RMarkdown for Scientists
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
0.1 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.
0.2 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
- 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
0.3 Where has this course been taught?
So far I have taught this rmarkdown for science course at the following locations:
- Melbourne, November for SSA Victoria
- Melbourne, April, for Monash University
- Canberra, July, for SSA Victoria
- Melbourne, November, for AIMOS2019
- Melbourne, December, for Plant Pathology Conference
- Seattle, February, for University of Washington
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.