I explored different packages (such as mgcv, MCMCglmm, glmmADMB, etc) but they all have limitations. Either they don't allow for zero-inflated, zero-altered distributions or they don't allow for temporal auto-correlation through functions as corAR() or corARMA().
The most feature-rich regression engine these days is provided by the brms package by Paul Buerkner. It covers zero-inflated distributions and autoregressive structures. Not sure about generalized additive, though.
Hi @Renan, yes you are right about this book. There is also "Beginner's guide to GAMMA with R" that could be interesting to explore. Thanks
Hi @Martin, I didn't know about this package and it seems to be amazing. After a first and quick exploration it seems to deal with non-linear models and smoothing terms. It seems to be the package that I need. Thanks a lot
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