Alain Zuur & Elena N. Ieno 
Mixed Effects Models and Extensions in Ecology with R [PDF ebook] 

Limitations of Linear Regression Applied on Ecological Data.- Things are not Always Linear; Additive Modelling.- Dealing with Heterogeneity.- Mixed Effects Modelling for Nested Data.- Violation of Independence – Part I.- Violation of Independence – Part II.- Meet the Exponential Family.- GLM and GAM for Count Data.- GLM and GAM for Absence–Presence and Proportional Data.- Zero-Truncated and Zero-Inflated Models for Count Data.- Generalised Estimation Equations.- GLMM and GAMM.- Estimating Trends for Antarctic Birds in Relation to Climate Change.- Large-Scale Impacts of Land-Use Change in a Scottish Farming Catchment.- Negative Binomial GAM and GAMM to Analyse Amphibian Roadkills.- Additive Mixed Modelling Applied on Deep-Sea Pelagic Bioluminescent Organisms.- Additive Mixed Modelling Applied on Phytoplankton Time Series Data.- Mixed Effects Modelling Applied on American Foulbrood Affecting Honey Bees Larvae.- Three-Way Nested Data for Age Determination Techniques Applied to Cetaceans.- GLMM Applied on the Spatial Distribution of Koalas in a Fragmented Landscape.- A Comparison of GLM, GEE, and GLMM Applied to Badger Activity Data.- Incorporating Temporal Correlation in Seal Abundance Data with MCMC.