Reproducible web documents with R, knitr & Markdown

Follow along at - http://cpsievert.github.io/slides/markdown

• Easy to learn and use.
• Focus on content, rather than coding and debugging errors.
• It's flexible. Markdown was created to simplify HTML, but with the right tools, your Markdown files can easily be converted to many different formats!
• Fastest way to internet!
  

• Markdown is a particular type of markup language.
• Markup languages are designed produce documents from plain text.
• Some of you may be familiar with LaTeX. This is another (less human friendly) markup language for creating pdf documents.
• LaTeX gives you much greater control, but it is restricted to pdf and has a much greater learning curve.
• As I mentioned, there are tools (mainly pandoc) that allow you to render markdown in different formats (for example, HTML/pdf/word)

• rmarkdown is a new package from RStudio that merges a lot of technologies in an exciting way.
• In fact, in RStudio now, you integrate R code into your Markdown document and render as HTML/pdf/Word in the click of a button!
  
• You can even embed your shiny apps in HTML documents generated with rmarkdown!

• R learning resources at UCLA by Joshua Wiley et al
• Advanced R programming by Hadley
• The rmarkdown website
• Tufte style HTML and pdf documents.
• shiny apps!
• Inject custom JavaScript for interactive visualizations.

Header 2

Header 3

This is regular text.

This is a blockquote.

This is the second paragraph in the blockquote.

This is an H2 in a blockquote

• It's easy to customize styling using the markdownToHTML function from the markdown package.

knit("index.Rmd") #generates 'index.md' file
library(markdown)
markdownToHTML("index.md", "index.html", stylesheet='custom.css')

• If you have rmarkdown, there are some nice templates you can use (File -> New File -> R Markdown -> From Template)

• Go to: File -> New File -> R Markdown
• Try out different output formats and pick one that you like!

Title
====================

This is an R Markdown document.

```{{r results='asis'}}
library(knitr)
kable(head(cars), 'html')
```

You can also embed plots, for example:

```{{r fig.width=7, fig.height=6, echo=FALSE}}
plot(cars)
```

library(rCharts)
dat <- subset(as.data.frame(HairEyeColor), Sex == "Male")
n1 <- nPlot(Freq ~ Hair, group = "Eye", data = dat, type = "multiBarChart")
n1$print("nvd3mbar")

Leveraging JavaScript, it's “easy” to make interactive stuff. Thanks to Yihui for source.

• Markdown Quick Reference
• Daring Fireball Markdown Basics
• Markdown Cheat Sheet
• Using R Markdown with RStudio
• knitr website
• Markdown example with knitr and rCharts by Ricardo Chavelas