R Markdown: The Definitive Guide, 1st Edition (Paperback) book cover

R Markdown

The Definitive Guide, 1st Edition

By Yihui Xie, J.J. Allaire, Garrett Grolemund

Chapman and Hall/CRC

304 pages

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pub: 2018-07-17
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Description

R Markdown: The Definitive Guide is the first official book authored by the core R Markdown developers that provides a comprehensive and accurate reference to the R Markdown ecosystem. With R Markdown, you can easily create reproducible data analysis reports, presentations, dashboards, interactive applications, books, dissertations, websites, and journal articles, while enjoying the simplicity of Markdown and the great power of R and other languages.

In this book, you will learn

  • Basics: Syntax of Markdown and R code chunks, how to generate figures and tables, and how to use other computing languages
  • Built-in output formats of R Markdown: PDF/HTML/Word/RTF/Markdown documents and ioslides/Slidy/Beamer/PowerPoint presentations
  • Extensions and applications: Dashboards, Tufte handouts, xaringan/reveal.js presentations, websites, books, journal articles, and interactive tutorials
  • Advanced topics: Parameterized reports, HTML widgets, document templates, custom output formats, and Shiny documents.

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.

Reviews

"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

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 Authors

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.

About the Series

Chapman & Hall/CRC The R Series

Learn more…

Subject Categories

BISAC Subject Codes/Headings:
MAT029000
MATHEMATICS / Probability & Statistics / General