EPPS Math Coding Camp

Quarto & LaTex

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Published

August 19, 2025

Instructor: Dongeun Kim

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Quarto & LaTeX

This document will provide you a very brief introduction to using Quarto and LaTex to improve your reports and presentation of your data analyses.

Quarto

Quarto is an expanded version of R Markdown for rendering reports with integrated code like the one you are currently reading. To create a quarto document, select Create a new Quarto document from the New File drop down in RStudio.

As this is a markdown style, most of the options this gives you access to are ways to modify text or add other embellishments to your report. Below are a few examples on how to change the text.

LaTeX

LaTeX is a high-quality typesetting system that is widely used for producing scientific and mathematical documents. It is especially useful when your report includes complex equations, tables, and citations.

To create a LaTeX document, you typically start with a .tex file and compile it into a PDF using a TeX engine such as pdflatex, xelatex, or lualatex.

While Quarto is excellent for combining code and text, LaTeX is the go-to tool when you want full control over formatting in academic writing, especially for papers with complex equations.

Quarto & LaTeX — How They Fit Together

  • Quarto is a publishing system that takes .qmd and produces HTML / PDF / Word / slides.
  • For PDF, Quarto converts Markdown → LaTeX and calls a LaTeX engine (pdflatex, xelatex, or lualatex).
  • For HTML, LaTeX isn’t required; math renders via MathJax/KaTeX in the browser.

Render flow (PDF): .qmd → Pandoc Markdown → LaTeX → PDF.

Getting Started in RStudio (Step-by-step)

  1. New File ▶ Quarto Document…
  2. Pick a title and author; choose HTML to start.
  3. Click Render. Confirm an .html appears in your project folder.
  4. Switch to PDF (requires LaTeX installed; TinyTeX recommended).

Core Markdown Formatting

Text

Markdown Renders as
*italics* italics
**bold** bold
***bold italics*** bold italics
superscript^2^ superscript2
subscript~i~ subscripti
~~strike~~ strike
`verbatim` verbatim

Headings

Markdown Heading
# Heading 1 # Heading 1
## Heading 2 ## Heading 2
### Heading 3 ### Heading 3
#### Heading 4 #### Heading 4
##### Heading 5 ##### Heading 5
###### Heading 6 ###### Heading 6

Tables (Markdown)

Markdown source:

| Right | Left | Default | Center |
|------:|:-----|---------|:------:|
|    12 | 12   | 12      |   12   |
|   123 | 123  | 123     |  123   |
|     1 | 1    | 1       |   1    |

Rendered:

Right Left Default Center
12 12 12 12
123 123 123 123
1 1 1 1

Source Code & Runnable Chunks

Use a fenced code block for plain code (not executed):

```r
#### plain code, not evaluated
1 + 1

Use a **runnable** chunk with options (note the `{r}` + `#|` lines):
::: {.cell}

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

A simple demo figure

:::

Useful options: - #| eval: false → show code but don’t run - #| echo: false → hide code, show results - #| warning: false, #| message: false → suppress output noise - #| fig-cap: "Caption" → caption figures - #| tbl-cap: "Caption" → caption tables

Working Directory (Reproducible Paths)

Prefer project‑root execution so all paths are consistent:

execute:
  dir: project

If absolutely needed, set a custom path in a setup chunk:

Math & LaTeX in Quarto

Inline vs Display

Inline math: \( E = mc^2 \) → ( E = mc^2 ).

Display math:

$$
y = \beta_0 + \beta_1 x + \epsilon
$$

Align Environment & Cross-refs

\begin{align}
y &= \beta_0 + \beta_1 x + \epsilon \\
\hat{y} &= \beta_0 + \beta_1 x
\end{align}

Number and reference:

$$
E = mc^2
(\#eq-einstein)
$$

As shown in @eq-einstein, mass–energy equivalence holds.
Tip

Label equations with (\#eq-name), then cite with @eq-name.

Figures & Tables with Cross-refs

Figure (label via label: and caption via fig-cap:):

Code 
plot(cars)
Figure 1: Speed vs Stopping Distance

Refer to Figure 1 in text.

Table (create an R table and label it):

Code 
head(mtcars, 6)
Table 1: First rows of mtcars 
                   mpg cyl disp  hp drat    wt  qsec vs am gear carb
Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1

Refer to Table 1 in text.

Showing LaTeX Commands Literally (Escaping)

Use inline code for short commands:

- `\documentclass` sets the type of document.
- `\usepackage{amsmath}` adds math support.
- `\maketitle` prints title/author/date.
- `\begin{document}` starts visible content.

Use a fenced code block for longer examples:

```latex
\documentclass{article}
\usepackage{amsmath}
\title{My First LaTeX Doc}
\author{Your Name}
\date{\today}

\begin{document}
\maketitle
Hello World!
\end{document}
```
Warning

If you type a backslash in plain text (not code), escape it as \.

Customizing PDF with LaTeX

Add packages/macros via preamble.tex

YAML in your .qmd:

format:
  pdf:
    include-in-header: preamble.tex

Create preamble.tex (project root or same folder):

% preamble.tex
\usepackage{amsmath, amssymb}
\usepackage{booktabs}
\newcommand{\R}{\mathbb{R}}

Use a custom LaTeX template

format:
  pdf:
    template: templates/custom.tex
    include-in-header: preamble.tex

Project-wide defaults (_quarto.yml)

project:
  type: default

format:
  html:
    toc: true
  pdf:
    pdf-engine: lualatex
    toc: true

execute:
  dir: project

Citations (Brief)

Add a bibliography in YAML:

bibliography: references.bib
csl: apa.csl   # optional style

Cite with @key and include a refs section:

## References

(Quarto/Pandoc will print the bibliography automatically at the end.)