
execute:
  keep-md: true       # Keep intermediate .md
  keep-ipynb: true    # Keep intermediate .ipynb
---

3) Minimal Document Templates

Basic HTML Document

---
title: "My Document"
format: html
---

Analysis Notebook (Jupyter-first, no re-execution)

Save as a Raw cell in your .ipynb:

---
title: "Analysis 310: Baseline Model"
author: "Your Name"
date: today
format:
  html:
    toc: true
    code-fold: true
    embed-resources: true
execute:
  echo: true
---

Render: quarto render notebook.ipynb

Multi-Format Document

---
title: "My Document"
toc: true
format:
  html:
    code-fold: true
    theme: cosmo
  pdf:
    documentclass: scrartcl
    papersize: letter
  docx: default
---

Render all: quarto render doc.qmd Render one: quarto render doc.qmd --to pdf

4) Journal and Academic Paper Formatting

Available Journal Templates

Template	Command	Publisher
ACM	`quarto use template quarto-journals/acm`	Association for Computing Machinery
PLOS	`quarto use template quarto-journals/plos`	Public Library of Science
ASA/JASA	`quarto use template quarto-journals/asa`	American Statistical Association
Elsevier	`quarto use template quarto-journals/elsevier`	Elsevier journals
ACS	`quarto use template quarto-journals/acs`	American Chemical Society
JSS	`quarto use template quarto-journals/jss`	Journal of Statistical Software
Biophysical	`quarto use template quarto-journals/biophysical`	Biophysical Journal

Using a Journal Template

# Create new project from template (creates directory with starter files)
quarto use template quarto-journals/elsevier

# Add template to existing project (extension only, no starter files)
quarto add quarto-journals/elsevier

In your document:

---
title: "My Paper"
format:
  elsevier-pdf:
    toc: true
    keep-tex: true
  elsevier-html: default
---

Render:

quarto render paper.qmd --to elsevier-pdf

When No Official Template Exists

Word/Docx Route (most journals accept Word)

---
title: "My Paper"
format:
  docx:
    reference-doc: templates/journal-reference.docx
bibliography: refs/library.bib
csl: csl/target-journal.csl
link-citations: true
---

Create a reference Word document with journal-required styles
Download the journal’s CSL from the Zotero Style Repository
Render: quarto render paper.qmd --to docx

Custom Typst/PDF Route (Recommended for New Templates)

Typst is a modern typesetting system bundled with Quarto (no separate install). Faster compilation, better error messages, and simpler template syntax than LaTeX. Preferred when building a custom template from scratch.

---
format:
  typst:
    papersize: us-letter
    margin:
      x: 1in
      y: 1in
    mainfont: "Linux Libertine"
    fontsize: 11pt
    columns: 1
    keep-typ: true               # Retain .typ for debugging
bibliography: refs/library.bib
csl: csl/target-journal.csl
citeproc: true                   # Use Pandoc/CSL for citations (not Typst's built-in)
---

Create a custom Typst format extension:

quarto create extension format    # select "typst", provide a name

This generates:

_extensions/myjournal/
├── _extension.yml          # Format metadata and defaults
├── typst-template.typ      # Core template function (layout, styles)
├── typst-show.typ          # Maps Pandoc metadata to template arguments
├── template.qmd            # Starter document
└── README.md

Render: quarto render paper.qmd --to myjournal-typst

When to choose Typst over LaTeX: - Building a new custom template (simpler syntax, faster iteration) - No existing LaTeX class to reuse - Want faster compile times - Don’t need niche LaTeX packages

When to stick with LaTeX: - Journal provides a .cls or .sty file - Heavy use of specialized LaTeX packages (e.g., tikz, mhchem) - Existing LaTeX template you want to reuse

Custom LaTeX/PDF Route

---
format:
  pdf:
    template: templates/journal.latex
    documentclass: article
    papersize: letter
    include-in-header:
      - text: |
          \usepackage{amsmath}
          \usepackage{booktabs}
    keep-tex: true
bibliography: refs/library.bib
csl: csl/target-journal.csl
---

Author and Affiliation Metadata

---
title: "A Novel Approach to the Problem"
subtitle: "With Applications"
date: 2026-02-06

abstract: |
  Background: Description of the problem.
  Methods: What we did.
  Results: What we found.
  Conclusions: What it means.

keywords:
  - keyword1
  - keyword2
  - keyword3

author:
  - name: Your Name
    email: author@example.org
    orcid: 0000-0000-0000-0000
    corresponding: true
    roles:
      - conceptualization
      - methodology
      - writing
    affiliation:
      - ref: inst1
      - ref: inst2

  - name: Jane Doe
    equal-contributor: true
    affiliation:
      - ref: inst1

affiliations:
  - id: inst1
    name: Acme Health System
    department: Department of Research
    city: Anytown
    state: NY
    country: US

  - id: inst2
    name: State University
    city: Anytown
    state: NY
    country: US

copyright:
  holder: Your Name
  year: 2026
license: "CC BY"

funding:
  statement: "This work was supported by..."

citation:
  container-title: Journal Name
  volume: 1
  issue: 1
  doi: 10.5555/example
---

Manuscript Project Type

For complex papers with multiple notebooks/documents:

quarto create project manuscript

# _quarto.yml
project:
  type: manuscript

manuscript:
  meca-bundle: true    # MECA submission package (if journal supports it)

format:
  docx:
    reference-doc: templates/journal-reference.docx
  pdf:
    documentclass: scrartcl
    keep-tex: true

bibliography: refs/library.bib
csl: csl/journal.csl
link-citations: true

5) Citations and Bibliography

Setup

---
bibliography: references.bib       # or multiple: [refs1.bib, refs2.bib]
csl: style.csl                     # optional, defaults to Chicago author-date
link-citations: true
---

Citation Syntax

Syntax	Result
`[@knuth1984]`	Parenthetical: (Knuth, 1984)
`@knuth1984`	Narrative: Knuth (1984)
`[-@knuth1984]`	Year only: (1984)
`[see @knuth1984, pp. 33-35]`	With prefix and locator
`[@knuth1984; @wickham2015]`	Multiple citations

Include uncited items in bibliography

nocite: |
  @item1, @item2

Include everything: nocite: | @*

Control bibliography placement

## References

::: {#refs}
:::

## Appendix
Content after references...

PDF Citation Methods

format:
  pdf:
    cite-method: citeproc    # default, portable
    # cite-method: natbib    # LaTeX natbib
    # cite-method: biblatex  # LaTeX biblatex

6) Cross-References

Label Prefixes

Element	Label Prefix	Reference	Output
Figure	`#fig-`	`@fig-name`	Figure 1
Table	`#tbl-`	`@tbl-name`	Table 1
Equation	`#eq-`	`@eq-name`	Equation 1
Section	`#sec-`	`@sec-name`	Section 1
Code Listing	`#lst-`	`@lst-name`	Listing 1
Theorem	`#thm-`	`@thm-name`	Theorem 1

Labels must be lowercase. Use hyphens, not underscores (underscores break LaTeX/PDF).

Figures

Static image:

![An Elephant](elephant.png){#fig-elephant}

As shown in @fig-elephant, elephants are large.

Computed figure:

#| label: fig-scatter
#| fig-cap: "Scatter plot of X vs Y"
#| fig-alt: "Dots showing positive correlation"

import matplotlib.pyplot as plt
plt.scatter(x, y)
plt.show()

Subfigures:

::: {#fig-panels layout-ncol=2}
![Panel A](panelA.png){#fig-panelA}
![Panel B](panelB.png){#fig-panelB}

Main caption for both panels
:::

Computed subfigures:

#| label: fig-plots
#| fig-cap: "Analysis Results"
#| fig-subcap:
#|   - "Distribution"
#|   - "Trend"
#| layout-ncol: 2

Tables

| Col A | Col B | Col C |
|:------|:-----:|------:|
| left  | center| right |

: Summary Statistics {#tbl-summary}

See @tbl-summary for details.

Computed table:

#| label: tbl-results
#| tbl-cap: "Model Results"

from IPython.display import Markdown
Markdown(df.to_markdown(index=False))

Equations

$$
y = \beta_0 + \beta_1 x + \epsilon
$$ {#eq-model}

The linear model (@eq-model) is fundamental.

Sections (requires `number-sections: true`)

## Introduction {#sec-intro}

As discussed in @sec-intro...

7) Figure and Table Options

Figure Sizing and Layout

#| fig-width: 8              # Width in inches
#| fig-height: 6             # Height in inches
#| fig-asp: 0.618            # Aspect ratio (golden ratio)
#| fig-dpi: 300              # Resolution
#| fig-align: center         # left, center, right
#| fig-format: png           # png, pdf, svg, retina
#| fig-pos: "H"              # LaTeX placement: h, t, b, H, p
#| fig-cap-location: bottom  # top, bottom, margin

Document-level defaults:

---
fig-width: 8
fig-height: 6
fig-cap-location: bottom
---

Layout for Multiple Items

::: {layout-ncol=2}
![](image1.png)
![](image2.png)
:::

Custom layout with relative widths (negative = spacing):

::: {layout="[[40,-20,40], [100]]"}
![](img1.png)
![](img2.png)
![](img3.png)
:::

Table Options

#| tbl-colwidths: [60, 40]       # Column width percentages
#| tbl-cap-location: top         # top, bottom, margin
#| classes: plain                # Disable default styling

Grid tables (for complex content like lists, code blocks):

+---------------+---------------+
| Column 1      | Column 2      |
+===============+===============+
| - Item 1      | Some text     |
| - Item 2      | More text     |
+---------------+---------------+

: Complex Table {#tbl-complex}

DataFrame Print Style

df-print: kable    # default, kable, tibble, paged

8) Code Display Options

Per-Cell

#| code-fold: true           # Collapsible code (HTML only)
#| code-summary: "Show code" # Label for collapsed code
#| code-overflow: wrap       # wrap or scroll
#| code-line-numbers: true   # Show line numbers

Document-Level

---
format:
  html:
    code-fold: true
    code-tools: true         # Global show/hide + source download
    code-line-numbers: true
    code-overflow: scroll
    highlight-style: github  # tango, pygments, kate, monokai, etc.
---

9) PDF Output Configuration

Basic PDF

---
format:
  pdf:
    documentclass: scrartcl       # scrartcl, article, report, book
    papersize: letter             # letter, a4
    fontsize: 11pt
    number-sections: true
    colorlinks: true
    toc: true
    toc-depth: 3
    lof: true                    # List of Figures
    lot: true                    # List of Tables
    keep-tex: true               # Retain .tex for debugging
---

Fonts

format:
  pdf:
    mainfont: "Times New Roman"
    sansfont: "Open Sans"
    monofont: "Roboto Mono"
    mathfont: "TeX Gyre Termes Math"
    fontsize: 12pt
    linestretch: 1.5

Page Geometry

format:
  pdf:
    geometry:
      - top=30mm
      - bottom=30mm
      - left=25mm
      - right=25mm
      - heightrounded

PDF Engine

format:
  pdf:
    pdf-engine: lualatex    # lualatex (default), pdflatex, xelatex, tectonic

LaTeX Includes

format:
  pdf:
    include-in-header:
      - text: |
          \usepackage{amsmath}
          \usepackage{booktabs}
          \usepackage{longtable}
      - file: custom-preamble.tex
    include-before-body:
      - file: before-body.tex
    include-after-body:
      - file: appendix.tex

Raw LaTeX in Document Body

```{=latex}
\begin{tabular}{|l|l|}\hline
Age & Frequency \\ \hline
18--25 & 15 \\
26--35 & 33 \\ \hline
\end{tabular}
```

Typst PDF Output (Alternative to LaTeX)

Typst is a modern typesetting system bundled with Quarto – no separate TeX installation needed. It produces PDF output with faster compilation, clearer error messages, and a simpler template language than LaTeX.

Basic Typst

---
format:
  typst:
    papersize: us-letter
    margin:
      x: 1in
      y: 1in
    mainfont: "Linux Libertine"
    fontsize: 11pt
    number-sections: true
    toc: true
    columns: 1
    keep-typ: true         # Retain intermediate .typ file for debugging
---

Render: quarto render doc.qmd --to typst

Typst Fonts

format:
  typst:
    mainfont: "Times New Roman"
    fontsize: 12pt
    font-paths:
      - fonts/              # Local directory with .ttf/.otf files

Typst searches system fonts by default. Use font-paths for bundled fonts.

Typst Page Layout

format:
  typst:
    papersize: a4
    margin:
      top: 2.5cm
      bottom: 2.5cm
      left: 2cm
      right: 2cm
    columns: 2             # Two-column layout

Citations in Typst

Two citation processing options:

# Option A: Pandoc/CSL (recommended -- use your journal's CSL file)
format:
  typst: default
bibliography: refs/library.bib
csl: csl/target-journal.csl
citeproc: true

# Option B: Typst's built-in citation system
format:
  typst:
    bibliographystyle: apa
bibliography: refs.bib

Use Option A (Pandoc/CSL) when you need a specific journal citation style.

Raw Typst in Document Body

```{=typst}
#table(
  columns: 2,
  [*Age*], [*Frequency*],
  [18--25], [15],
  [26--35], [33],
)
```

Custom Typst Format (Extension)

quarto create extension format    # select "typst"

Generates _extensions/name/ with typst-template.typ (layout) and typst-show.typ (metadata mapping). Package as a Quarto extension for reuse across papers.

LaTeX vs Typst Decision Guide

Factor	LaTeX (`pdf`)	Typst (`typst`)
Install	Requires TeX distribution	Bundled with Quarto
Compile speed	Slower (multiple passes)	Fast (single pass, Rust)
Error messages	Cryptic	Clear, with line numbers
Template syntax	Complex (`.cls`/`.sty`)	Simple (`.typ` functions)
Package ecosystem	Massive (CTAN)	Growing, smaller
Math typesetting	Excellent	Good, improving
Journal `.cls` files	Use LaTeX	Use Typst
New custom templates	Consider Typst	Preferred

10) HTML Output Configuration

Feature-Rich HTML

---
format:
  html:
    toc: true
    toc-depth: 3
    toc-location: left          # left, body, right
    toc-expand: 2
    number-sections: true
    code-fold: true
    code-tools: true
    anchor-sections: true
    smooth-scroll: true
    theme: cosmo                # Bootswatch theme
    css: styles.css
    embed-resources: true       # Self-contained single file
    link-external-icon: true
    link-external-newwindow: true
---

Tabsets

::: {.panel-tabset}
## Python
```python
print("Hello")

R

cat("Hello")

:::


### Callout Blocks

```markdown
:::{.callout-note}
Important information here.
:::

:::{.callout-warning}
## Custom Title
Watch out for this.
:::

Types: note, tip, warning, caution, important

11) Projects (`_quarto.yml`)

Creating a Project

quarto create project default myproject
quarto create project website mysite
quarto create project book mybook
quarto create project manuscript mypaper

Project Configuration

# _quarto.yml
project:
  type: website
  output-dir: _site
  render:
    - "*.qmd"
    - "!drafts/"          # exclude drafts directory

# Shared settings (all documents inherit)
toc: true
number-sections: true
bibliography: references.bib

# Execution control
execute:
  freeze: auto

# Format defaults
format:
  html:
    theme: cosmo
    css: styles.css
  pdf:
    documentclass: scrartcl

Metadata Hierarchy (highest priority wins)

Document YAML front matter
Directory _metadata.yml
Project _quarto.yml

Working Directory

project:
  execute-dir: project    # Execute from project root (default: file's directory)

Access project root in code: os.environ["QUARTO_PROJECT_DIR"]

12) All Output Formats

Documents

html, pdf, typst, docx, odt, epub

Presentations

revealjs (HTML slides), pptx (PowerPoint), beamer (LaTeX PDF slides)

Markdown Variants

gfm (GitHub), commonmark, hugo, docusaurus, markua

Scholarly

jats (Journal Article Tag Suite), latex (LaTeX source instead of PDF)

13) Markdown Essentials

Text Formatting

Effect	Syntax
Italics	`italics`
Bold	`bold`
*Bold italics*	`*bold italics*`
Superscript	`text^2^`
Subscript	`text~2~`
~~Strikethrough~~	`~~text~~`
`Code`	`code`

Links and Images

[Link text](https://url)
![Caption](image.png)
![](image.png){fig-alt="Alt text" width=80%}
[![Clickable image](image.png)](https://url)

Footnotes

Text with a footnote.[^1]

[^1]: Footnote content.

Text with inline footnote.^[Inline footnote content.]

Equations

Inline: $E = mc^{2}$

Display:
$$
\hat{\beta} = (X'X)^{-1}X'y
$$

Diagrams (Mermaid)

```{mermaid}
flowchart LR
  A[Data] --> B[Clean]
  B --> C[Model]
  C --> D[Report]
```

Divs and Spans

::: {.classname}
Block content
:::

[Inline content]{.classname}

Special Characters

En-dash: --
Em-dash: ---
Page break:

14) CLI Commands Reference

# Render
quarto render doc.qmd                    # all formats defined in YAML
quarto render doc.qmd --to pdf           # specific format
quarto render doc.qmd --to html          # specific format
quarto render                            # entire project

# Preview (live reload)
quarto preview doc.qmd
quarto preview                           # entire project

# Execution control
quarto render doc.ipynb                  # .ipynb: NO re-execution (default)
quarto render doc.ipynb --execute        # .ipynb: FORCE re-execution
quarto render doc.qmd                    # .qmd: DOES execute (default)
quarto render doc.qmd --cache            # enable caching
quarto render doc.qmd --no-cache         # disable caching
quarto render doc.qmd --cache-refresh    # invalidate and re-execute cached

# Projects
quarto create project website mysite
quarto create project manuscript mypaper

# Templates
quarto use template quarto-journals/acm  # new project from template
quarto add quarto-journals/acm           # add extension to existing project

# Publishing
quarto publish quarto-pub                # Quarto Pub
quarto publish gh-pages                  # GitHub Pages
quarto publish netlify                   # Netlify
quarto publish connect                   # Posit Connect

# Extensions
quarto create extension journal          # create your own journal extension

15) Common Patterns and Recipes

Self-Contained HTML Report (Email/Share)

---
title: "Analysis Report"
date: today
format:
  html:
    toc: true
    code-fold: true
    embed-resources: true
    theme: cosmo
---

Jupyter Notebook Rendered Without Re-Execution

Raw cell in .ipynb:

---
title: "310 - Baseline Model"
author: "Your Name"
date: today
format:
  html:
    toc: true
    code-fold: true
    embed-resources: true
---

quarto render 310-Baseline-Model.ipynb

Academic Paper (Quick Start)

---
title: "Paper Title"
author:
  - name: Your Name
    corresponding: true
    affiliation:
      - name: Institution Name
abstract: |
  Abstract text here.
bibliography: references.bib
csl: journal-style.csl
format:
  pdf:
    documentclass: scrartcl
    number-sections: true
    keep-tex: true
  docx:
    reference-doc: templates/reference.docx
---

Presentation (Reveal.js)

---
title: "My Presentation"
format:
  revealjs:
    theme: dark
    slide-number: true
    transition: slide
---

## Slide 1

Content here.

## Slide 2

More content.

Project with Frozen Execution

# _quarto.yml
project:
  type: website

execute:
  freeze: auto

format:
  html:
    toc: true
    theme: cosmo

16) Inline Code

Embed computed values in narrative text:

Python (Jupyter):

The mean age was `{python} mean_age` years.

R (Knitr):

The mean age was `{r} mean(data$age)` years.

Limitations: - Keep expressions simple (pre-computed values) - Not supported inside YAML strings (titles, captions) - In .ipynb files, inline expressions only evaluate during quarto render with execute: enabled: true

17) Summary: Execution Decision Tree

Want to render without re-executing code?
│
├── Using .ipynb?
│   └── Just run: quarto render notebook.ipynb
│       (Default behavior: outputs preserved)
│
├── Using .qmd in a project?
│   └── Set freeze: auto in _quarto.yml
│       Run once, then project renders skip re-execution
│
├── Using .qmd standalone?
│   ├── execute: enabled: false  (never run)
│   ├── execute: cache: true     (re-run only on code changes)
│   └── eval: false per-cell     (skip specific cells)
│
└── Want to FORCE execution?
    └── quarto render file.ipynb --execute

Quarto Document Skill

1) Document Types and When to Use Each

2) Execution Control (Critical for Jupyter Workflows)

The Problem

For .ipynb Files (Simplest Path)

For .qmd Files (Must Opt Out of Execution)

Option A: execute: enabled: false (Document-Level)

Option B: freeze (Project-Level, Recommended for Multi-Doc Projects)

Option C: cache (Cell-Level Caching)

Recommended Workflow: Jupyter-First Analysis

Cell-Level Execution Options

Intermediate File Preservation (Debugging)

3) Minimal Document Templates

Basic HTML Document

Analysis Notebook (Jupyter-first, no re-execution)

Multi-Format Document

4) Journal and Academic Paper Formatting

Available Journal Templates

Using a Journal Template

When No Official Template Exists

Word/Docx Route (most journals accept Word)

Custom Typst/PDF Route (Recommended for New Templates)

Custom LaTeX/PDF Route

Author and Affiliation Metadata

Manuscript Project Type

5) Citations and Bibliography

Setup

Citation Syntax

Include uncited items in bibliography

Control bibliography placement

PDF Citation Methods

6) Cross-References

Label Prefixes

Figures

Tables

Equations

Sections (requires number-sections: true)

7) Figure and Table Options

Figure Sizing and Layout

Layout for Multiple Items

Table Options

DataFrame Print Style

8) Code Display Options

Per-Cell

Document-Level

9) PDF Output Configuration

Basic PDF

Fonts

Page Geometry

PDF Engine

LaTeX Includes

Raw LaTeX in Document Body

Typst PDF Output (Alternative to LaTeX)

Basic Typst

Typst Fonts

Typst Page Layout

Citations in Typst

Raw Typst in Document Body

Custom Typst Format (Extension)

LaTeX vs Typst Decision Guide

10) HTML Output Configuration

Feature-Rich HTML

Tabsets

R

11) Projects (_quarto.yml)

Creating a Project

Project Configuration

Metadata Hierarchy (highest priority wins)

Working Directory

12) All Output Formats

Documents

Presentations

Markdown Variants

Scholarly

13) Markdown Essentials

Text Formatting

Links and Images

Footnotes

Equations

Diagrams (Mermaid)

For `.ipynb` Files (Simplest Path)

For `.qmd` Files (Must Opt Out of Execution)

Option A: `execute: enabled: false` (Document-Level)

Option B: `freeze` (Project-Level, Recommended for Multi-Doc Projects)

Option C: `cache` (Cell-Level Caching)

Sections (requires `number-sections: true`)

11) Projects (`_quarto.yml`)