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

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Outline:

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 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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Reviewer comments

Comments from Prof. Joe Hilbe and Dr. Aaron Macneil.

Data sets used in the book

The current (July 2012) errata list of the book can be found here.

All data sets used in the book are provided as *.txt files. Right-mouse click on a data file and click on Save-As.

Support material for readers of 'Beginner's Guide to GLM and GLMM with R' (2013). Zuur, Hilbe and Ieno.

Readers of the book 'Beginner's Guide to GLM and GLMM with R' (2013) by Zuur, Hilbe and Ieno have free access to Chapter 1 of Zero Inflated Models and Generalized Linear Mixed Models with R (2012). Zuur AF, Saveliev AA, Ieno EN. This chapter contains an introduction to Bayesian statistics and MCMC. Chapter 1 of Zuur (2012b) provides an introduction to multiple linear regression, which is also prerequisite knowledge for Beginner's Guide to GLM and GLMM with R. These two chapters are downloadable from:

Both chapters are password protected. The password is given on page vi in the preface of Beginner's Guide to GLM and GLMM with R. See the paragraph labelled "Chapter 1 of Zuur et al. (2012a) and Zuur (2012b)".