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R Markdown: The Definitive Guide (Chapman & Hall/CRC


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Table of Contents

Preface How to read this book Structure of the book Software information and conventions Acknowledgments
About the Authors Yihui Xie J.J. Allaire Garrett Grolemund I Get Started
1 Installation 2 Basics 2.1 Example applications 2.2 Compile an R Markdown document 2.3 Cheat sheets 2.4 Output formats 2.5 Markdown syntax 2.6 R code chunks and inline R code 2.7 Other language engines 2.8 Interactive documents
II Output Formats 3 Documents
3.1 HTML document 3.2 Notebook 3.3 PDF document 3.4 Word document 3.5 OpenDocument Text document 3.6 Rich Text Format document 3.7 Markdown document 3.8 R package vignette 4 Presentations 4.1 ioslides presentation 4.2 Slidy presentation 4.3 Beamer presentation 4.4 PowerPoint presentation III Extensions
5 Dashboards 5.1 Layout 5.2 Components 5.3 Shiny 6 Tufte Handouts 6.1 Headings 6.2 Figures 6.3 Sidenotes 6.4 References 6.5 Tables 6.6 Block quotes 6.7 Responsiveness 6.8 Sans-serif fonts and epigraphs 6.9 Customize CSS styles 7 xaringan Presentations 7.1 Get started 7.2 Keyboard shortcuts 7.3 Slide formatting 7.4 Build and preview slides 7.5 CSS and themes 7.6 Some tips 8 reveal.js Presentations 8.1 Display modes 8.2 Appearance and style 8.3 Slide transitions 8.4 Slide backgrounds 8.5 2-D presentations 8.6 Custom CSS 8.7 reveal.js options 8.8 reveal.js plugins 8.9 Other features
9 Community Formats 9.1 Lightweight Pretty HTML Documents 9.2 The rmdformats package 9.3 Shower presentations 10 Websites 10.1 Get started 10.2 The directory structure 10.3 Deployment 10.4 Other site generators 10.5 rmarkdown's site generator 11 HTML Documentation for R Packages 11.1 Get started 11.2 Components
12 Books 12.1 Get started 12.2 Project structure 12.3 Markdown extensions 12.4 Output Formats 12.5 Editing 12.6 Publishing
13 Journals 13.1 Get started 13.2 Articles templates 13.3 Using a template 13.4 LaTeX content 13.5 Linking with bookdown 13.6 Contributing templates
14 Interactive Tutorials 14.1 Get started 14.2 Tutorial types 14.3 Exercises 14.4 Quiz questions 14.5 Videos 14.6 Shiny components 14.7 Navigation and progress tracking
IV Other Topics 15 Parameterized reports 15.1 Declaring parameters 15.2 Using parameters 15.3 Knitting with parameters 15.4 Publishing
16 HTML Widgets 16.1 Overview 16.2 A widget example (sigma.js) 16.3 Creating your own widgets 16.4 Widget sizing 16.5 Advanced topics
17 Document Templates 17.1 Template structure 17.2 Supporting files 17.3 Custom Pandoc templates 17.4 Sharing your templates 18 Creating New Formats 18.1 Deriving from built-in formats 18.2 Fully custom formats 18.3 Using a new format 19 Shiny Documents 19.1 Getting started 19.2 Deployment 19.3 Embedded Shiny apps 19.4 Shiny widgets 19.5 Multiple pages 19.6 Delayed rendering 19.7 Output arguments for render functions

About the Author

Yihui Xie is a software engineer at RStudio. He has authored and co-authored several R packages, including knitr, rmarkdown, bookdown, blogdown, shiny, xaringan, and animation. He has published three other books, Dynamic Documents with R and knitr, bookdown: Authoring Books and Technical Documents with R Markdown, and blogdown: Creating Websites with R Markdown. J.J. Allaire is the founder of RStudio and the creator of the RStudio IDE. He is an author of several packages in the R Markdown ecosystem including rmarkdown, flexdashboard, learnr, and radix. Garrett Grolemund is the co-author of R for Data Science and author of Hands-On Programming with R. He wrote the lubridate R package and works for RStudio as an advocate who trains engineers to do data science with R and the Tidyverse.


"The manuscript offers a detailed documentation of the R Markdown document format and its related packages for R (e.g. knitr, rmarkdown, flexdashboard, shiny). These packages form an important ecosystem for reproducible research using R and are widely used across academia and the private sector. All the authors have been key contributors to developing the core R Markdown packages and are knowledgable about the inner workings of these functions and all the available options to customize published documents...The target audience for this manuscript would be experienced R users who frequently use R Markdown to generate publications for a variety of mediums (articles, books, information dashboards, interactive web applications, etc.)...While this book is strongly related to the author's previous book (Dynamic Documents with R and knitr), a wider range of readers should find this new manuscript useful for its focus on the broad range of output formats generated by R Markdown and how to customize those outputs." ~Benjamin Soltoff, Department of Computational Social Science, University of Chicago

"A main strength of the software described herein is that it facilitates reproducible documents incorporating analyses and figures. The first topics covered in chapters 6-13 include handout and presentation formats that could be used effectively for teaching or presenting statistical results. The other topics focus on larger scale documents such as complex websites, books, and academic journal articles. From academic teaching and research to industry and other settings, the material covered by this book allows statisticians and data scientists to disseminate results in a highly effective manner." ~David Whitney, Department of Biostatistics, University of Washington

"This book will be a valuable reference for students, academics, and professionals using R - that is to say, any one in a wide (and growing) variety of fields focused on practical data analysis including statistics, machine learning, the social sciences, etc. There is increasing awareness that nearly any occasion calling for analysis code also calls for some amount of corresponding documentation, explanation, and/or interpretation. Rapid improvement in tools for R markdown has made integrating code and text less and less of a chore, and therefore more and more common - even among users new to R. R markdown is a popular choice now for a range of formats including blog posts, user manuals, books, dissertations, and undergraduate homework assignments. I personally use R markdown for nearly all of my website content, presentations, research papers, and to generate reports for the clients of my statistical consulting business. Because of its many applications, however, the ecosystem of R markdown tools has become unwieldy, and many tutorials reference outdated techniques or unnecessary workarounds. A definitive guide has been long needed." ~Rose Hartman, UnderstandingData

"This book is so far the most comprehensive reference for the R Markdown format and its associated extensions and tools. On a high level, Part I and II (Chapter 1-4) of this book cover the basic use of the R Markdown document and the knitr and rmarkdown packages, which are helpful for new users to quickly get started. Part III (Chapter 5-13) introduces a lot of new developments and powerful tools for R Markdown, including creating presentations, authoring books, building websites, writing journal articles, etc. In my personal point of view this is the most attractive part of this book, as it opens a new world for users who have only used R Markdown to create ordinary documents." ~Yixuan Qui, Department of Statistics, Purdue University

"This book represents a valuable contribution to the target field due to its exploration of a wide range of features in the markdown language. If other books on this topic exist, this one has the advantage that the authors have already made significant contributions to the markdown language in the R platform and certainly have a comprehensive understanding of the topic...I recommend this book for publication because the topic is sophisticated and complex, and the interested audience will certainly be satisfied with the clarity of presentation and the depth that the authors reach in their exploratory examples" ~Jon Katz, data analyst

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