Uncovering ecological state dynamics with hidden Markov models

Type Article
Date 2020-12
Language English
Author(s) McClintock Brett T.1, Langrock Roland2, Gimenez Olivier3, Cam Emmanuelle4, Borchers David L.5, Glennie Richard5, Patterson Toby A.6, Coulson Tim
Affiliation(s) 1 : NOAA National Marine Fisheries Service Seattle WA ,USA
2 : Department of Business Administration and Economics Bielefeld University Bielefeld ,Germany
3 : CNRS Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, France
4 : Laboratoire des Sciences de l'Environnement Marin Institut Universitaire Européen de la Mer Univ. Brest, CNRS, IRD Ifremer ,France
5 : School of Mathematics and Statistics University of St Andrews St Andrews, UK
6 : CSIRO Oceans and Atmosphere Hobart, Australia
Source Ecology Letters (1461-023X) (Wiley), 2020-12 , Vol. 23 , N. 12 , P. 1878-1903
DOI 10.1111/ele.13610
WOS© Times Cited 72
Keyword(s) Behavioural ecology, community ecology, ecosystem ecology, hierarchical model, movement ecology, observation error, population ecology, state-space model, time series

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.

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Supplementary Material 14 173 KB Open access
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How to cite 

McClintock Brett T., Langrock Roland, Gimenez Olivier, Cam Emmanuelle, Borchers David L., Glennie Richard, Patterson Toby A., Coulson Tim (2020). Uncovering ecological state dynamics with hidden Markov models. Ecology Letters, 23(12), 1878-1903. Publisher's official version : https://doi.org/10.1111/ele.13610 , Open Access version : https://archimer.ifremer.fr/doc/00655/76692/