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.
Preface
How to read this book
Structure of the book
Software information and conventions
Acknowledgments
About the Authors
?Yihui Xie
?J.J. Allaire
?Garrett Grolemund
I Get Started
1 Installation
2 Basics
?2.1 Example applications
?2.1.1 Airbnbs knowledge repository
?2.1.2 Homework assignments on RPubs
?2.1.3 Personalized mails
?2.1.4 2017 Employer Health Benefits Survey
?2.1.5 Journal articles
?2.1.6 Dashboards at eelloo
?2.1.7 Books
?2.1.8 Websites
?2.2 Compile an R Markdown document
?2.3 Cheat sheets
?2.4 Output formats
?2.5 Markdown syntax
?2.5.1 Inline formatting
?2.5.2 Block-level elements
?2.5.3 Math expressions
?2.6 R code chunks and inline R code
?2.6.1 Figures
?2.6.2 Tables
?2.7 Other language engines
?2.7.1 Python
?2.7.2 Shell scripts
?2.7.3 SQL
?2.7.4 Rcpp
?2.7.5 Stan
?2.7.6 JavaScript and CSS
?2.7.7 Julia
?2.7.8 C and Fortran
?2.8 Interactive documents
?2.8.1 HTML widgets
?2.8.2 Shiny documents
II Output Formats
3 Documents
?3.1 HTML document
?3.1.1 Table of contents
?3.1.2 Section numbering
?3.1.3 Tabbed sections
?3.1.4 Appearance and style
?3.1.5 Figure options
?3.1.6 Data frame printing
?3.1.7 Code folding
?3.1.8 MathJax equations
?3.1.9 Document dependencies
?3.1.10 Advanced customization
?3.1.11 Shared options
?3.1.12 HTML fragments
?3.2 Notebook
?3.2.1 Using Notebooks
?3.2.2 Saving and sharing
?3.2.3 Notebook format
?3.3 PDF document
?3.3.1 Table of contents
?3.3.2 Figure options
?3.3.3 Data frame printing
?3.3.4 Syntax highlighting
?3.3.5 LaTeX options
?3.3.6 LaTeX packages for citations
?3.3.7 Advanced customization
?3.3.8 Other features
?3.4 Word document
?3.4.1 Other features
?3.5 OpenDocument Text document
?3.5.1 Other features
?3.6 Rich Text Format document
?3.6.1 Other features
?3.7 Markdown document
?3.7.1 Markdown variants
?3.7.2 Other features
?3.8 R package vignette
4 Presentations
?4.1 ioslides presentation
?4.1.1 Display modes
?4.1.2 Incremental bullets
?4.1.3 Visual appearance
?4.1.4 Code highlighting
?4.1.5 Adding a logo
?4.1.6 Tables
?4.1.7 Advanced layout
?4.1.8 Text color
?4.1.9 Presenter mode
?4.1.10 Printing and PDF output
?4.1.11 Custom templates
?4.1.12 Other features
?4.2 Slidy presentation
?4.2.1 Display modes
?4.2.2 Text size
?4.2.3 Footer elements
?4.2.4 Other features
?4.3 Beamer presentation
?4.3.1 Themes
?4.3.2 Slide level
?4.3.3 Other features
?4.4 PowerPoint presentation
?4.4.1 Custom templates
?4.4.2 Other features
III Extensions
5 Dashboards
?5.1 Layout
?5.1.1 Row-based layouts
?5.1.2 Attributes on sections
?5.1.3 Multiple pages
?5.1.4 Story boards
?5.2 Components
?5.2.1 Value boxes
?5.2.2 Gauges
?5.2.3 Text annotations
?5.2.4 Navigation bar
?5.3 Shiny
?5.3.1 Getting started
?5.3.2 A Shiny dashboard example
?5.3.3 Input sidebar
?5.3.4 Learning more
6 Tufte Handouts
?6.1 Headings
?6.2 Figures
?6.2.1 Margin figures
?6.2.2 Arbitrary margin content
?6.2.3 Full-width figures
?6.2.4 Main column figures
?6.3 Sidenotes
?6.4 References
?6.5 Tables
?6.6 Block quotes
?6.7 Responsiveness
?6.8 Sans-serif fonts and epigraphs
?6.9 Customize CSS styles
7 xaringan Presentations
?7.1 Get started
?7.2 Keyboard shortcuts
?7.3 Slide formatting
?7.3.1 Slides and properties
?7.3.2 The title slide
?7.3.3 Content classes
?7.3.4 Incremental slides
?7.3.5 Presenter notes
?7.3.6 yolo: true
?7.4 Build and preview slides
?7.5 CSS and themes
?7.6 Some tips
?7.6.1 Autoplay slides
?7.6.2 Countdown timer
?7.6.3 Highlight code lines
?7.6.4 Working offline
?7.6.5 Macros
?7.6.6 Disadvantages
8 reveal.js Presentations
?8.1 Display modes
?8.2 Appearance and style
?8.2.1 Smaller text
?8.3 Slide transitions
?8.4 Slide backgrounds
?8.5 2-D presenations
?8.6 Custom CSS
?8.6.1 Slide IDs and classes
?8.6.2 Styling text spans
?8.7 reveal.js options
?8.8 reveal.js plugins
?8.9 Other features
9 Community Formats
?9.1 Lightweight Pretty HTML Documents
?9.1.1 Usage
?9.1.2 Package vignettes
?9.2 The rmdformats package
?9.3 Shower presentations
10 Websites
?10.1 Get started
?10.2 The directory structure
?10.3 Deployment
?10.4 Other site generators
?10.5 rmarkdowns site generator
?10.5.1 A simple example
?10.5.2 Site authoring
?10.5.3 Common elements
?10.5.4 Site navigation
?10.5.5 HTML generation
?10.5.6 Site configuration
?10.5.7 Publishing websites
?10.5.8 Additional examples
?10.5.9 Custom site generators
11 HTML Documentation for R Packages
?11.1 Get started
?11.2 Components
?11.2.1 Home page
?11.2.2 Function reference
?11.2.3 Articles
?11.2.4 News
?11.2.5 Navigation bar
12 Books
?12.1 Get started
?12.2 Project structure
?12.2.1 Index file
?12.2.2 Rmd files
?12.2.3 _bookdown.yml
?12.2.4 _output.yml
?12.3 Markdown extensions
?12.3.1 Number and reference equations
?12.3.2 Theorems and proofs
?12.3.3 Special headers
?12.3.4 Text references
?12.3.5 Cross referencing
?12.4 Output Formats
?12.4.1 HTML
?12.4.2 LaTeX/PDF
?12.4.3 E-books
?12.4.4 A single document
?12.5 Editing
?12.5.1 Build the book
?12.5.2 Preview a chapter
?12.5.3 Serve the book
?12.5.4 RStudio addins
?12.6 Publishing
?12.6.1 RStudio Connect
?12.6.2 Other services
?12.6.3 Publishers
13 Journals
?13.1 Get started
?13.2 rticles templates
?13.3 Using a template
?13.4 LaTeX content
?13.5 Linking with bookdown
?13.6 Contributing templates
14 Interactive Tutorials
?14.1 Get started
?14.2 Tutorial types
?14.3 Exercises
?14.3.1 Solutions
?14.3.2 Hints
?14.4 Quiz questions
?14.5 Videos
?14.6 Shiny components
?14.7 Navigation and progress tracking
IV Other Topics
15 Parameterized reports
?15.1 Declaring parameters
?15.2 Using parameters
?15.3 Knitting with parameters
?15.3.1 The Knit button
?15.3.2 Knit with custom parameters
?15.3.3 The interactive user interface
?15.4 Publishing
16 HTML Widgets
?16.1 Overview
?16.2 A widget example (sigma.js)
?16.2.1 File layout
?16.2.2 Dependencies
?16.2.3 R binding
?16.2.4 JavaScript binding
?16.2.5 Demo
?16.3 Creating your own widgets
?16.3.1 Requirements
?16.3.2 Scaffolding
?16.3.3 Other packages
?16.4 Widget sizing
?16.4.1 Specifying a sizing policy
?16.4.2 JavaScript resize method
?16.5 Advanced topics
?16.5.1 Data transformation
?16.5.2 Passing JavaScript functions
?16.5.3 Custom widget HTML
?16.5.4 Create a widget without an R package
17 Document Templates
?17.1 Template structure
?17.2 Supporting files
?17.3 Custom Pandoc templates
?17.4 Sharing your templates
18 Creating New Formats
?18.1 Deriving from built-in formats
?18.2 Fully custom formats
?18.3 Using a new format
19 Shiny Documents
?19.1 Getting started
?19.2 Deployment
?19.2.1 ShinyApps.io
?19.2.2 Shiny Server / RStudio Connect
?19.3 Embedded Shiny apps
?19.3.1 Inline applications
?19.3.2 External applications
?19.4 Shiny widgets
?19.4.1 The shinyApp() function
?19.4.2 Example: k-Means clustering
?19.4.3 Widget size and layout
?19.5 Multiple pages
?19.6 Delayed rendering
?19.7 Output arguments for render functions
?19.7.1 A caveat
References
