R Markdown

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

• I Get Started 1.Installation 2. Basics Example applications Airbnb’s knowledge repository Homework assignments on RPubs Personalized mails Employer Health Benefits Survey Journal articles Dashboards at eelloo Books Websites Compile an R Markdown document Cheat sheets Output formats Markdown syntax Inline formatting Block-level elements Math expressions R code chunks and inline R code Figures Tables Other language engines Python Shell scripts SQL Rcpp Stan JavaScript and CSS Julia C and Fortran Interactive documents HTML widgets Shiny documents II Output Formats 3. Documents HTML document Table of contents Section numbering Tabbed sections Appearance and style Figure options Data frame printing Code folding MathJax equations Document dependencies Advanced customization Shared options HTML fragments Notebook Using Notebooks Saving and sharing Notebook format PDF document Table of contents Figure options Data frame printing Syntax highlighting LaTeX options LaTeX packages for citations Advanced customization Other features Word document Other features OpenDocument Text document Other features Rich Text Format document Other features Markdown document Markdown variants Other features R package vignette 4. Presentations ioslides presentation Display modes Incremental bullets Visual appearance Code highlighting Adding a logo Tables Advanced layout Text color Presenter mode Printing and PDF output Custom templates Other features Slidy presentation Display modes Text size Footer elements Other features Beamer presentation Themes Slide level Other features PowerPoint presentation Custom templates Other features III Extensions 5. Dashboards Layout Row-based layouts Attributes on sections Multiple pages Story boards Components Value boxes Gauges Text annotations Navigation bar Shiny Getting started A Shiny dashboard example Input sidebar Learning more 6. Tufte Handouts Headings Figures Margin figures Arbitrary margin content Full-width figures Main column figures Sidenotes References Tables Block quotes Responsiveness Sans-serif fonts and epigraphs Customize CSS styles 7. xaringan Presentations Get started Keyboard shortcuts Slide formatting Slides and properties The title slide Content classes Incremental slides Presenter notes yolo: true Build and preview slides CSS and themes Some tips Autoplay slides Countdown timer Highlight code lines Working offline Macros Disadvantages 8. revealjs Presentations Display modes Appearance and style Smaller text Slide transitions Slide backgrounds -D presentations Custom CSS Slide IDs and classes Styling text spans revealjs options revealjs plugins Other features 9. Community Formats Lightweight Pretty HTML Documents Usage Package vignettes The rmdformats package Shower presentations 10. Websites Get started The directory structure Deployment Other site generators rmarkdown’s site generator A simple example Site authoring Common elements Site navigation HTML generation Site configuration Publishing websites Additional examples Custom site generators 11. HTML Documentation for R Packages Get started Components Home page Function reference Articles News Navigation bar 12. Books Get started Project structure Index file Rmd files _bookdownyml _outputyml Markdown extensions Number and reference equations Theorems and proofs Special headers Text references Cross referencing Output Formats HTML LaTeX/PDF E-books A single document Editing Build the book Preview a chapter Serve the book RStudio addins Publishing RStudio Connect Other services Publishers 13. Journals Get started Articles templates Using a template LaTeX content Linking with bookdown Contributing templates 14. Interactive Tutorials Get started Tutorial types Exercises Solutions Hints Quiz questions Videos Shiny components Navigation and progress tracking IV Advanced Topics 15. Parameterized reports Declaring parameters Using parameters Knitting with parameters The Knit button Knit with custom parameters The interactive user interface Publishing 16. HTML Widgets Overview A widget example (sigmajs) File layout Dependencies R binding JavaScript binding Demo Creating your own widgets Requirements Scaffolding Other packages Widget sizing Specifying a sizing policy JavaScript resize method Advanced topics Data transformation Passing JavaScript functions Custom widget HTML Create a widget without an R package 17. Document Templates Template structure Supporting files Custom Pandoc templates Sharing your templates 18. Creating New Formats Deriving from built-in formats Fully custom formats Using a new format 19. Shiny Documents Getting started Deployment ShinyAppsio Shiny Server / RStudio Connect Embedded Shiny apps Inline applications External applications Shiny widgets The shinyApp() function Example: k-Means clustering Widget size and layout Multiple pages Delayed rendering Output arguments for render functions A caveat