Uncovering ecological state dynamics with hidden Markov models
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Ecological systems can often be characterised by changes among a finite set of underlying states pertaining to individuals, populations, communities or entire ecosystems through time. Owing to the inherent difficulty of empirical field studies, ecological state dynamics operating at any level of this hierarchy can often be unobservable or ?hidden?. Ecologists must therefore often contend with incomplete or indirect observations that are somehow related to these underlying processes. By formally disentangling state and observation processes based on simple yet powerful mathematical properties that can be used to describe many ecological phenomena, hidden Markov models (HMMs) can facilitate inferences about complex system state dynamics that might otherwise be intractable. However, HMMs have only recently begun to gain traction within the broader ecological community. We provide a gentle introduction to HMMs, establish some common terminology, review the immense scope of HMMs for applied ecological research and provide a tutorial on implementation and interpretation. By illustrating how practitioners can use a simple conceptual template to customise HMMs for their specific systems of interest, revealing methodological links between existing applications, and highlighting some practical considerations and limitations of these approaches, our goal is to help establish HMMs as a fundamental inferential tool for ecologists.
McClintock , B T , Langrock , R , Gimenez , O , Cam , E , Borchers , D L , Glennie , R & Patterson , T A 2020 , ' Uncovering ecological state dynamics with hidden Markov models ' , Ecology Letters , vol. Early View . https://doi.org/10.1111/ele.13610 , https://doi.org/10.1111/ele.13610
This article is a U.S. Government work and is in the public domain in the USA. Ecology Letters published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
DescriptionThis research was inspired in part by the SFB TRR 212 (NC3), which is funded by the German Research Foundation (DFG).
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