(This article was first published on Frank Davenport's Blog on R, Statistics, and all Things Spatial - R, and kindly contributed to R-bloggers)
This post by Suraj Gupta explains it all. This is the firs time I have seen a concise and accessible explanation of the R environment structure and why it matters.
Addendum: This one by Digithead is also pretty good
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Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).