A Beginner's Guide to Generalized Additive Mixed Models with R

de Alain F. Zuur, Anatoly A. Saveliev, Elena N. Ieno

A Beginner's Guide to GAMM with R is the third in Highland Statistics' Beginner's Guide series, following the well-received A Beginner's Guide to Generalized Additive Models with R and A Beginner's Guide to GLM and GLMM with R. In this book we take the reader on an exciting voyage into the world of generalized additive mixed effects models (GAMM). Keywords are GAM, mgcv, gamm4, random effects, Poisson and negative binomial GAMM, gamma GAMM, binomial GAMM, NB-P models, GAMMs with generalized extreme value distributions, overdispersion, underdispersion, two-dimensional smoothers, zero-inflated GAMMs, spatial correlation, INLA, Markov chain Monte Carlo techniques, JAGS, and two-way nested GAMMs. The book includes three chapters on the analysis of zero-inflated data. Across the book frequentist approaches (gam, gamm, gamm4, lme4) are compared with Bayesian techniques (MCMC in JAGS and INLA). Datasets on squid, polar bears, coral reefs, ruddy turnstones, parasites in anchovy, common guillemots, harbor porpoises, forestry, brood parasitism, maximum cod length, and Common Scoters are used in case studies. The R code to construct, fit, interpret, and comparatively evaluate models is provided at every stage.