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Dedication
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Dedication
by Yihui Xie
Dynamic Documents with R and knitr, 2nd Edition
Cover
Title Page
Copyright Page
Dedication
Table of 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 LATEX
3.2.2 An Example in Markdown
3.3 Quick Reporting
3.4 Extracting R Code
4 Editors
4.1 RStudio
4.2 LYX
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 LATEX
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 PythonTEX
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
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To my parents
Shaobai Xie
and
Guolan Xie
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