These are the lecture notes from my course OCN 683, 'Advanced Statistics in R'. The course is mostly about analyzing ecological data using GLMs, GAMs, and GLMMs, plus sections on simulation, model selection, and multivariate community analysis. I'm putting the notes here because they might be useful.
Disclaimer: I borrow heavily from Bolker, Ecological Models and Data in R, Princeton University Press; Fox and Weisberg, An R Companion to Applied Regression, SAGE Publications; Zuur et al., Mixed Effects Models and Extensions in Ecology with R, Springer; Gelman and Hill, Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge University Press. Go to these sources for definitive material; the lecture notes are condensed/simplified for pedagogical purposes.