Quarto for Scientists

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 be reproduced by anyone with a computer.

About this

This is a book on rmarkdown, aimed for scientists. It was initially developed as a 3 hour workshop, but is now developed into a resource that will grow and change over time as a living book.

This book aims to teach the following:

• Getting started with your own R Markdown document
• Improve workflow:
  • With RStudio projects
  • Using keyboard shortcuts
• Export your R Markdown document 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 creating an R Markdown 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 R Markdown
• Next steps in working with rmarkdown - how to extend yourself to other rmarkdown formats

Why write this as a book?

There are many great books on R Markdown and it’s various features, such as “Rmarkdown: The definitive guide”, “bookdown: Authoring Books and Technical Documents with R Markdown”, and “Dynamic Documents with R and knitr, Second edition”, and Yihui Xie’s thesis, “Dynamic Graphics and Reporting for Statistics”.

So why write a book?

Good question. The answer is that writing this as a book provides a way for me to structure the content in the form of a workshop, in a way suitable for learning in a few hours.

How to use this book

This book was written to provide course materials for a 3 hour course on R Markdown.

We worked through the following sections in the book in 3 hours:

• Why use R Markdown
• Installation
• what is RStudio?
• suggested workflow and hygiene
• how to use R Markdown
• using R Markdown with pdf, html, and Word
• what are some useful keyboard shortcuts
• Adding captions to tables and figures
• Changing figures
• Adding mathematics
• Citing figures and tables
• Changing citations and styles

With the remaining sections being used as extra material, or have since been written after the course:

• Fixing some common problems in R Markdown
• What are some alternative outputs of R Markdown?
• Where to go next?
• Suggested references

Course materials can be downloaded by using the following command from the usethis package:

usethis::use_course("bit.ly/rmd4sci-materials")

Where has this course been taught?

So far I have taught this rmarkdown for science course at the following locations:

• 2018
  • Melbourne, November for SSA Victoria
• 2019
  • Melbourne, April, for Monash University
  • Canberra, July, for SSA Victoria
  • Melbourne, November, for AIMOS2019
  • Melbourne, December, for Plant Pathology Conference
• 2020
  • Seattle, February, for University of Washington

Licence

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