book

Dynamic Documents with R and knitr, 2nd Edition

Name: Dynamic Documents with R and knitr, 2nd Edition
Author: Yihui Xie
ISBN: 9781315360706

by Yihui Xie

July 2017

Intermediate to advanced

294 pages

5h 43m

English

Chapman and Hall/CRC

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Cover
Title Page
Copyright Page
Dedication
Table of Contents
Preface
Author
List of Figures
List of Tables
1 Introduction

2 Reproducible Research
2.1 Literature2.2 Good and Bad Practices2.3 Barriers
3 A First Look
3.1 Setup3.2 Minimal Examples3.2.1 An Example in LATEX3.2.2 An Example in Markdown3.3 Quick Reporting3.4 Extracting R Code
4 Editors
4.1 RStudio4.2 LYX4.3 Emacs/ESS4.4 Other Editors
5 Document Formats
5.1 Input Syntax5.1.1 Chunk Options5.1.2 Chunk Label5.1.3 Global Options5.1.4 Chunk Syntax5.2 Document Formats5.2.1 Markdown5.2.2 LATEX5.2.3 HTML5.2.4 reStructuredText5.2.5 AsciiDoc5.2.6 Textile5.2.7 Customization5.3 Output Renderers5.4 R Scripts
6 Text Output
6.1 Inline Output6.2 Chunk Output6.2.1 Chunk Evaluation6.2.2 Code Formatting6.2.3 Code Decoration6.2.4 Show/Hide Output6.2.5 Collapse Output6.2.6 Trim Blank Lines6.3 Tables6.4 Automatic Printing6.5 Themes
7 Graphics
7.1 Graphical Devices7.1.1 Custom Device7.1.2 Choose a Device7.1.3 Device Size7.1.4 More Device Options7.1.5 Encoding7.1.6 The Dingbats Font7.2 Plot Recording7.3 Plot Rearrangement7.3.1 Animation7.3.2 Alignment7.4 Plot Size in Output7.5 Extra Output Options7.6 The tikz() Device7.7 Figure Environment7.8 Figure Path
8 Cache
8.1 Implementation8.2 Write Cache8.3 When to Update Cache8.4 Side Effects8.5 Chunk Dependencies8.5.1 Manual Dependency8.5.2 Automatic Dependency8.6 Load Cache Manually8.7 Other Options
9 Cross Reference
9.1 Chunk Reference9.1.1 Embed Code Chunks9.1.2 Reuse Whole Chunks9.2 Code Externalization9.2.1 Labeled Chunks9.2.2 Line-Based Chunks9.3 Child Documents9.3.1 Input Child Documents9.3.2 Child Documents as Templates9.3.3 Standalone Mode
10 Hooks
10.1 Chunk Hooks10.1.1 Create Chunk Hooks10.1.2 Trigger Chunk Hooks10.1.3 Hook Arguments10.1.4 Hooks and Chunk Options10.1.5 Write Output10.2 Examples10.2.1 Crop Plots10.2.2 rgl Plots10.2.3 Manually Save Plots10.2.4 Optimize PNG Plots10.2.5 Close an rgl Device10.2.6 WebGL
11 Language Engines
11.1 Design11.1.1 The Engine Function11.1.2 Engine Options11.2 Languages and Tools11.2.1 C++11.2.2 C/Fortran11.2.3 Interpreted Languages11.2.4 Stan11.2.5 TikZ11.2.6 Graphviz11.2.7 Highlight11.2.8 Other Engines11.3 Persistent Sessions
12 Tricks and Solutions
12.1 Chunk Options12.1.1 Option Aliases12.1.2 Option Templates12.1.3 Program Chunk Options12.1.4 Code in Appendix12.1.5 Local R Options12.1.6 Dynamic Code12.2 Package Options12.3 Typesetting12.3.1 Output Width12.3.2 Message Colors12.3.3 Box Padding12.3.4 Beamer12.3.5 Suppress Long Output12.3.6 Escape Special Characters12.3.7 The Example Environment12.3.8 The Docco Style12.4 Utilities12.4.1 R Package Citation12.4.2 Image URI12.4.3 Upload Images12.4.4 Compile Documents12.4.5 Construct Code Chunks12.4.6 Extract Source Code12.4.7 Reproducible Simulation12.4.8 R Documentation12.4.9 Rst2pdf12.4.10 Package Demos12.4.11 Pretty Printing12.4.12 A Macro Preprocessor12.4.13 Exit Knitting Early12.4.14 Literal knitr Source Code12.4.15 Spell Checking12.5 Debugging12.6 Multilingual Support
13 Publishing Reports
13.1 RStudio13.2 Pandoc13.3 HTML5 Slides13.4 Jekyll13.5 WordPress
14 R Markdown
14.1 Overview14.2 Pandoc’s Markdown Extensions14.2.1 Basic Syntax14.2.2 YAML Metadata14.3 Output Formats14.3.1 HTML Document14.3.2 LATEX/PDF Document14.3.3 Word Document14.3.4 Markdown Documents14.3.5 ioslides Presentation14.3.6 Slidy Presentation14.3.7 Beamer Presentation14.3.8 Other Formats14.4 Interactive Documents with Shiny14.5 Extending R Markdown v214.5.1 Templates14.5.2 New Formats14.5.3 HTML Widgets14.6 Changes in R Markdown from v1 to v2
15 Applications
15.1 Homework15.2 Serve Dynamic Documents15.3 Website and Blogging15.3.1 Vistat and Rcpp Gallery15.3.2 UCLA R Tutorial15.3.3 The cda and RHadoop Wiki15.3.4 The ggbio Package15.3.5 Geospatial Data in R and Beyond15.4 Package Vignettes15.4.1 Vignette Metadata and Engines15.4.2 Vignette Examples15.4.3 PDF Vignette15.4.4 HTML Vignette15.5 Books15.5.1 This Book15.5.2 The Analysis of Data15.5.3 The Statistical Sleuth in R15.5.4 Text Analysis with R for Students of Literature15.6 Literate Programming for R Packages
16 Other Tools
16.1 Sweave16.1.1 Syntax16.1.2 Options16.1.3 Problems16.2 Other R Packages16.3 Python Packages16.3.1 Dexy16.3.2 PythonTEX16.3.3 IPython16.4 More Tools16.4.1 Org-mode16.4.2 SASweave16.4.3 Office
Appendix
A InternalsA.1 DocumentationA.2 ClosuresA.3 ImplementationA.3.1 ParserA.3.2 Chunk HooksA.3.3 Option AliasesA.3.4 CacheA.3.5 Compatibility with SweaveA.3.6 ConcordanceA.4 Syntax
Bibliography
Index

Content preview from Dynamic Documents with R and knitr, 2nd Edition

List of Figures

1.1	A simulation of Brownian motion
3.1	The source of a minimal Rnw document
3.2	A minimal example in
3.3	The source of a minimal Rmd document
3.4	A minimal example in Markdown
4.1	Edit an Rnw document in RStudio
4.2	Edit an Rmd document in RStudio
4.3	Using knitr in L_YX
5.1	The Sweave style in knitr
5.2	The listings style in knitr
7.1	A plot created in ggplot2 that does not need to be printed explicitly
7.2	A plot using the Bookman font family
7.3	A table of the Windows-1250 code page
7.4	Three expressions produced two plots
7.5	All high-level plots are captured
7.6	Show plots right below the ...

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Reproducible Research and Reports with R Markdown

Publisher Resources

ISBN: 9781315360706

Cloud Computing

Data Engineering

Data Science

AI & ML

Programming Languages

Software Architecture

IT/Ops

Security

Design

Business

Soft Skills

Dynamic Documents with R and knitr, 2nd Edition

by Yihui Xie

Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
and much more.