Dynamic Documents with R and knitr
1st Edition
Published on 10. September 2013
Book
Paperback/Softback
216 pages
978-1-4822-0353-0 (ISBN)
Description
The cut-and-paste approach to writing statistical reports is not only tedious and laborious, but also can be harmful to scientific research, because it is inconvenient to reproduce the results. Dynamic Documents with R and knitr introduces a new approach via dynamic documents, i.e. integrating computing directly with reporting. A comprehensive guide to the R package knitr, the book covers examples, document editors, basic usage, detailed explanations of a wide range of options, tricks and solutions, extensions, and complete applications of this package.
The book provides an overview of dynamic documents, introducing the idea of literate programming. It then explains the importance of dynamic documents to scientific research and its impact on reproducible research. Building on this, the author covers basic concepts, common text editors that support knitr, and the syntax for different document formats such as LaTeX, HTML, and Markdown before going on to discuss core functionality, how to control text and graphics output, caching mechanisms that can reduce computation time, and reuse of source code. He then explores advanced topics such as chunk hooks, integrating other languages such as Python and awk into one report in the knitr framework, and useful tricks that make it easier to write documents with knitr. Discussions of how to publish reports in a variety of formats, applications, and other tools complete the coverage.
Suitable for both beginners and advanced users, this book shows you how to write reports in simple languages such as Markdown. The reports range from homework, projects, exams, books, blogs, and web pages to any documents related to statistical graphics, computing, and data analysis. While familiarity with LaTeX and HTML is helpful, the book requires no prior experience with advanced programs or languages. For beginners, the text provides enough features to get started on basic applications. For power users, the last several chapters enable an understanding of the extensibility of the knitr package.
The book provides an overview of dynamic documents, introducing the idea of literate programming. It then explains the importance of dynamic documents to scientific research and its impact on reproducible research. Building on this, the author covers basic concepts, common text editors that support knitr, and the syntax for different document formats such as LaTeX, HTML, and Markdown before going on to discuss core functionality, how to control text and graphics output, caching mechanisms that can reduce computation time, and reuse of source code. He then explores advanced topics such as chunk hooks, integrating other languages such as Python and awk into one report in the knitr framework, and useful tricks that make it easier to write documents with knitr. Discussions of how to publish reports in a variety of formats, applications, and other tools complete the coverage.
Suitable for both beginners and advanced users, this book shows you how to write reports in simple languages such as Markdown. The reports range from homework, projects, exams, books, blogs, and web pages to any documents related to statistical graphics, computing, and data analysis. While familiarity with LaTeX and HTML is helpful, the book requires no prior experience with advanced programs or languages. For beginners, the text provides enough features to get started on basic applications. For power users, the last several chapters enable an understanding of the extensibility of the knitr package.
Reviews / Votes
"... 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
More details
Series
Language
English
Place of publication
London
United Kingdom
Publishing group
Taylor & Francis Ltd
Target group
College/higher education
Authors and students from any discipline who want to document their research.
Illustrations
4 s/w Tabellen, 46 s/w Abbildungen
4 Tables, black and white; 46 Illustrations, black and white
Dimensions
Height: 234 mm
Width: 156 mm
Weight
363 gr
ISBN-13
978-1-4822-0353-0 (9781482203530)
Copyright in bibliographic data and cover images is held by Nielsen Book Services Limited or by the publishers or by their respective licensors: all rights reserved.
Schweitzer Classification
Other editions
New editions
Yihui Xie
Dynamic Documents with R and knitr
Book
06/2015
2nd Edition
Chapman & Hall/CRC
€112.30
Shipment within 15-20 days
Person
Content
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
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