Multi-species distribution modeling using penalized mixture of regressions

DOI10.1214/15-AOAS813zbMATH Open1397.62263arXiv1509.04834OpenAlexW1839582124WikidataQ57239139 ScholiaQ57239139MaRDI QIDQ746675FDOQ746675

Authors: Francis K. C. Hui, David I. Warton, Scott D. Foster 

Publication date: 28 October 2015

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: Multi-species distribution modeling, which relates the occurrence of multiple species to environmental variables, is an important tool used by ecologists for both predicting the distribution of species in a community and identifying the important variables driving species co-occurrences. Recently, Dunstan, Foster and Darnell [Ecol. Model. 222 (2011) 955-963] proposed using finite mixture of regression (FMR) models for multi-species distribution modeling, where species are clustered based on their environmental response to form a small number of "archetypal responses." As an illustrative example, they applied their mixture model approach to a presence-absence data set of 200 marine organisms, collected along the Great Barrier Reef in Australia. Little attention, however, was given to the problem of model selection - since the archetypes (mixture components) may depend on different but likely overlapping sets of covariates, a method is needed for performing variable selection on all components simultaneously. In this article, we consider using penalized likelihood functions for variable selection in FMR models. We propose two penalties which exploit the grouped structure of the covariates, that is, each covariate is represented by a group of coefficients, one for each component. This leads to an attractive form of shrinkage that allows a covariate to be removed from all components simultaneously. Both penalties are shown to possess specific forms of variable selection consistency, with simulations indicating they outperform other methods which do not take into account the grouped structure. When applied to the Great Barrier Reef data set, penalized FMR models offer more insight into the important variables driving species co-occurrence in the marine community (compared to previous results where no model selection was conducted), while offering a computationally stable method of modeling complex species-environment relationships (through regularization).

Full work available at URL: https://arxiv.org/abs/1509.04834

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zbMATH Keywords

variable selectionpenalized likelihoodregularizationfinite mixture modelscommunity level modelsspecies archetype models

Mathematics Subject Classification ID

Generalized linear models (logistic models) (62J12) Applications of statistics to environmental and related topics (62P12)

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Cited In (15)

• A globally convergent algorithm for Lasso-penalized mixture of linear regression models
• Grouped heterogeneous mixture modeling for clustered data
• Additive multivariate Gaussian processes for joint species distribution modeling with heterogeneous data
• Mixing it up: new methods for finite mixture modelling of multi-species data in ecology. (Abstract of thesis)
• Multivariate Bayesian clustering using covariate‐informed components with application to boreal vegetation sensitivity
• Sparse pairwise likelihood estimation for multivariate longitudinal mixed models
• Model-based simultaneous clustering and ordination of multivariate abundance data in ecology
• Heterogeneity Analysis via Integrating Multi-Sources High-Dimensional Data With Applications to Cancer Studies
• Finite mixture of regression modeling for high-dimensional count and biomass data in ecology
• Modelling the covariance structure in marginal multivariate count models: hunting in Bioko Island
• Pursuing Sources of Heterogeneity in Modeling Clustered Population
• Joint species distribution modeling: dimension reduction using Dirichlet processes
• Estimation of multiple networks with common structures in heterogeneous subgroups
• Investigation of a generalized multinomial model for species data
• Tuning parameter selection for a penalized estimator of species richness

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