(This article was first published on Dataninja » R, and kindly contributed to R-bloggers)
Quick-R, by Robert Kabacoff, is a wonderful R introduction site. It covers data management, basic and advanced statistics, and graphing in R, and it is aimed at an audience that has previous experience using other packages (such as SAS or Stata) that work differently than R.
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Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).