Why R Markdown?

• Reproducible
  • Save time generating the same report each month
• Reduces errors (and makes it easier to fix them)
  • Easily check whether the tables or graphs are using the correct version of data
  • If it is not, easily change it
• Flexibility
  • You can be explicit about anything, and design a product that looks EXACTLY how you want
  • Because all of your decisions are expressed in code, creating a new product with those same designs is easy

Some Drawbacks

• Time (especially in the beginning)
  • Changing any default options will take you a lot of time
  • Weird problems can arise and be difficult to diagnose
• Compatibility for sharing
  • Some co-authors may not want a PDF or HTML
  • Output to Microsoft products (PPT, DOC) is possible, but not optimized

Two Main Output Types:

• HTML
  • Default for R Markdown
  • Included with initial installation
• PDF
  • Requires additional installations

Sharing Options

• Files
• RPubs
• Shiny

HTML Default Outputs

• Web page (default)
  • Can be interactive
• Presentation
  • Can be rendered using several programs (ioslides, Slidy, R Presentations)

Advantages of HTML Outputs

• Very easy to create something basic, but professional looking
• (Sort of) easy to customize
  • If you know CSS or HTML, you can do elaborate customizations
• Best for anything interactive

Useful HTML Extensions

• Bookdown
  • Create multi-paged HTML documents, with tabs
• Blogdown
  • Create a full website
  • Can be hosted through GitHub
• RevealJS
  • My personal favorite for presentations (used for this one!)
  • Provides tons of customization options
• Flexdashboard

Getting Started with PDFs

• PDFs are generated using Latex
• You need to install a distribution of Latex on your machine to use this software
• I recommend TinyTeX, as it is easy to install and use

To install TinyTex:

# Install the R Package
install.packages("tinytex")

# Use the package to install Latex
tinytex::install_tinytex()

Default PDF Ouputs

• PDF Documents
  • Very professional looking
  • Have a cool, Latex-exclusive font (Computer Modern)
  • Easy to include formatted tables, figures, and in-line code
• PDF Presentations (Beamer)
  • NOT attractive

Great PDF Extension

• Bookdown!
  • Designed to help you write an entire book in R, but also provides some useful extensions
  • Link to figures in text, automatically number figures and tables, and more

Background Images

• Display static images that automatically change size with the presentation

Background Videos

• Display dynamic video behind text

Introductory Materials (all by Yihui Xie)

• R Markdown: The Definitive Guide, https://bookdown.org/yihui/rmarkdown/
• Bookdown: Authoring Books and Technical Documents with R Markdown, https://bookdown.org/yihui/bookdown/
• Blogdown: Creating Websites with R Markdown, https://bookdown.org/yihui/blogdown/

More Advanced Reading

• R Markdown Cookbook, https://bookdown.org/yihui/rmarkdown-cookbook/
• Officedown, an in-development project to enhance Office compatibility: https://davidgohel.github.io/officedown/
• knitr documentation: https://yihui.org/knitr/
• Animations for statistical concepts: https://yihui.org/animation/examples/

Examples:

• A dashboard (by our own Greg Chambers!): https://rpubs.com/gchambe1/c
• A survey results report: http://files.kff.org/attachment/Report-Employer-Health-Benefits-Annual-Survey-2017
• A website: https://emitanaka.org/