I’m not very familiar with S4 classes and methods, but I assume it’s the recommended way to write new packages since it is newer than S3; this of course is open to debate. I’ll outline my experience of programming with S4 classes and methods in a later post, but in the mean time, I...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).