• knitr

• R markdown

• Usign knitr via Rmd

• Rnw knitr style

It's a framework for producing reproducible reports

• Code and text
• Runs R code and includes the output

• Prettier out of the box
  • Code re-formating: tidy
  • Code highlighting
  • Simple copy-paste enabled
• Better approach to dealing with plots
• Under active development by @xieyihui

Mark-down (md) advantages

• It's simple: little overhead
• Main result is HTML which opens new horizons besides PDF

knitr main outputs

• PDF: mostly through Rnw files
• HTML: via R Markdown files (Rmd)
  • Reports
  • Tutorials: ggplot2 intro
  • Presentations:
    • RPubs example
    • My first Rmd presentation

More at the knitr showcase

slidify

• How this presentation was made and published on the web.

knitcitations

• Useful for creating HTML citations: example

RStudio

• Everything works out of the box
• You can use knitr instead of Sweave() (change the option)
• Easily publish your reports via RPubs

Blogging

• knit2wp() introduced here
• through Jekyll: check this
• doable at Tumblr: Jeffrey Horner part I, part II, wrap-up

Markdown's syntax is simple

• That's also partly why LaTeX (Rnw) is still superior for PDF output if you want more control.

The only major change in Rmd are the R code chunks

RStudio (desktop) has a great syntax description. They have another great page online. Check it out!

This blog post goes over the basics pretty well.

Your first Rmd file

1. In RStudio: File, New, R Markdown
2. Click on Knit HTML

Your 2nd file

1. In RStudio: File, New, R Markdown
2. Click on MD (Markdown quick reference)
3. Edit the title, text, code, add chunks as you wish
4. Click on Knit HTML

Basic chunk

```r

hola()
```

You can add chunk labels after r

http://yihui.name/knitr/options

• Figure
  • fig.width, fig.height: R control
  • out.width, out.height: output control
  • fig.keep: useful for >=2 plots in 1 chunk
  • fig.cap: caption in Rnw only
    
• Cache
  • cache: whether to cache a chunk
  • dependson: which other chunks this chunk depends on

• Results
  • results: similar to the same option in Sweave()
  • message, error, warning: whether to print them or not
• Global options

opts_chunk$set(fig.width = 5, fig.height = 5, cache = TRUE)

For EDA

• fellgernon.tumblr.com example which you can view here

For sharing quick code

• ORFs example visible through RPubs
• Scrapping Ravens data from ESPN example

For quick presentations: no LaTeX

For blogging

It's almost like native R files!

• Change the setting in RStudio to weave with knitr
  • Preferences, Sweave, Weave Rnw files using knitr
• Use knitr options instead of the Sweave options
  • Sexpr() works for in-line code
• Enjoy your PDF output!

Quick example through RStudio

Longer template

• Rnw
• PDF

library(slidify)
author("Rmd-intro")
## Edit the text
slidify("index.Rmd")
## Created the GitHub repo 'Rmd-intro'

## Initialized my git repository locally

## Added the github repo as a remote

## These steps are described here
## https://github.com/ramnathv/slidify/issues/99
publish("lcolladotor", "Rmd-intro")
## Slides are live at http://lcolladotor.github.com/Rmd-intro/

Thanks!