Quarto for Scholarly Writing
Technology Committee Professional Development
November 14, 2023

Ryan Straight, Ph.D

College of Applied Science and Technology
University of Arizona

Let’s Get Started

The Plan for Today

Follow along with this slide deck at:

https://ryanstraight.github.io/tc-quarto/

Images via Adobe Firefly.

Access the source files on GitHub

Quarto

What is Quarto?

• Description
• Scholarly relevance
• Quarto’s evolution

Code

```{r}
#| label: fig-mtcars
#| fig-cap: A scatterplot rendered on-the-fly.
plot(mtcars$mpg)
```

Figure 1: A scatterplot rendered on-the-fly.

Quarto vs. Traditional Tools

• Data integration
• Dynamic content
• Output versatility

Images via dream.ai.

Human Services

Data-Driven Reports and Policy Papers:

Professionals in human services often deal with data related to social issues, demographics, and service outcomes. Quarto can be used to integrate this data directly into reports and policy papers. For example, a report on community health outcomes could include live-updated graphs and charts.

Case Study Documentation:

Case studies are a crucial part of human services education and practice. Quarto allows for the integration of qualitative data, such as interview transcripts or field notes, alongside quantitative data. This feature supports a more holistic and nuanced presentation of case studies.

Educational Materials and Training Guides:

Quarto’s flexibility in output formats (like slides, PDFs, and web pages) makes it ideal for creating diverse educational materials. Training guides for new social work methodologies or community engagement strategies can be crafted with rich multimedia content.

Organizational Leadership

Organizational Analysis and Strategy Documents:

Leaders often need to analyze organizational data like employee performance metrics, market analysis, or financial reports. Quarto can embed these data analyses directly into strategic documents, enabling dynamic and data-informed leadership decision-making.

Training and Development Materials:

For leadership training programs, Quarto can be used to create interactive training materials. It can combine theoretical content with real-world data, helping to bridge the gap between theory and practice.

Internal Communications and Presentations:

Quarto’s versatility in creating slides and reports is beneficial for internal communication. Leaders can use it to present complex organizational data in an easily digestible format, enhancing transparency and informed decision-making within the organization.

Academic Applications

Data visualization

Visualizations are rendered in the Quarto document, not pre-rendered, saved, and loaded. For example, Figure 2 below.

Code

```{r}
#| label: fig-airquality
#| fig-cap: "Temperature and ozone level."
#| out-width: 83%
#| output-location: column
#| code-fold: true

library(ggplot2)

ggplot(airquality, aes(Temp, Ozone)) + 
  geom_point() + 
  geom_smooth(method = "loess")
```

Figure 2: Temperature and ozone level.

Teaching materials

Cross-referencing is also useful for teaching. For example, we can link directly to Section 2.1 on “What is Quarto?” or to Figure 1, the scatterplot from earlier. Or perhaps we want to reference Table 1. Where’s Table 1? Later in the deck!

Note that we’re not actually typing “Table 1.” Here’s the source code for the paragraph above:

Cross-referencing is also useful for teaching.
For example, we can link directly to @sec-whatisquarto on "What is Quarto?" or to @fig-mtcars, the scatterplot from earlier.
Or perhaps we want to reference @tbl-iris.
Where's @tbl-iris?
Later in the deck!

Research & Publication

The bread and butter. Easy integration with Google Scholar, DOI, ORCID, and Zotero. We’ll be delving deeper into this later. It’s worth noting here that you can cite references in a slide deck just as you would a document. For example, we might cite Taddeo (2016), Kline (1985), and Ihde (1990), and they would automatically be listed in the References section (Section 7.3).¹ First, though…

1. And, since we’ve specified we want to use APA style in the YAML by including apa.csl, we know the references are perfectly formatted.

Installation and Use

Installing Quarto

• Download & install
• Initial setup¹
• Basic configuration

Images via dream.ai.

1. There is none! It lives in the background.

Basic Features

• Document types
• Tool integrations
• Portable and replicable

• Quarto lets you create virtually any type of document, whether that’s a slide deck (like this one), a webpage, a book, interactive dashboards, a Confluence site, or, as we’ll see, manuscripts.
• It also natively integrates into platforms like RStudio and Jupyter notebooks, so think of it as simply a way of writing rather than a platform for doing so.
• Since you’re writing in plain text and building your manuscript, code, graphs, analysis, even references right there in the file, you can just give it to the world and it should work as intended. Replicability and reproducability are really the key, here.

Advanced Features

Advanced Data Handling

Code

library(dygraphs)
dygraph(fdeaths, "Female Deaths")
dygraph(mdeaths, "Male Deaths")
dygraph(ldeaths, "All Deaths")

• Embedding code
• Live data updates
• Enhanced visualization

Iris table

Remember we talked about this earlier?

Table 1: A table displaying 75 rows of the iris dataset.

Sepal.Length	Sepal.Width	Petal.Length	Petal.Width	Species
5.1	3.5	1.4	0.2	setosa
4.9	3.0	1.4	0.2	setosa
4.7	3.2	1.3	0.2	setosa
4.6	3.1	1.5	0.2	setosa
5.0	3.6	1.4	0.2	setosa
5.4	3.9	1.7	0.4	setosa
4.6	3.4	1.4	0.3	setosa
5.0	3.4	1.5	0.2	setosa
4.4	2.9	1.4	0.2	setosa
4.9	3.1	1.5	0.1	setosa
5.4	3.7	1.5	0.2	setosa
4.8	3.4	1.6	0.2	setosa
4.8	3.0	1.4	0.1	setosa
4.3	3.0	1.1	0.1	setosa
5.8	4.0	1.2	0.2	setosa
5.7	4.4	1.5	0.4	setosa
5.4	3.9	1.3	0.4	setosa
5.1	3.5	1.4	0.3	setosa
5.7	3.8	1.7	0.3	setosa
5.1	3.8	1.5	0.3	setosa
5.4	3.4	1.7	0.2	setosa
5.1	3.7	1.5	0.4	setosa
4.6	3.6	1.0	0.2	setosa
5.1	3.3	1.7	0.5	setosa
4.8	3.4	1.9	0.2	setosa
5.0	3.0	1.6	0.2	setosa
5.0	3.4	1.6	0.4	setosa
5.2	3.5	1.5	0.2	setosa
5.2	3.4	1.4	0.2	setosa
4.7	3.2	1.6	0.2	setosa
4.8	3.1	1.6	0.2	setosa
5.4	3.4	1.5	0.4	setosa
5.2	4.1	1.5	0.1	setosa
5.5	4.2	1.4	0.2	setosa
4.9	3.1	1.5	0.2	setosa
5.0	3.2	1.2	0.2	setosa
5.5	3.5	1.3	0.2	setosa
4.9	3.6	1.4	0.1	setosa
4.4	3.0	1.3	0.2	setosa
5.1	3.4	1.5	0.2	setosa
5.0	3.5	1.3	0.3	setosa
4.5	2.3	1.3	0.3	setosa
4.4	3.2	1.3	0.2	setosa
5.0	3.5	1.6	0.6	setosa
5.1	3.8	1.9	0.4	setosa
4.8	3.0	1.4	0.3	setosa
5.1	3.8	1.6	0.2	setosa
4.6	3.2	1.4	0.2	setosa
5.3	3.7	1.5	0.2	setosa
5.0	3.3	1.4	0.2	setosa
7.0	3.2	4.7	1.4	versicolor
6.4	3.2	4.5	1.5	versicolor
6.9	3.1	4.9	1.5	versicolor
5.5	2.3	4.0	1.3	versicolor
6.5	2.8	4.6	1.5	versicolor
5.7	2.8	4.5	1.3	versicolor
6.3	3.3	4.7	1.6	versicolor
4.9	2.4	3.3	1.0	versicolor
6.6	2.9	4.6	1.3	versicolor
5.2	2.7	3.9	1.4	versicolor
5.0	2.0	3.5	1.0	versicolor
5.9	3.0	4.2	1.5	versicolor
6.0	2.2	4.0	1.0	versicolor
6.1	2.9	4.7	1.4	versicolor
5.6	2.9	3.6	1.3	versicolor
6.7	3.1	4.4	1.4	versicolor
5.6	3.0	4.5	1.5	versicolor
5.8	2.7	4.1	1.0	versicolor
6.2	2.2	4.5	1.5	versicolor
5.6	2.5	3.9	1.1	versicolor
5.9	3.2	4.8	1.8	versicolor
6.1	2.8	4.0	1.3	versicolor
6.3	2.5	4.9	1.5	versicolor
6.1	2.8	4.7	1.2	versicolor
6.4	2.9	4.3	1.3	versicolor

Customization in Quarto

• Academic templates
• Styling & formatting
• Layout tips

Images via dream.ai.

Scholarly writing

Live Demonstration

• Create document
• Embed data
• Format output
• Zotero integration
• Native citation
• Cross-referencing

Images via dream.ai.

Examples

Quarto now has a manuscript project type to make this even easier!

Let’s look at two examples: one external and one internal!

Here I’ll show you an actual Quarto document and how it’s built into the format the outlet requires just by adding a couple lines of code.

Adoption Support

Learning resources

Most of what you’ll need to know can be found on the Quarto website’s Guide.

Troubleshooting

Google is your friend! You can also try using LLMs like ChatGPT to help troubleshoot syntax errors.

Community resources

Check out the #quartopub hashtag on social media for a vibrant community of folks using this platform!

• The guide is indispensible. Quarto can be intimidating at first, especially if you’re not used to using plain text for writing and building, so having walkthroughs is fantastic.
• Honestly, just Google whatever problem you’re having. I’ve found 99% of my issues can be solved by:
  • Undoing my last thing and trying again. (It’s usually user error.)
  • Updating packages and whatnot.
  • And, failing that, just Googling the issue.
• The community around Quarto is great. People genuinely love using it to do really cool things.

Conclusion

Q&A Session

• Questions?
• Let’s clarify
• Thoughts?

That’s a wrap!

Thanks, everybody! We hope this was useful!

What do you want to see? Tell us what you’d like us to cover by taking this brief survey. Use this QR code:

Image via GIPHY

References

Ihde, D. (1990). Technology and the Lifeworld: From Garden to Earth. Indiana University Press.

Kline, S. J. (1985). What is Technology? Bulletin of Science, Technology & Society, 1, 215–218.

Taddeo, M. (2016). Just Information Warfare. Topoi, 35(1), 213–224. https://doi.org/10.1007/s11245-014-9245-8