Quarto for Scientific Reporting

an introduction and overview

Andrew Van Domelen
vandomea@myumanitoba.ca

University of Manitoba, Department of Biochemistry and Medical Genetics

2024-09-24

Land Acknowledgement

Land Acknowledgments

Overview

Scientific Reporting

Quarto and Rstudio

Quarto outputs

Extensions

Resources

Takeaways

Key Takeaways

  • Don’t quit the familiar tools!
  • Excelling at Quarto (and scientific communication) is an iterative process.
  • You are not alone
  • Make it easy for your audience

Scientific Reporting

Scientific Reporting

Reproducibility and Transparency

  • Methodological Documentation
  • Open Data and Code Sharing
  • Robust Data Management
  • Comprehensive Reporting of Results

Scientific Reporting

Our Role as Graduate Students

  • Methodological Documentation
  • Communication
    • Advisor, committee
    • Publications
    • Conferences
  • Mentoring other students

RStudio and Quarto

What is Rstudio?

  • Developed by Posit
  • User-friendly Integrated Development Environment (IDE)
    • write code, analyze data, and create visuals
  • R, python, command-line, others

What is Rstudio?

What is Quarto?

Brief Introduction

Developed by Posit

Publishing system

Wide variety of outputs

Transparent

Reproducible

What is Quarto?

Authoring Tools

Rstudio IDE

Jupyter Notebooks

Visual Studio Code

Neovim

Other text editors

What is Quarto?

Our Current System

Without Quarto
  • Google Docs
  • Microsoft Office
  • Data analysis platform
    • “cut-and-paste”
Using Quarto

Examples

Revealjs slides

Open source HTML framework

Endlessly customizable

Learning curve

source

See more at the Revealjs site

and on quarto.org

More RevealJS examples

Revealjs slides

Let’s look at an example Revealjs presentation

Other options for slides

Microsoft PowerPoint

Beamer (PDF)

HTML documents

Open source framework

Endlessly customizable

(smaller) learning curve

source

HTML documents

Let’s look at an example HTML document

Websites

Some great websites made in Quarto:

Websites with Quarto

PDF documents

HTML documents easily convert to PDFs

‘Article’ PDF

‘Report’ PDF

Two more great examples here:

PDFs with Quarto

Other options for documents

Microsoft Word

Typst

Still in development!

Dashboards

Have a lot of data to communicate?

Make it:

Interesting

Attractive

Accessible

Dashboards with Quarto

Extensions

Extensions

Pointer

Quiz

Molstar

FontAwesome

Journal Formatting

Extensions in Quarto

Helpful Resources

A Quarto tutorial website for UM students and staff

Key Takeaways

  • Don’t quit the familiar tools! Quarto makes beautiful, publication-quality outputs, but we still need Google Docs and Microsoft Office.
  • Excelling at Quarto (and scientific communication) is an iterative process. Learn what works then reuse it!
  • Quarto can be frustrating, but you’re not alone. We’re all solving problems.
  • Make it easy for your audience. We communicate for their sake.

Thank you!