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

Chapter 1 provides a basic introduction to Bayesian statistics and Markov Chain Monte Carlo (MCMC), as we will need this for most analyses.

In Chapter 2 we analyse nested zero inflated data of sibling negotiation of barn owl chicks. We explain the application of a Poisson GLMM for 1-way nested data and discuss the observation-level random intercept to allow for overdispersion. We show that the data are zero-inflated and introduce zero-inflated GLMM. 

Data of sandeel otolith presence in seal scat is analysed in Chapter 3. We present a flowchart of steps in selecting the appropriate technique: Poisson GLM, negative binomial GLM, Poisson or negative binomial GAM, or GLMs with zero-inflated distribution.

Chapter 4 is relevant for readers interested in the analysis of (zero inflated) 2-way nested data. The chapter takes us to marmot colonies: multiple colonies with multiple animals sampled repeatedly over time.

Chapters 5 – 7 address GLMs with spatial correlation. Chapter 5 presents an analysis of Common Murre density data and introduces hurdle models using GAM. Random effects are used to model spatial correlation. In Chapter 6 we analyse zero-inflated skate abundance recorded at approximately 250 sites along the coastal and continental shelf waters of Argentina. Chapter 7 also involves spatial correlation (parrotfish abundance) with data collected around islands, which increases the complexity of the analysis. GLMs with residual conditional auto-regressive correlation structures are used.

In Chapter 8 we apply zero-inflated models to click beetle data.

Chapter 9 is relevant for readers interested in GAM, zero inflation, and temporal auto-correlation. We analyse a time series of zero-inflated whale strandings.

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