Dynamic Documents with R and knitr

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.

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