Table of Contents

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
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

Cross Reference 79
Chunk Reference
Code Externalization
Child Documents

Hooks
Chunk Hooks
Examples

Language Engines
Design
Languages and Tools

Tricks and Solutions
Chunk Options
Package Options
Typesetting
Utilities
Debugging
Multilingual Support

Publishing Reports
RStudio
Pandoc
HTML5 Slides
Jekyll
WordPress

Applications
Homework
Web Site and Blogging
Package Vignettes
Books

Other Tools
Sweave
Other R Packages
Python Packages
More Tools

Internals
Documentation
Closures
Implementation
A.4 Syntax
Bibliography
Index

Reviews

"… a great source for beginners and advanced users of knitr alike. The author writes with much wit and charm. … a valuable resource for everybody who is interested in reproducible research in general and who wants to easily generate reproducible reports in particular, i.e., a must read for every applied statistician! Learning knitr and getting some tips and tricks is, most of the time, easy and fun with this book."
—ISCB News, 59, June 2015 "After reading Dynamic Documents with R and knitr, … I became a fan of this package and its flexibility. The book is written in a conversational style that gives a clear and practical introduction to knitr for both beginners and advanced users. … Compared with Sweave, knitr is more powerful. … Furthermore, knitr is more flexible than Sweave. … Most impressively, caching can be incorporated in a simple way by knitr. … The book is readable with a clear overall structure. … this book allows us to enhance our knowledge of knitr’s usage and quickly find what we want."
—The American Statistician, February 2015 "The book provides a systematic description of the package [knitr], including its concepts, design principles, and philosophy. It also has many examples, well-thought out advice, and useful tips and tricks. … The book is well written. It has introductory material useful for novices as well as advice for more seasoned users, all explained in conversational English without unnecessary technical jargon. … While I have been using Sweave and then knitr for several years, I still learned many new useful things from the book. … the book deserves a place on the bookshelves of both new and experienced R and TeX users."
—Boris Veytsman, TUGboat, Volume 35, 2014 "If you are looking to learn how to use knitr, this book is for you. There are a limited number of resources for learning knitr because the package is relatively new and the documentation produced by Xie is so good. … I think this book will continue to be the best resource about knitr …easy to understand … this is a great read and handy desk reference for the regular knitr user."
—Journal of Statistical Software, January 2014 "Three recent books have significantly influenced how I use R in reproducible work: Dynamic Documents with R and knitr by Yihui Xie, Reproducible Research with R and RStudio by Christopher Gandrud, and Implementing Reproducible Research edited by Victoria Stodden, Friedrich Leisch, and Roger D. Peng … I recommend all three books to R users at any level. There really is something here for everyone."
—Richard Layton, PhD, PE, Rose-Hulman Institute of Technology, Terre Haute, Indiana, USA