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A hierarchical zero-inflated model for species compositional data—from individual taxon responses to community response

Song S. Qian, Thomas F. Cuffney

Limnol. Oceanogr. Methods 12:498-506 (2014) | DOI: 10.4319/lom.2014.12.498

ABSTRACT: Healthy macroinvertebrate communities are typically composed of a few abundant taxa and many relatively rare taxa. These rare taxa tend to be sensitive to pollution and, in aggregate, are important indicators of water quality (e.g., EPT taxa richness that combines Ephemeroptera, Plecoptera, and Trichoptera taxa). Rare taxa lead to community data sets that contain large numbers of zero values that are often a source of difficulty in data processing and analysis. A hierarchical zero-inflated Poisson model is developed to study the responses to watershed urbanization of a group of macroinvertebrates taxa (EPT taxa) often used as indicators of good water quality and a healthy stream ecosystem. The zero-inflated Poisson model is parameterized with a unimodal curve for the abundance model and a logit-linear model for the zero model. The hierarchical model is used to integrate responses of individual taxa into a community level response. The emphasis of the model is on estimating the probability that an observed 0 represents the true absence of a taxon. By modeling the probability of true absence as a function of watershed level urbanization intensity both at individual taxon level and at the community level, we are able to develop a stressor-specific tolerance indicator to (1) separate truly sensitive EPT taxa from more tolerant taxa, and (2) compare the responses of different communities to the same stressor or responses of the same community in different regions. We document the development of the model and the process of integrating individual taxon models into a community model. The model is applied to a data set collected for study of the effect of urbanization on stream ecosystems.