I have just uploaded the new version of my "Statistics with R": http://zoonek2.free.fr/UNIX/48_R/all.htmlThe previous version was one year and a half old, so in spite of the fact I have not had much time to devote to it in the past two years, it might ...

Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).