Quarto: A tool for open scholarship

Part I

Rick Gilmore

Preliminaries

Follow-along

Figure 1: https://penn-state-open-science.github.io/bootcamp-2025-quarto-I/

Agenda

  • Motivation
  • Installing the tools
  • Case study
  • Under the hood

Motivation

flowchart LR
  A(["Idea"]) --> B["Proposal"]
  B --> C("Project_1")
  B --> D("Project_2")
  C --> E["IRB_protocol"]
  D --> E
  C --> F["Lab_protocol"]
  D --> F
  C --> G["Data_pipeline_1"]
  D --> H["Data_pipeline_2"]
  B --> I["Conference_presentation"]
  F --> I
  G --> I
  C --> I
  I --> J["Journal_manuscript"]
  H --> K["Lab_mtg_report"]
  K --> J
  F --> J
Figure 2: A sample scholarly workflow

Documents have many parts…

flowchart LR
  A("Data") --> B["Data_pipeline"]
  B --> C("Figure_1")
  B --> D("Figure_2")
  B --> E("Table_1")
  F("Text") --> G["Document"]
  H("References") --> G
  C --> G
  D --> G
  E --> G
Figure 3: Components of a scholarly document

Challenges

“I just found a typo in our data file. We need to re-run all of the analyses and regenerate all of the stats, figures, and tables ASAP. The submission deadline is tomorrow!”

“Can we make the typefaces and axes the same in Figures 1 and 2? The submission deadline is tomorrow!”

“We need to submit our grant progress report by tomorrow!”

More challenges

  • Reducing duplication of effort
  • Re-using our own hard work
  • Making our own work reproducible1…
  • & transparent2

Solution

  • DRY WIT
    • Don’t Repeat Yourself
    • Write It Down

Computational notebooks

  • Automate as much as possible
  • Re-use text, code, figures

https://quarto.org

Wilson et al. (2014)

Wilson et al. (2014)

Wilson et al. (2014)

Installing the tools

Install R

https://cran.rstudio.com

Install RStudio

https://posit.co/download/rstudio-desktop/

Install Quarto

https://quarto.org/docs/get-started/

Launch RStudio

Case studies

Template repository

  • Hosted on GitHub
  • Sample files for you to explore
  • Hello World
  • Slides

https://github.com/penn-state-open-science/bootcamp-2025-quarto-I-template

In RStudio

Load the R packages

Open hello-world.qmd

Render the document

Inspect the HTML output

Edit, save, render, inspect (repeat)

Wrap-up

flowchart LR
  A(["Idea"]) --> B["Proposal"]
  B --> C("Project_1")
  B --> D("Project_2")
  C --> E["IRB_protocol"]
  D --> E
  C --> F["Lab_protocol"]
  D --> F
  C --> G["Data_pipeline_1"]
  D --> H["Data_pipeline_2"]
  B --> I["Conference_presentation"]
  F --> I
  G --> I
  C --> I
  I --> J["Journal_manuscript"]
  H --> K["Lab_mtg_report"]
  K --> J
  F --> J

A sample scholarly workflow

You have the power.

FAQs

  • Do I have to learn R?
  • What’s wrong with X (alternative tools)?
  • My adviser prefers X, what should I do?

Take homes

  • Quarto \(\rightarrow\) DRY WIT
  • Save time!
  • Reproducible to you \(\rightarrow\) reproducible to others
  • Quarto (Part II): Reproducible research reports (tomorrow 1:15p)

…If I have seen further it is by standing on the shoulders of Giants.

Newton to Robert Hooke, 1675

Sir Isaac Newton from Wikipedia

Resources

About

This talk was produced using Quarto, using the RStudio Integrated Development Environment (IDE), version 2025.5.1.513.

The source files are in R and R Markdown, then rendered to HTML using the revealJS framework. The HTML slides are hosted in a GitHub repo and served by GitHub pages: https://penn-state-open-science.github.io/bootcamp-2025-quarto-I/

References

Wilson, G., Aruliah, D. A., Brown, C. T., Chue Hong, N. P., Davis, M., Guy, R. T., … Wilson, P. (2014). Best practices for scientific computing. PLoS Biology, 12, e1001745. https://doi.org/10.1371/journal.pbio.1001745