We have put together the following guides on writing niceR code

1. A general introduction to R
2. Version control in R with git
3. Using functions to simplify your scripts
4. Different ways of repeating things.
5. Plotting.
6. Writing reports with knitr and markdown

We have also put together a list of

1. General R resources to help you continue learning.
2. A non-exhaustive list of bad habits that you should avoid and tips you should follow.

Other topics, covered by other people

1. Overview of R Data structures

We have also written guides on

1. Markov Chain Monte Carlo