(This article was first published on Search Results for R, and kindly contributed to R-bloggers)
I use R for just about everything, including exploratory data analysis and graphics. The only other package with which I have any familiarity is Mathematica. I've been generally satisfied with R graphics, although there are things that I always struggle...
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Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).