What is R Markdown?

How does it work?

Similar to a regular R document except the code is broken up into chunks to which you can apply different options. For example, you can choose to execute a chunk of code but not to display it in the report by selecting the option ‘echo = FALSE’
Outside of the chunks you can add headers, pictures, links or text explaining your code
R Markdown Cheat Sheet

To use it you need:

Not necessary now but if you want to produce PDFs then you will need LaTeX software:

Once you have downloaded and installed everything you are ready to create an R Markdown document.

In RStudio go to:
File -> New File -> R Markdown….
Give it a name and select html as the default output format
This will open an R Markdown document with some default information included and some chunks set up:

The first chunk is the setup chunk, you can use this load libraries, functions and data
You can use {r, eval = FALSE} to skip chunks that take a long time to run and {r, echo = FALSE} to run chunks but not show the code in the output
There are lots of other options you can set at the beginning of each chunk - have a look at the R Markdown cheat sheet
You can have headers for each section by using “#”, the more you use (up to 6), the smaller your header is
These headers are collected into a table of contents you can use to navigate through your code - you can find this in the bottom-left and top-right corners of the script window

Once you have finished splitting your code up into chunks and adding explanatory text and pictures, you are ready to knit your document! (Ctrl+Shift+K)

Once you have knitted your html document you will be able to publish it online at rpubs.com

If you want to make your knitted html a bit fancier you can use a prettydoc template
To do this replace output: html_document with: