Writing academically

Jayani P. G. Lakshika

Department of Econometrics and Business Statistics, Monash University, Australia.

🎯 Objectives

  • Understand how to use the Quarto journal and thesis templates.
  • Manage references and citations.
  • Add and customize code chunks, equations, figures, and tables in Quarto.

📝 Quarto Template for Journal Paper

With Quarto, you can create fully formatted and reproducible journal articles with ease.

You have two options:

  • ✨ Start fresh using a journal-specific template.
  • 🔧 Apply the format to an existing Quarto project.

In this workshop, we will use the official template for the Journal of Statistical Software (JSS).

This template includes:

  • A pre-configured YAML header
  • Sample .qmd content
  • A bibliography file (references.bib)

You’ll be able to write, cite, and format your article — ready for submission — all in Quarto!

🚀 Let’s Begin…

🆕 Creating a New Article

To start a new article using the Journal of Statistical Software (JSS) template, run this command in your terminal or RStudio console:

quarto use template quarto-journals/jss

This will:

  • Install the JSS extension

  • Create a new folder with:

    • A sample .qmd file
    • A sample bibliography (references.bib)

You’ll be ready to write your article right away!

🛠️ Applying the Format to an Existing Project

Already have a Quarto document or project? Install the JSS format with:

quarto add quarto-journals/jss

Then, update your YAML header to use the new format.

✅ Now you’re ready to write and render in the JSS style!

🧪 Let’s Try It Together!

Now it’s your turn to try creating a Quarto journal article using the JSS template.

🧭 Steps to Follow

  1. Open RStudio or your terminal
  2. Run this command to create a new project:
quarto use template quarto-journals/jss

  1. Open the new folder and locate:

    • index.qmd (main article)
    • references.bib (sample bibliography)

  2. Click Render to preview the document as PDF or HTML

🙋 Raise your hand or drop a question if you need help!

🎓 Monash Quarto Thesis Template

The Monash Quarto Thesis Template helps you create a well-structured, submission-ready thesis following Monash University guidelines.

🆕 Create a New Thesis Project

To get started, run the following command in your terminal or RStudio console:

quarto use template quarto-monash/thesis

This will:

  • Install the Monash thesis extension

  • Create a new project folder with:

    • A pre-configured index.qmd
    • Chapter files (chapters/)
    • Front matter and bibliography
    • A ready-to-render thesis structure

📚 Adding a Bibliography to .qmd Files

### 1. Create a `.bib` File (BibTeX Format)

```bibtex
@article{smith2021,
  title = {A Method for Data Analysis},
  author = {Smith, Jane},
  journal = {Journal of Statistics},
  year = {2021}
}

💡 Save as: references.bib

bibliography: references.bib
csl: apa.csl  # Optional: adds citation style (e.g., APA, IEEE)

3. Cite in the Text

As shown in recent work [@smith2021], the method is effective.

🔄 Quarto will automatically format the in-text citation and generate a reference list.

⚙️ Quarto Quirks & Power Tips

📐 LaTeX Equation in a Figure Caption

![This figure demonstrates the equation $E = mc^2$.](figure.png){#fig-einstein}

✅ You can embed LaTeX-style equations directly using dollar signs ($...$) in the caption.

✅ Works in both HTML and PDF outputs.

Refer to Another Figure in a Caption

![Here we compare this with Figure @fig-einstein.](comparison.png){#fig-compare}

📝 @fig-einstein will resolve to the numbered figure reference (e.g., Figure 1) in PDF/HTML.

📌 Make sure the first figure has an ID like {#fig-einstein}.

| Tool   | Link                              |
|--------|-----------------------------------|
| Quarto | [quarto.org](https://quarto.org) |

✅ Use standard Markdown syntax inside tables: [text](url)

✅ Works for external links, local files, and section anchors.

🖼 Alt-Text in Figure Chunk

![Scatterplot of speed vs. distance](cars-plot.png){fig-alt="A scatterplot showing car stopping distances by speed."}

✅ Use fig-alt="..." to improve accessibility and support screen readers.

👍 Highly recommended for academic publishing and accessibility standards.

🎯 What We Learned

  • 📝 Journal Articles – You can create a JSS-formatted article using quarto use template quarto-journals/jss.
  • 🎓 Monash Thesis – The Monash thesis template gives you a structured, submission-ready format out of the box.
  • 📚 Citations – Bibliographies are managed with .bib files and citations inserted using [@key] syntax.
  • 📊 Code & Output – Quarto lets you embed R code, equations, figures, and tables with full formatting control.

Keep writing and keep it reproducible 💡