Journal of Data Science 8(2010), 379-396 A Mixed Effects Model for Overdispersed Zero Inflated Poisson Data with an Application in Animal Breeding Mariana Rodrigues-Motta 1 , Daniel Gianola 2,3 and Bjørg Heringstad 3 1 University of Campinas-UNICAMP, 2 DUniversity of Wisconsin and 3 Norwegian University of Life Sciences Abstract: Response variables that are scored as counts, for example, number of mastitis cases in dairy cattle, often arise in quantitative genetic analysis. When the number of zeros exceeds the amount expected such as under the Poisson density, the zero-inflated Poisson (ZIP) model is more appropri- ate. In using the ZIP model in animal breeding studies, it is necessary to accommodate genetic and environmental covariances. For that, this study proposes to model the mixture and Poisson parameters hierarchically, each as a function of two random effects, representing the genetic and environ- mental sources of variability, respectively. The genetic random effects are allowed to be correlated, leading to a correlation within and between clusters. The environmental effects are introduced by independent residual terms, ac- counting for overdispersion above that caused by extra-zeros. In addition, an inter correlation structure between random genetic effects affecting mix- ture and Poisson parameters is used to infer pleiotropy, an expression of the extent to which these parameters are influenced by common genes. The methods described here are illustrated with data on number of mastitis cases from Norwegian Red cows. Bayesian analysis yields posterior distributions useful for studying environmental and genetic variability, as well as genetic correlation. Key words: Count data, overdispersion, random effects, ZIP models. 1. Introduction Some traits in animal breeding are scored as counts, for example, litter size in pigs, embryo yield produced after superovulation, and number of mastitis cases in dairy cattle. When the number of zeros exceeds the amount expected under a certain density, as for example, the Poisson density, a possibility for modeling the extra-zeros has been proposed by Lambert (1992). In using the ZIP model in animal breeding studies, it is necessary to accommodate genetic and environmental covariances. For that, this study proposes to model the mixture