R Markdown

The Definitive Guide

Yihui Xie, J.J. Allaire, Garrett Grolemund

• Publisher: Chapman and Hall/CRC
• Year: 2018
• Print ISBN: 9781138359420
• eBook ISBN: 9780429782961
• Topic: Mathematics
• Subtopic: Probability & Statistics
• Index: Mathematics

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.

Contents

List of Figures

List of Tables

Preface

About the Authors

I Get Started

1 Installation

2 Basics

2.1 Example apppcations

2.1.1 Airbnb’s knowledge repository

2.1.3 Personapzed mail

2.1.4 2017 Employer Health Benefits Survey

2.1.5 Journal articles

2.1.6 Dashboards at eelloo

2.1.7 Books

2.1.8 Websites

2.2 Compile an R Markdown document

2.3 Cheat sheets

2.4 Output formats

2.5 Markdown syntax

2.5.1 Inpne formatting

2.5.2 Block-level elements

2.5.3 Math expressions

2.6 R code chunks and inpne R code

2.6.1 Figures

2.6.2 Tables

2.7 Other language engines

2.7.1 Python

2.7.2 Shell scripts

2.7.3 SQL

2.7.4 Rcpp

2.7.5 Stan

2.7.6 JavaScript and CSS

2.7.7 Jupa

2.7.8 C and Fortran

2.8 Interactive documents

2.8.1 HTML widgets

2.8.2 Shiny documents

II Output Formats

3 Documents

3.1 HTML document

3.1.1 Table of contents

3.1.2 Section numbering

3.1.3 Tabbed sections

3.1.4 Appearance and style

3.1.5 Figure options

3.1.6 Data frame printing

3.1.7 Code folding

3.1.8 MathJax equations

3.1.9 Document dependencies

3.1.10 Advanced customization

3.1.11 Shared options

3.1.12 HTML fragments

3.2 Notebook

3.2.1 Using Notebooks

3.2.2 Saving and sharing

3.2.3 Notebook format

3.3 PDF document

3.3.1 Table of

3.3.2 Figure options

3.3.3 Data frame printing

3.3.4 Syntax highpghting

3.3.5 LaTeX options

3.3.6 LaTeX packages for citations

3.3.7 Advanced customization

3.3.8 Other features

3.4 Word document

3.4.1 Other features

3.5 OpenDocument Text document

3.5.1 Other features

3.6 Rich Text Format document

3.6.1 Other features

3.7 Markdown document

3.7.1 Markdown variants

3.7.2 Other features

3.8 R package vignette

4 Presentations

4.1 iospdes presentation

4.1.1 Display modes

4.1.2 Incremental bullets

4.1.3 Visual appearance

4.1.4 Code highpghting

4.1.5 Adding a logo

4.1.6 Tables

4.1.7 Advanced layout

4.1.8 Text color

4.1.9 Presenter mode

4.1.10 Printing and PDF output

4.1.11 Custom templates

4.1.12 Other features

4.2 Spdy presentation

4.2.1 Display modes

4.2.2 Text size

4.2.3 Footer elements

4.2.4 Other features

4.3 Beamer presentation

4.3.1 Themes

4.3.2 Spde level

4.3.3 Other features

4.4 PowerPoint presentation

4.4.1 Custom templates

4.4.2 Other features

III Extensions

5 Dashboards

5.1 Layout

5.1.1 Row-based layouts

5.1.2 Attributes on sections

5.1.3 Multiple pages

5.1.4 Story boards

5.2 Components

5.2.1 Value boxes

5.2.2 Gauges

5.2.3 Text annotations

5.2.4 Navigation bar

5.3 Shiny

5.3.1 Getting started

5.3.2 A Shiny dashboard example

5.3.3 Input sidebar

5.3.4 Learning more

6 Tufte Handouts

6.1 Headings

6.2 Figures

6.2.1 Margin figures

6.2.2 Arbitrary margin content

6.2.3 Full-width figures

6.2.4 Main column 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 Spde formatting

7.3.1 Spdes and properties

7.3.2 The title spde

7.3.3 Content classes

7.3.4 Incremental spdes

7.3.5 Presenter notes

7.3.6 yolo: true

7.4 Build and preview spdes

7.5 CSS and themes

7.6 Some tips

7.6.1 Autoplay spdes

7.6.2 Countdown timer

7.6.3 Highpght code pnes

7.6.4 Working offpne

7.6.5 Macros

7.6.6 Disadvantages

8 reveal.js Presentations

8.1 Display modes

8.2 Appearance and style

8.2.1 Smaller text

8.3 Spde transitions

8.4 Spde backgrounds

8.5 2-D presenations

8.6 Custom CSS

8.6.1 Spde IDs and classes

8.6.2 Stypng text spans

8.7 reveal.js options

8.8 reveal.js plugins

8.9 Other features

9 Community Formats

9.1 Pghtweight Pretty HTML Documents

9.1.1 Usage

9.1.2 Package vignettes

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

10.5.1 A simple example

10.5.2 Site authoring

10.5.3 Common elements

10.5.4 Site navigation

10.5.5 HTML generation

10.5.6 Site configuration

10.5.7 Pubpshing websites

10.5.8 Additional examples

10.5.9 Custom site generators

11 HTML Documentation for R Packages

11.1 Get started

11.2 Components

11.2.1 Home page

11.2.2 Function reference

11.2.3 Articles

11.2.4 News

11.2.5 Navigation...

Table of contents

• Cover
• Halftitle Page
• Title Page
• Copyright
• Table of Contents