Contents

Preface

Author

List of Figures

List of Tables

1      Introduction

2      Reproducible Research

2.1      Literature

2.2      Good and Bad Practices

2.3      Barriers

3      A First Look

3.1      Setup

3.2      Minimal Examples

3.2.1      An Example in

3.2.2      An Example in Markdown

3.3      Quick Reporting

3.4      Extracting R Code

4      Editors

4.1      RStudio

4.2      L_YX

4.3      Emacs/ESS

4.4      Other Editors

5      Document Formats

5.1      Input Syntax

5.1.1      Chunk Options

5.1.2      Chunk Label

5.1.3      Global Options

5.1.4      Chunk Syntax

5.2      Document Formats

5.2.1      Markdown

5.2.2      L^ATEX

5.2.3      HTML

5.2.4      reStructuredText

5.2.5      AsciiDoc

5.2.6      Textile

5.2.7      Customization

5.3      Output Renderers

5.4      R Scripts

6      Text Output

6.1      Inline Output

6.2      Chunk Output

6.2.1      Chunk Evaluation

6.2.2      Code Formatting

6.2.3      Code Decoration

6.2.4      Show/Hide Output

6.2.5      Collapse Output

6.2.6      Trim Blank Lines

6.3      Tables

6.4      Automatic Printing

6.5      Themes

7      Graphics

7.1      Graphical Devices

7.1.1      Custom Device

7.1.2      Choose a Device

7.1.3      Device Size

7.1.4      More Device Options

7.1.5      Encoding

7.1.6      The Dingbats Font

7.2      Plot Recording

7.3      Plot Rearrangement

7.3.1      Animation

7.3.2      Alignment

7.4      Plot Size in Output

7.5      Extra Output Options

7.6      The tikz() Device

7.7      Figure Environment

7.8      Figure Path

8      Cache

8.1      Implementation

8.2      Write Cache

8.3      When to Update Cache

8.4      Side Effects

8.5      Chunk Dependencies

8.5.1      Manual Dependency

8.5.2      Automatic Dependency

8.6      Load Cache Manually

8.7      Other Options

9      Cross Reference

9.1      Chunk Reference

9.1.1      Embed Code Chunks

9.1.2      Reuse Whole Chunks

9.2      Code Externalization

9.2.1      Labeled Chunks

9.2.2      Line-Based Chunks

9.3      Child Documents

9.3.1      Input Child Documents

9.3.2      Child Documents as Templates

9.3.3      Standalone Mode

10    Hooks

10.1    Chunk Hooks

10.1.1    Create Chunk Hooks

10.1.2    Trigger Chunk Hooks

10.1.3    Hook Arguments

10.1.4    Hooks and Chunk Options

10.1.5    Write Output

10.2    Examples

10.2.1    Crop Plots

10.2.2    rgl Plots

10.2.3    Manually Save Plots

10.2.4    Optimize PNG Plots

10.2.5    Close an rgl Device

10.2.6    WebGL

11    Language Engines

11.1    Design

11.1.1    The Engine Function

11.1.2    Engine Options

11.2    Languages and Tools

11.2.1    C++

11.2.2    C/Fortran

11.2.3    Interpreted Languages

11.2.4    Stan

11.2.5    TikZ

11.2.6    Graphviz

11.2.7    Highlight

11.2.8    Other Engines

11.3    Persistent Sessions

12    Tricks and Solutions

12.1    Chunk Options

12.1.1    Option Aliases

12.1.2    Option Templates

12.1.3    Program Chunk Options

12.1.4    Code in Appendix

12.1.5    Local R Options

12.1.6    Dynamic Code

12.2    Package Options

12.3    Typesetting

12.3.1    Output Width

12.3.2    Message Colors

12.3.3    Box Padding

12.3.4    Beamer

12.3.5    Suppress Long Output

12.3.6    Escape Special Characters

12.3.7    The Example Environment

12.3.8    The Docco Style

12.4    Utilities

12.4.1    R Package Citation

12.4.2    Image URI

12.4.3    Upload Images

12.4.4    Compile Documents

12.4.5    Construct Code Chunks

12.4.6    Extract Source Code

12.4.7    Reproducible Simulation

12.4.8    R Documentation

12.4.9    Rst2pdf

12.4.10  Package Demos

12.4.11  Pretty Printing

12.4.12  A Macro Preprocessor

12.4.13  Exit Knitting Early

12.4.14  Literal knitr Source Code

12.4.15  Spell Checking

12.5    Debugging

12.6    Multilingual Support

13    Publishing Reports

13.1    RStudio

13.2    Pandoc

13.3    HTML5 Slides

13.4    Jekyll

13.5    WordPress

14    R Markdown

14.1    Overview

14.2    Pandoc’s Markdown Extensions

14.2.1    Basic Syntax

14.2.2    YAML Metadata

14.3    Output Formats

14.3.1    HTML Document

14.3.2    LATEX/PDF Document

14.3.3    Word Document

14.3.4    Markdown Documents

14.3.5    ioslides Presentation

14.3.6    Slidy Presentation

14.3.7    Beamer Presentation

14.3.8    Other Formats

14.4    Interactive Documents with Shiny

14.5    Extending R Markdown v2

14.5.1    Templates

14.5.2    New Formats

14.5.3    HTML Widgets

14.6    Changes in R Markdown from v1 to v2

15    Applications

15.1    Homework

15.2    Serve Dynamic Documents

15.3    Website and Blogging

15.3.1    Vistat and Rcpp Gallery

15.3.2    UCLA R Tutorial

15.3.3    The cda and RHadoop Wiki

15.3.4    The ggbio Package

15.3.5    Geospatial Data in R and Beyond

15.4    Package Vignettes

15.4.1    Vignette Metadata and Engines

15.4.2    Vignette Examples

15.4.3    PDF Vignette

15.4.4    HTML Vignette

15.5    Books

15.5.1    This Book

15.5.2    The Analysis of Data

15.5.3    The Statistical Sleuth in R

15.5.4    Text Analysis with R for Students of Literature

15.6    Literate Programming for R Packages

16    Other Tools

16.1    Sweave

16.1.1    Syntax

16.1.2    Options

16.1.3    Problems

16.2    Other R Packages

16.3    Python Packages

16.3.1    Dexy

16.3.2    PythonT_EX

16.3.3    IPython

16.4    More Tools

16.4.1    Org-mode

16.4.2    SASweave

16.4.3    Office

Appendix

A      Internals

A.1      Documentation

A.2      Closures

A.3      Implementation

A.3.1      Parser

A.3.2      Chunk Hooks

A.3.3      Option Aliases

A.3.4      Cache

A.3.5      Compatibility with Sweave

A.3.6      Concordance

A.4      Syntax

Bibliography

Index