swirl (no not that one Sematic Webbers)

swirl is a way to learn R and data science interactively.

Try it out here.

knitr

For dynamic report generation in R.

Link for knitr

References for graphs in R

This link provides pretty simple examples but useful. Adding error bars is not completely straightforward, this link gives a good explanation.

LDA - Step by Step in R

Was able to get an example running very quickly with this tutorial. http://www.rtexttools.com/1/post/2011/08/getting-started-with-latent-dirichlet-allocation-using-rtexttools-topicmodels.html