Thesis using Quarto

Dr. Ajay Kumar Koli \(\cdot\) 2nd SARA Bootcamp

Thesis
Structure

Set Up GitHub Repo

Create a new GitHub repository (repo) for your book project.

 

Create Version Control RStudio Project

Paste the Repo Link/URL

Set Up RStudio Project

Create a file named _quarto.yml. It will contain the configuration settings for your thesis.

Configure _quarto.yml:

project:
  type: book

book:
  title: "My Book Title"
  author: "Author Name"
  date: "2023-10-01"
  chapters:
    - index.qmd
    - chapter1.qmd
    - chapter2.qmd

format:
  html:
    theme: cosmo
  pdf:
    documentclass: scrreprt

Create Content Files

  • Create the content files for your chapters (e.g., index.qmd, chapter1.qmd, chapter2.qmd).

  • Write your content using Markdown syntax. You can also include code, figures, and other elements.

Example index.qmd

---
format: html
---

# Introduction

Welcome to my book. This is the introduction chapter.

Example chapter1.qmd

---
format: html
---

# Chapter 1

This is the content of Chapter 1.

Render the Book

Preview and Iterate (html)

Preview and Iterate (pdf)

Thesis Text
Formating

Markdown


Markdown is a lightweight markup language for creating formatted text using a plain-text editor. Developed by John Gruber in 2004.

Source: https://en.wikipedia.org/wiki/Markdown

Text formatting


Markdown Syntax Output 
normal
 normal 
*italics*
 italics 
**bold**
 bold 
***bold italics***
 bold italics

Source: Quarto guide

Text formatting


Markdown Syntax Output 
superscript^2^
 superscript2 
subscript~2~
 subscript2 
~~strike through~~
 strike through 
`verbatim code`
 verbatim code

Source: Quarto guide

Headings


Markdown Syntax Output 
# Header 1

Header 1

 
## Header 2

Header 2

 
### Header 3

Header 3

 
#### Header 4

Header 4

 
##### Header 5
Header 5
 
###### Header 6
Header 6

Add images

If image is saved in your computer,
![](add image path here)


Markdown Syntax Output 
![](banner.png)
 |

Add images

If image is taken from the internet,
![](add image link here)


![](https://images.unsplash.com/photo-1627130595904-ebeeb6540a93?q=80&w=1974&auto=format&fit=crop&ixlib=rb-4.0.3&ixid=M3wxMjA3fDB8MHxwaG90by1wYWdlfHx8fGVufDB8fHx8fA%3D%3D)

Unordered list


Markdown Syntax Output 
* Item 1
* Item 2
* Item 3
  • Item 1
  • Item 2
  • Item 3

Unordered list: Sub-items


Markdown Syntax Output 
* Main items
    + Sub-item 1
    + Sub-item 2
        - Sub-sub-item 1
  • Main items
    • Sub-item 1
    • Sub-item 2
      • Sub-sub-item 1

Ordered list


Markdown Syntax Output 
1. Eggs
1. Tea
1. Fish
1. Milk
  1. Eggs
  2. Tea
  3. Fish
  4. Milk

List


Markdown Syntax Output 
(@)  A list whose numbering

continues after

(@)  an interruption
  1. A list whose numbering

continues after

  1. an interruption

List


Markdown Syntax Output 
::: {}
1. A item
1. B item
:::

::: {}
1. Followed by another list
:::
  1. A item
  2. A item
  1. Followed by another list

Equations

Use $ delimiters for inline math.


Markdown Syntax Output 
It is a great equation $E = mc^{2}$
 It is a great equation \(E=mc^{2}\)

Equations

Use $$ delimiters for display math.


Markdown Syntax Output 
It is a great equation $$E = mc^{2}$$
 It is a great equation \[E=mc^{2}\]

In-line coding

`{r} `

```{r}

age <- c(1, 2, 3, 4, 5)

```

Input: The mean age of the participants is `{r} mean(age)`.

Output: The mean age of the participants is 3.

Tables,
Figures &
Data in
a Thesis

What We Will Cover Now

  • 📊 Adding Tables (Markdown → kable → kableExtra)
  • 🖼️ Adding Figures (Images → Code → ggplot)
  • 🔗 Cross-Referencing Tables & Figures
  • 📁 Loading & Displaying Real Data
  • 🎯 Hands-on Your Turn Exercises

📊 Adding Tables

Step 1: Markdown Table (Simplest)

Type this in your .qmd file:

| Name  | Age | City     |
|-------|-----|----------|
| Ajay  | 25  | Delhi    |
| Kiram | 30  | Sonipat  |

Output:

Name Age City
Ajay 25 Delhi
Kiram 30 Sonipat

Step 2: kable Table

```{r}
# call the r package
library(knitr)

kable(head(mtcars), 
      caption = "My First Table")
```


Note

kable() is the go-to function for simple, clean tables in R.

Step 3: kableExtra (Styled Tables)

```{r}
library(kableExtra)

kable(head(mtcars), caption = "Styled Table") |>
  kable_styling(
    bootstrap_options = "striped",
    full_width = FALSE
  )
```
  • striped — alternating row colors
  • hover — highlight on mouse hover
  • condensed — compact layout

🎯 Your Turn: Tables

Exercise 1

Create a table showing 5 rows of any dataset of your choice.

✅ Add a caption
✅ Make it striped
✅ Set full_width = FALSE

🖼️ Adding Figures

Step 1: Insert an External Image

![Figure Caption](images/my-photo.png){
  fig-alt="description" 
  width="70%"
}


Tip

Always add fig-alt for accessibility — it’s good research practice!

Step 2: Figure from R Code

```{r}
#| label: fig-cars
#| fig-cap: "Relationship between Speed and Distance"

plot(cars$speed, cars$dist,
     xlab = "Speed", ylab = "Distance")
```
  • label — must start with fig- for cross-referencing
  • fig-cap — your figure caption

Step 3: ggplot Figure

```{r}
#| label: fig-ggplot
#| fig-cap: "MPG by Cylinder Count"
#| fig-width: 6
#| fig-height: 4
#| eval: false

library(ggplot2)

ggplot(mtcars, aes(x = factor(cyl), y = mpg)) +
  geom_boxplot(fill = "steelblue") +
  labs(x = "Cylinders", y = "MPG")
```

🎯 Your Turn: Figures

Exercise 2

  1. Insert any image from your computer
  2. Create a ggplot figure using the iris dataset
  3. Add a proper caption using fig-cap
  4. Set figure width and height

🔗 Cross-Referencing

Why Cross-Reference?

In a thesis, you write:

“As shown in Figure 3.2, the results indicate…”

Quarto handles the numbering automatically - you just use labels!

Cross-Referencing Figures

In your code chunk:

#| label: fig-scatter

In your text:

As shown in @fig-scatter, there is a positive trend...


Important Rule

Figure labels must start with fig-
Table labels must start with tbl-

Cross-Referencing Tables

In your code chunk:

#| label: tbl-summary

In your text:

As seen in @tbl-summary, the results indicate...


Quarto automatically converts @tbl-summary \(\rightarrow\) Table 1

🎯 Your Turn: Cross-Referencing

Exercise 3

  1. Create one table with a tbl- label
  2. Create one figure with a fig- label
  3. Reference both somewhere in your text using @
  4. Render and check the automatic numbering

📁 Real Data in Your Thesis

Loading Data

```{r}
# CSV file
data <- read.csv("data/survey.csv")

# Excel file
library(readxl)
data <- read_excel("data/survey.xlsx")

# Built-in dataset
data <- mtcars
```

Displaying Data as a Table

```{r}
#| label: tbl-data
#| tbl-cap: "Summary of Survey Data"

library(knitr)

kable(head(data))
```

Creating a Figure from Real Data

```{r}
#| label: fig-data
#| fig-cap: "Distribution of Responses"

hist(data$age, 
     main = "", 
     xlab = "Age",
     col = "steelblue")
```

🎯 Your Turn: Real Data

Exercise 4

Using the built-in airquality dataset:

  1. Display the first 6 rows as a kable table
  2. Create a histogram of the Temp column
  3. Add proper captions to both
  4. Cross-reference them in a short paragraph

📐 Thesis-Specific Settings

Global Settings in _quarto.yml

execute:
  echo: false       # hide code in final thesis
  warning: false    # hide warnings
  message: false    # hide messages

format:
  html:
    fig-width: 7
    fig-height: 5


Tip

Set echo: false globally so your thesis shows only output, not code.

Useful Chunk Options

Option Purpose
echo: false Hide code, show output
eval: false Show code, don’t run it
fig-width: 7 Set figure width
fig-height: 5 Set figure height
tbl-cap Add table caption
fig-cap Add figure caption

Key Takeaway

In a Quarto thesis, everything is connected

Your data, code, and writing live in one place.

When data changes → tables and figures update automatically.

Note

That is Reproducible Research in action! 🎉

Add
References

What We Will Cover Now

  • 📖 What is Zotero and why use it?
  • ⚙️ Setting up Zotero with Quarto
  • 📝 Adding a bibliography to your thesis
  • ✍️ Inserting citations in your text
  • 🎨 Changing citation styles (APA, Chicago, etc.)
  • 🔗 Connecting Zotero directly in RStudio
  • 🎯 Hands-on Your Turn Exercises

📖 What is Zotero?

Zotero — Simply Put

Think of Zotero as a smart bookshelf for your research.

  • 📚 Saves all your papers, books, and articles in one place
  • 🏷️ Stores author, year, title, journal — automatically
  • 📤 Exports references in any format Quarto needs
  • 🔄 Syncs across devices via zotero.org

Note

Zotero is free and open source — perfect for researchers!

Why Zotero + Quarto?

Without Zotero With Zotero + Quarto
Type references manually References inserted automatically
Format APA by hand Style applied instantly
Risk of typos Always accurate
Hard to update One click to refresh
Separate reference list Auto-generated bibliography

⚙️ Setting Up Zotero

Step 1: Install Zotero

  1. Go to zotero.org and download Zotero
  2. Install the Zotero Connector browser extension
  3. Create a free account at zotero.org/user/register
  4. Sign in inside the Zotero app

Tip

The browser extension lets you save a paper in one click while browsing Google Scholar or any journal website.

Step 2: Add References to Zotero

Three easy ways:

  • 🌐 Browser Connector — click the Zotero icon while on any paper page
  • 🔍 Search by DOI/ISBN — Edit → Add Item by Identifier
  • 📄 Import PDF — drag and drop a PDF into Zotero

Step 3: Install Better BibTeX Plugin

This plugin exports your library in a format Quarto understands.

  1. Go to github.com/retorquere/zotero-better-bibtex
  2. Download the .xpi file
  3. In Zotero → Tools → Add-ons → Install Add-on From File
  4. Select the downloaded .xpi file
  5. Restart Zotero

Step 4: Export Your Library as .bib

  1. In Zotero, right-click your collection
  2. Select Export Collection
  3. Choose format: Better BibTeX
  4. ✅ Check Keep Updated — auto-syncs when you add new references!
  5. Save as references.bib inside your Quarto project folder

Warning

Save the .bib file in the same folder as your _quarto.yml

📝 Linking Bibliography in Quarto

Add Bibliography to _quarto.yml

project:
  type: book

book:
  title: "My Thesis"
  author: "Your Name"

bibliography: references.bib
csl: apa.csl                  # citation style (optional)

format:
  html:
    theme: cosmo
  pdf:
    documentclass: scrreprt

Note

bibliography: tells Quarto where your references file lives.

Or Add to a Single Chapter’s YAML

If you only want bibliography in one .qmd file:

---
title: "Literature Review"
bibliography: references.bib
csl: apa.csl
---

✍️ Inserting Citations in Text

Citation Syntax — The Basics

Every reference in your .bib file has a citation key like:

@peng2011reproducible
@wickham2016ggplot2
@gandrud2016reproducible

How to Cite in Text

What you want Syntax Output
Author (Year) @peng2011 Peng (2011)
(Author, Year) [@peng2011] (Peng, 2011)
Multiple sources [@peng2011; @knuth1984] (Peng, 2011; Knuth, 1984)
Page number [@peng2011, p. 45] (Peng, 2011, p. 45)
Suppress author [-@peng2011] (2011)

Example in Your Thesis Text

Reproducible research has been defined as sharing data and 
code alongside findings [@peng2011].

As @buckheit1995 argued, the actual scholarship is the 
complete software environment that produced the results.

Several studies [@peng2011; @gandrud2016; @knuth1984] 
have emphasized the importance of literate programming.

The Bibliography Appears Automatically!

At the end of your document, Quarto automatically generates:

## References

Peng, R. D. (2011). Reproducible research in computational 
science. *Science*, 334(6060), 1226–1227.

Buckheit, J., & Donoho, D. (1995). WaveLab and reproducible 
research. *Wavelets and Statistics*, 55–81.

Tip

No need to type the reference list — Quarto does it for you! 🎉

🎯 Your Turn: First Citation

Exercise 1

  1. Add 3 references to your Zotero library
  2. Export as references.bib to your project folder
  3. Link it in your _quarto.yml
  4. Write one paragraph and cite all 3 sources
  5. Render and check the bibliography at the end

🎨 Citation Styles

What is a CSL File?

CSL = Citation Style Language

It controls how your citations look:

  • APA → (Peng, 2011)
  • Chicago → Peng, Roger D. 2011. “Reproducible Research…”
  • Vancouver → [1]
  • Harvard → Peng (2011)
  • IEEE → [1] R. D. Peng…

Download a CSL File

  1. Go to zotero.org/styles
  2. Search for your required style (e.g., APA 7th)
  3. Download the .csl file
  4. Place it in your Quarto project folder
  5. Add to _quarto.yml:
csl: apa.csl

Common CSL Files

Style File Name Used In
APA 7th apa.csl Social sciences
Chicago chicago-author-date.csl Humanities
Vancouver vancouver.csl Medicine
Harvard harvard-cite-them-right.csl General
IEEE ieee.csl Engineering

Tip

Check with your university which style they require for your thesis!

🎯 Your Turn: Change Citation Style

Exercise 2

  1. Download the APA 7th CSL file from zotero.org/styles
  2. Place it in your project folder
  3. Add csl: apa.csl to your _quarto.yml
  4. Render your document
  5. Now switch to Chicago style and render again
  6. Compare the difference!

🔗 Zotero Direct Integration in RStudio

The Easiest Way — Visual Editor

RStudio’s Visual Editor connects directly to Zotero!

  1. Open your .qmd file in RStudio
  2. Switch to Visual mode (top-left toggle)
  3. Go to Insert → Citation
  4. Search your Zotero library directly!
  5. Click Insert — citation key added automatically

Note

No need to remember citation keys — RStudio finds them for you!

Visual Editor Citation Dialog

Insert → Citation

┌─────────────────────────────────┐
│  🔍 Search: reproducible        │
│                                 │
│  📚 My Library                  │
│  ├── Peng 2011                  │
│  ├── Buckheit 1995              │
│  └── Gandrud 2016               │
│                                 │
│  [ Insert ]  [ Cancel ]         │
└─────────────────────────────────┘

Setting Up Zotero in RStudio

Make sure RStudio can find your Zotero:

  1. Tools → Global Options → R Markdown → Citations
  2. Set Zotero Library to: Local or Web
  3. If Web: add your Zotero API key from zotero.org/settings/keys
  4. Click OK

Auto-Complete Citation Keys

In Source mode, type @ and start typing:

As shown by @pen...

RStudio will autocomplete from your .bib file:

@peng2011reproducible  ← select this!
@penman2019...

Tip

This works like autocomplete in coding — fast and accurate!

🎯 Your Turn: Visual Editor Citations

Exercise 3

  1. Open a .qmd file in Visual mode
  2. Use Insert → Citation to search your Zotero library
  3. Insert 2 citations into a paragraph
  4. Switch to Source mode and observe the citation keys
  5. Render and check the output

📁 Your .bib File — A Closer Look

What a .bib File Looks Like

@article{peng2011reproducible,
  title   = {Reproducible Research in Computational Science},
  author  = {Peng, Roger D},
  journal = {Science},
  volume  = {334},
  number  = {6060},
  pages   = {1226--1227},
  year    = {2011}
}

@book{gandrud2016reproducible,
  title     = {Reproducible Research with R and RStudio},
  author    = {Gandrud, Christopher},
  publisher = {CRC Press},
  year      = {2016}
}

Anatomy of a Citation Key

@article{peng2011reproducible,
          ^^^^^^^^^^^^^^^^^^^^
          This is the citation key you use in text
          
          Convention: AuthorYearKeyword
          e.g., peng2011reproducible
               wickham2016ggplot
               gandrud2016reproducible

Note

Better BibTeX generates these keys automatically for you!

🛠️ Troubleshooting

Common Problems & Fixes

Problem Fix
Citation not found Check the key matches exactly in .bib
Bibliography not showing Add bibliography: references.bib to YAML
Wrong style Check .csl file name and path
.bib not updating Re-export from Zotero with Keep Updated
RStudio can’t find Zotero Check Global Options → Citations

Checklist Before Rendering

  • ✅ references.bib is in the project folder
  • ✅ bibliography: references.bib is in _quarto.yml
  • ✅ Citation keys in text match keys in .bib file
  • ✅ .csl file is downloaded and path is correct
  • ✅ Zotero is open (for live sync)

Key Takeaway 🔑

Never format a reference manually again!

Zotero + Quarto means:

  • ✍️ You write — Quarto formats
  • 📚 You collect — Zotero organizes
  • 🎨 You choose the style — CSL applies it
  • 🔄 You add a source — bibliography updates automatically

💛 Benefits of using Quarto

  1. Reproducibility

  2. Iterative Workflow

  3. Customization and Flexibility

  4. Multi-Format Output

  5. Collaboration

  6. Reduced Formatting Issues

  7. Integration with Other Tools

  8. Documentation and Support