R Markdown
The Definitive Guide
Chapman & Hall/CRC The R Series

R Markdown: The Definitive Guide is the first official book authored by the core R Markdown developers that provides a comprehensive and accurate reference to the R Markdown ecosystem. With R Markdown, you can easily create reproducible data analysis reports, presentations, dashboards, interactive applications, books, dissertations, websites, and journal articles, while enjoying the simplicity of Markdown and the great power of R and other languages.

In this book, you will learn

• Basics: Syntax of Markdown and R code chunks, how to generate figures and tables, and how to use other computing languages
• Built-in output formats of R Markdown: PDF/HTML/Word/RTF/Markdown documents and ioslides/Slidy/Beamer/PowerPoint presentations
• Extensions and applications: Dashboards, Tufte handouts, xaringan/reveal.js presentations, websites, books, journal articles, and interactive tutorials
• Advanced topics: Parameterized reports, HTML widgets, document templates, custom output formats, and Shiny documents.

Yihui Xie is a software engineer at RStudio. He has authored and co-authored several R packages, including knitr, rmarkdown, bookdown, blogdown, shiny, xaringan, and animation. He has published three other books, Dynamic Documents with R and knitr, bookdown: Authoring Books and Technical Documents with R Markdown, and blogdown: Creating Websites with R Markdown.

J.J. Allaire is the founder of RStudio and the creator of the RStudio IDE. He is an author of several packages in the R Markdown ecosystem including rmarkdown, flexdashboard, learnr, and radix.

Garrett Grolemund is the co-author of R for Data Science and author of Hands-On Programming with R. He wrote the lubridate R package and works for RStudio as an advocate who trains engineers to do data science with R and the Tidyverse.

I Get Started

1.Installation

2. Basics
Example applications
Airbnb’s knowledge repository
Homework assignments on RPubs
Personalized mails
Employer Health Benefits Survey
Journal articles
Dashboards at eelloo
Books
Websites
Compile an R Markdown document
Cheat sheets
Output formats
Markdown syntax
Inline formatting
Block-level elements
Math expressions
R code chunks and inline R code
Figures
Tables
Other language engines
Python
Shell scripts
SQL
Rcpp
Stan
JavaScript and CSS
Julia
C and Fortran
Interactive documents
HTML widgets
Shiny documents

II Output Formats

3. Documents HTML document
Table of contents
Section numbering
Tabbed sections
Appearance and style
Figure options
Data frame printing
Code folding
MathJax equations
Document dependencies
Advanced customization
Shared options
HTML fragments
Notebook
Using Notebooks
Saving and sharing
Notebook format
PDF document
Table of contents
Figure options
Data frame printing
Syntax highlighting
LaTeX options
LaTeX packages for citations
Advanced customization
Other features
Word document
Other features
OpenDocument Text document
Other features
Rich Text Format document
Other features
Markdown document
Markdown variants
Other features
R package vignette

4. Presentations
ioslides presentation
Display modes
Incremental bullets
Visual appearance
Code highlighting
Adding a logo
Tables
Advanced layout
Text color
Presenter mode
Printing and PDF output
Custom templates
Other features
Slidy presentation
Display modes
Text size
Footer elements
Other features
Beamer presentation
Themes
Slide level
Other features
PowerPoint presentation
Custom templates
Other features

III Extensions

5. Dashboards
Layout
Row-based layouts
Attributes on sections
Multiple pages
Story boards
Components
Value boxes
Gauges
Text annotations
Navigation bar
Shiny
Getting started
A Shiny dashboard example
Input sidebar
Learning more

6. Tufte Handouts
Headings
Figures
Margin figures
Arbitrary margin content
Full-width figures
Main column figures
Sidenotes
References
Tables
Block quotes
Responsiveness
Sans-serif fonts and epigraphs
Customize CSS styles

7. xaringan Presentations
Get started
Keyboard shortcuts
Slide formatting
Slides and properties
The title slide
Content classes
Incremental slides
Presenter notes
yolo: true
Build and preview slides
CSS and themes
Some tips
Autoplay slides
Countdown timer
Highlight code lines
Working offline
Macros
Disadvantages

8. revealjs Presentations
Display modes
Appearance and style
Smaller text
Slide transitions
Slide backgrounds
-D presentations
Custom CSS
Slide IDs and classes
Styling text spans
revealjs options
revealjs plugins
Other features

9. Community Formats
Lightweight Pretty HTML Documents
Usage
Package vignettes
The rmdformats package
Shower presentations

10. Websites
Get started
The directory structure
Deployment
Other site generators
rmarkdown’s site generator
A simple example
Site authoring
Common elements
Site navigation
HTML generation
Site configuration
Publishing websites
Additional examples
Custom site generators

11. HTML Documentation for R Packages
Get started
Components
Home page
Function reference
Articles
News
Navigation bar

12. Books
Get started
Project structure
Index file
Rmd files
_bookdownyml
_outputyml
Markdown extensions
Number and reference equations
Theorems and proofs
Special headers
Text references
Cross referencing
Output Formats
HTML
LaTeX/PDF
E-books
A single document
Editing
Build the book
Preview a chapter
Serve the book
RStudio addins
Publishing
RStudio Connect
Other services
Publishers

13. Journals
Get started
Articles templates
Using a template
LaTeX content
Linking with bookdown
Contributing templates

14. Interactive Tutorials
Get started
Tutorial types
Exercises
Solutions
Hints
Quiz questions
Videos
Shiny components
Navigation and progress tracking

IV Advanced Topics

15. Parameterized reports
Declaring parameters
Using parameters
Knitting with parameters
The Knit button
Knit with custom parameters
The interactive user interface
Publishing

16. HTML Widgets
Overview
A widget example (sigmajs)
File layout
Dependencies
R binding
JavaScript binding
Demo
Creating your own widgets
Requirements
Scaffolding
Other packages
Widget sizing
Specifying a sizing policy
JavaScript resize method
Advanced topics
Data transformation
Passing JavaScript functions
Custom widget HTML
Create a widget without an R package

17. Document Templates
Template structure
Supporting files
Custom Pandoc templates
Sharing your templates

18. Creating New Formats
Deriving from built-in formats
Fully custom formats
Using a new format

19. Shiny Documents
Getting started
Deployment
ShinyAppsio
Shiny Server / RStudio Connect
Embedded Shiny apps
Inline applications
External applications
Shiny widgets
The shinyApp() function
Example: k-Means clustering
Widget size and layout
Multiple pages
Delayed rendering
Output arguments for render functions
A caveat

Yihui Xie is a software engineer at RStudio. He has authored and co-authored several R packages, including knitr, rmarkdown, bookdown, blogdown, shiny, xaringan, and animation. He has published three other books, Dynamic Documents with R and knitr, bookdown: Authoring Books and Technical Documents with R Markdown, and blogdown: Creating Websites with R Markdown.

J.J. Allaire is the founder of RStudio and the creator of the RStudio IDE. He is an author of several packages in the R Markdown ecosystem including rmarkdown, flexdashboard, learnr, and radix.

Garrett Grolemund is the co-author of R for Data Science and author of Hands-On Programming with R. He wrote the lubridate R package and works for RStudio as an advocate who trains engineers to do data science with R and the Tidyverse.