Introduction
Reproducible Research
Literature
Good and Bad Practices
Barriers
A First Look
Setup
Minimal Examples
Quick Reporting
Extracting R Code
Editors
RStudio
LYX
Emacs/ESS
Other Editors
Document Formats
Input Syntax
Document Formats
Output Renderers
R Scripts
Text Output
Inline Output
Chunk Output
Tables
Automatic Printing
Themes
Graphics
Graphical Devices
Plot Recording
Plot Rearrangement
Plot Size in Output
Extra Output Options
The tikz Device
Figure Environment
Figure Path
Cache
Implementation
Write Cache
When to Update Cache
Side Effects
Chunk Dependencies
Load Cache Manually
Other Options
Cross Reference
Chunk Reference
Code Externalization
Child Documents
Hooks
Chunk Hooks
Examples
Language Engines
Design
Languages and Tools
Persistent Sessions
Tricks and Solutions
Chunk Options
Package Options
Typesetting
Utilities
Debugging
Multilingual Support
Publishing Reports
RStudio
Pandoc
HTML5 Slides
Jekyll
WordPress
R Markdown
Overview
Pandoc’s Markdown Extensions
Output Formats
Interactive Documents with Shiny
Extending R Markdown v2
Changes in R Markdown from v1 to v2
Applications
Homework
Serve Dynamic Documents
Web Site and Blogging
Package Vignettes
Books
Literate Programming for R Packages
Other Tools
Sweave
Other R Packages
Python Packages
More Tools
Appendix: Internals
Bibliography
Index