Quarto for Scientists

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

This is a course on how to use Quarto, with the target audience being for scientists. This was first developed as a short workshop on rmarkdown, as the book "rmarkdown for scientists". The general structure will be the same, and it will grow and change over time as a living book.

Structure of the workshop

This online book covers more content than the workshop. Here's an example structure of a 3.5 hour course.

time	topic
1:30-1:40	Get started with your own Quarto document
1:40-2:00	Workflow when using Quarto documents and projects
2:00-2:20	Exporting Quarto documents to PDF, HTML, and Microsoft Word
2:30-3:00	BREAK
3:00-3:30	Managing captions, figures, tables
3:30-3:45	Managing equations and bibliographies
3:45-4:15	How to debug and handle common errors
3:45-5:00	Free time for discussion around aother Quarto formats: websites, blogs, slides, and more!

Learning outcomes

After completing this course, you will know how to:

Create your own Quarto document
Create figures and tables that you can reference in text, and update with - your data
Export your Quarto document to PDF, HTML, and Microsoft Word
Use keyboard shortcuts to improve workflow
Cite research articles and generate a bibliography

We may, depending on time, also cover the following areas:

Change the size and type of your figures
Create captions for your figures, and reference them in text
Cite research articles and generate a bibliography
Debug and handle common errors

Getting Started

See the installation chapter for details on software to be installed.

Working materials will be made available at github.com/njtierney/qmd4sci-materials.

Book

Book aims

This book aims to teach the following:

Getting started with your own Quarto document
- Using Rstudio
- Visual Studio Code
Improve workflow:
- RStudio
- Demonstrate rstudio projects
- Using keyboard shortcuts
- Quarto projects
Export your Quarto documents to PDF, HTML, and Microsoft Word
Better manage figures and tables
- Reference figures and tables in text so that they dynamically update
- Create captions for figures and tables
- Change the size and type of figures
- Save the figures to disk when rendering a document
Work with equations
- Inline and display
- Caption equations
- Reference equations
Manage bibliographies
- Cite articles in text
- Generate bibliographies
- Change bibliography styles
Debug and handle common errors with Quarto
Next steps in working with Quarto:
- How to extend yourself to other formats, such as slides, websites, books, and more

Abstract aka "why should you read this"

For a scientific report to be completely credible, it must be reproducible. The full computational environment used to derive the results, including the data and code used for statistical analysis should be available for others to reproduce.

Quarto is a tool that allows you integrate your code, text and figures in a single file in order to make high quality, reproducible reports. A paper published with an included Quarto file and data sets can (in principle) be reproduced by anyone with a computer.

Future / extensions

Tentatively, there will also be a new part to this book, which discusses how to use Quarto in a targets pipeline. This is now my preferred way to work when starting new projects, and it draws heavily from Miles McBain's ergonomic workflow packages, tflow, fnmate, capsule, most of which are demonstrated in his blog post, "Benefits of a function-based diet (The {drake} post)".

License