A comparison of joint species distribution models for percent cover data

Abstract

Joint species distribution models (JSDMs) have gained considerable traction among ecologists over the past decade, due to their capacity to answer a wide range of questions at both the species- and the community-level. The family of generalised linear latent variable models in particular has proven popular for building JSDMs, being able to handle many response types including presence-absence data, biomass, overdispersed and/or zero-inflated counts. We extend latent variable models to handle percent cover response variables, with vegetation, sessile invertebrate and macroalgal cover data representing the prime examples of such data arising in community ecology. Sparsity is a commonly encountered challenge with percent cover data. Responses are typically recorded as percentages covered per plot, though some species may be completely absent or present, that is, have 0% or 100% cover, respectively, rendering the use of beta distribution inadequate. We propose two JSDMs suitable for percent cover data, namely a hurdle beta model and an ordered beta model. We compare the two proposed approaches to a beta distribution for shifted responses, transformed presence-absence data and an ordinal model for percent cover classes. Results demonstrate the hurdle beta JSDM was generally the most accurate at retrieving the latent variables and predicting ecological percent cover data.