Quarto Essentials

Bogdan G. Popescu

John Cabot University

Introduction

What is Quarto

Quarto - open-source publishing system designed for creating dynamic, reproducible documents, including reports, presentations, and websites.

It supports multiple formats like HTML, PDF, Word, and slides.

Why Use Quarto?

Integrates well with R, Python, and Julia.

Enables embedding of code chunks directly in documents for dynamic content generation.

Facilitates reproducibility by linking code and results seamlessly.

Quarto Document Structure

YAML Header

The YAML header defines the document metadata, such as title, author, date, and output format.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
---

# Introduction

This is an example.

Quarto Document Structure

YAML Header

The YAML header defines the document metadata, such as title, author, date, and output format.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
---

# Introduction

This is an example.

Creating HTML Output

Basic YAML Configuration

To generate an HTML file, specify format: html in the YAML header.

Rendering the Document:

Use quarto render in R to generate the output.

Adding a Table of Contents

Enabling TOC:

Add toc: true in the YAML header to automatically generate a table of contents.
Control depth with toc-depth (e.g., 2 for two levels of headings).

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
---

# Introduction

This is an example.

Adding a Table of Contents

Customization

Rename the title with toc-title: "Contents".

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is an example.

Equations

You can easily add inline equations in the following way

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is an example.

This is an equation: $E=mc^{2}$

Equations

You can easily add inline equations in the following way

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is an example.

This is an equation: $E=mc^{2}$

This is also an equation: 

$$E=mc^{2}$$

Equations

You can easily add inline equations in the following way

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is an example.

This is an equation: $E=mc^{2}$

This is also an equation: 

$$E=mc^{2}$$

For more advanced equations, check: https://qmd4sci.njtierney.com/math

Code

Embedding Code

This is how we include code in our documents.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is an example.

This is an equation: $E=mc^{2}$

This is also an equation: 

$$E=mc^{2}$$

```{r}
summary(mtcars)
```

Code

Embedding Code

This is how we include code in our documents.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is an example.

This is an equation: $E=mc^{2}$

This is also an equation: 

$$E=mc^{2}$$

```{r echo=TRUE, eval=TRUE}
summary(mtcars)
```

Code

Embedding Code

This is how we only include code output in our documents.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is an example.

This is an equation: $E=mc^{2}$

This is also an equation: 

$$E=mc^{2}$$

```{r echo=FALSE, eval=TRUE}
summary(mtcars)
```

Code

Embedding Code

This is how we only include code without output in our documents.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is an example.

This is an equation: $E=mc^{2}$

This is also an equation: 

$$E=mc^{2}$$

```{r echo=TRUE, eval=FALSE}
summary(mtcars)
```

Code

Embedding Code

Many times you might have seen annoying library messages:

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is an example.

This is an equation: $E=mc^{2}$

This is also an equation: 

$$E=mc^{2}$$

```{r echo=TRUE, eval=FALSE}
summary(mtcars)
```

```{r}
library(dplyr)
```

Code

Embedding Code

To avoid them in printing, you should do:

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is an example.

This is an equation: $E=mc^{2}$

This is also an equation: 

$$E=mc^{2}$$

```{r echo=TRUE, eval=FALSE}
summary(mtcars)
```

```{r warning=FALSE, message=FALSE}
library(dplyr)
```

Embedding Resources

What is Self-Contained HTML?:

An HTML document that includes all dependencies (images, CSS, JavaScript) within a single file.

Why Use It?

Easy to share and view without requiring external resources.

This means that you will only see an html document being produced.

Embedding Resources

This a complicated document (with formulae, graphs) without resource-embedding.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is an example.

This is an equation: $E=mc^{2}$

This is also an equation: 

$$E=mc^{2}$$

```{r echo=TRUE, eval=FALSE}
summary(mtcars)
```

```{r}
library(dplyr)
```

Embedding Resources

This a complicated document (with formulae, graphs) with resource-embedding.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
embed-resources: true
---

# Introduction

This is an example.

This is an equation: $E=mc^{2}$

This is also an equation: 

$$E=mc^{2}$$

```{r echo=TRUE, eval=FALSE}
summary(mtcars)
```

```{r}
library(dplyr)
```

Text Formatting

This is how we format text within our document.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

```{r echo=TRUE, eval=FALSE}
summary(mtcars)
```

*This is italic text.*

**This is bold text.**

***This is bold and italic.***

This is reference to a `qmd` document.

Headings

This is how we add headings and subheadings.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

```{r echo=TRUE, eval=FALSE}
summary(mtcars)
```

The following are headers:

# Header 2
## Subheader 1
### Sub-subheader 1

Headings

This is how we can automatically number the headers.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
number-sections: true
---

# Introduction

```{r echo=TRUE, eval=FALSE}
summary(mtcars)
```

The following are headers:

# Header
## Subheader
### Sub-subheader

Headings

This is how we can remove some headers from being numbered.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
number-sections: true
---

# Introduction

```{r echo=TRUE, eval=FALSE}
summary(mtcars)
```

The following are headers:

# Header
## Subheader {.unnumbered}
### Sub-subheader {.unnumbered}

Headings

This is how we can remove some headers from being numbered and from the Table of Contents

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
number-sections: true
---

# Introduction

```{r echo=TRUE, eval=FALSE}
summary(mtcars)
```

The following are headers:

# Header
## Subheader {.unnumbered .unlisted}
### Sub-subheader {.unnumbered .unlisted}

Links

This is how we add links.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is how we can include links:

<https://quarto.org>

Another way is: [Quarto](https://quarto.org)

Pictures

This is how we add pictures.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is how we can include pictures:

![](figures/elephant.png){width="50%"}

Lists

This is how we add lists.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

* unordered list
  + sub-item 1
  + sub-item 2
    - sub-sub-item 1

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

Tables

This is how we add tables.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is a table.

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

Diagrams

Quarto has native support for embedding Mermaid and Graphviz diagrams.

This enables you to create flowcharts, sequence diagrams, state diagrams.

---
title: "Statistical Analysis Report"
author: "Your Name"
date: "2024-11-05"
format: html
toc: true
toc-title: "Contents"
---

# Introduction

This is a diagram.

```{mermaid}
%%| echo: fenced
flowchart LR
  A[Hard edge] --> B(Round edge)
  B --> C{Decision}
  C --> D[Result one]
  C --> E[Result two]
```

Videos

You can include videos in documents using the {{< video >}} shortcode. For example, here we embed a YouTube video:

Videos can refer to video files (e.g. MPEG) or can be links to videos published on YouTube, Vimeo, or Brightcove.

{{< video https://www.youtube.com/embed/wo9vZccmqwc >}}

Callout Blocks

Markdown Syntax

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

Output

Note

Note that there are five types of callouts, including note, tip, warning, caution, and important.

Word Basics

In order to create Word docs you will need to install:

Terminal

quarto tools install chromium

Word Basics

In order to create Word docs you will need to install:

Terminal

quarto tools install chromium

Word Basics

In order to create Word docs you will need to install:

Terminal

quarto tools install chromium