Integrated statistical models in ecology
Date
2023
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Abstract
The number of endangered and vulnerable species continues to grow globally as a result of habitat destruction, overharvesting, invasive species, and climate change. Understanding the drivers of population decline is pivotal for informing species conservation. Many datasets collected are restricted to a limited portion of the species range, may not include observations of other organisms in the community, or lack temporal breadth. When analyzed independently, these datasets often overlook drivers of population decline, muddle community responses to ecological threats, and poorly predict population trajectories. Over the last decade, thanks to efforts like The Long Term Ecological Research Network and National Ecological Observatory Network, citizen science surveys, and technological advances, ecological datasets that provide insights about collections of organisms or multiple characteristics of the same organism have become prevalent. The conglomerate of datasets has the potential to provide novel insights, improve predictive performance, and disentangle the contributions of confounded factors, but specifying joint models that assimilate all the available data sources is both intellectually daunting and computationally prohibitive. I develop methodology for specifying computationally efficient integrated models. I discuss datasets frequently collected in ecology, objectives common to many analyses, and the methodological challenges associated with specifying joint models in these contexts. I introduce a suite of model building and computational techniques I used to facilitate inference in three applied analyses of ecological data. In a case study of the joint mammalian response to the bark beetle epidemic in Colorado, I describe a restricted regression approach to deconfounding the effects of environmental factors and community structure on species distributions. I highlight that fitting certain joint species distribution models in a restricted parameterization improves sampling efficiency. To improve abundance estimates for a federally protected species, I specify an integrated model for analyzing independent aerial and ground surveys. I use a Markov melding approach to facilitate posterior inference and construct the joint distribution implied by the prior information, assumptions, and data expressed across a chain of submodels. I extend the integrated model by assimilating additional demographic surveys of the species that allow abundance estimates to be linked to annual variability in population vital rates. To reduce computation time, both models are fit using a multi-stage Markov chain Monte Carlo algorithm with parallelization. In each applied analysis, I uncover associations that would have been overlooked had the datasets been analyzed independently and improve predictive performance relative to models fit to individual datasets.
Description
Zip file contains Animation of annual survey effort.
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Subject
data assimilation
joint species distribution modeling
Markov melding
integrated population modeling
Bayesian hierarchical modeling
Lesser prairie-chicken