Modeling large scale species abundance with latent spatial processes

DOI10.1214/10-AOAS335MaRDI QIDQ614156zbMATH OpenWikidataFDO

Authors Avishek Chakraborty, Alan E. Gelfand, Adam M. Wilson, Andrew Latimer, John A. Silander

Publication date 27 December 2010

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

Full work available at URL https://arxiv.org/abs/1011.3327

zbMATH Keywords

conditional autoregressive priorlatent variablesmisalignmentordinal categorical dataparallel computing

Mathematics Subject Classification ID

Bayesian inference (62F15) Inference from spatial processes (62M30) Applications of statistics to environmental and related topics (62P12) Numerical analysis or methods applied to Markov chains (65C40)

Abstract: Modeling species abundance patterns using local environmental features is an important, current problem in ecology. The Cape Floristic Region (CFR) in South Africa is a global hot spot of diversity and endemism, and provides a rich class of species abundance data for such modeling. Here, we propose a multi-stage Bayesian hierarchical model for explaining species abundance over this region. Our model is specified at areal level, where the CFR is divided into roughly $\mathrm{37,000}$ one minute grid cells; species abundance is observed at some locations within some cells. The abundance values are ordinally categorized. Environmental and soil-type factors, likely to influence the abundance pattern, are included in the model. We formulate the empirical abundance pattern as a degraded version of the potential pattern, with the degradation effect accomplished in two stages. First, we adjust for land use transformation and then we adjust for measurement error, hence misclassification error, to yield the observed abundance classifications. An important point in this analysis is that only $28\mathrm{\%}$ of the grid cells have been sampled and that, for sampled grid cells, the number of sampled locations ranges from one to more than one hundred. Still, we are able to develop potential and transformed abundance surfaces over the entire region. In the hierarchical framework, categorical abundance classifications are induced by continuous latent surfaces. The degradation model above is built on the latent scale. On this scale, an areal level spatial regression model was used for modeling the dependence of species abundance on the environmental factors.

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Cited in

(16)

• Dependent species sampling models for spatial density estimation
• Joint species distribution modeling: dimension reduction using Dirichlet processes
• Additive multivariate Gaussian processes for joint species distribution modeling with heterogeneous data
• Spatial Species Sampling and Product Partition Models
• Spatial misalignment models for small area estimation: a simulation study
• scientific article; zbMATH DE number 4141869 (Why is no real title available?)
• Spatial regression modeling for compositional data with many zeros
• Multilevel latent Gaussian process model for mixed discrete and continuous multivariate response data
• Spatial Joint Species Distribution Modeling
• Modelling Species Diversity Through Species Level Hierarchical Modelling
• An adaptive spatial model for precipitation data from multiple satellites over large regions
• Bayesian modeling of discrete-time point-referenced spatio-temporal data
• Estimating seasonal onsets and peaks of bronchiolitis with spatially and temporally uncertain data
• Accounting for preferential sampling in geostatistical inference
• Joint modeling of climate niches for adult and juvenile trees
• Efficient modelling of presence-only species data via local background sampling

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