R Markdown: The Definitive Guide

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.

1133051929
R Markdown: The Definitive Guide

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.

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R Markdown: The Definitive Guide

R Markdown: The Definitive Guide

R Markdown: The Definitive Guide

R Markdown: The Definitive Guide

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Overview

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.


Product Details

ISBN-13: 9781138359338
Publisher: Taylor & Francis
Publication date: 07/17/2018
Series: Chapman & Hall/CRC The R Series
Pages: 338
Product dimensions: 6.10(w) x 9.10(h) x 0.80(d)

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.

Table of Contents

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                        

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