Year: 2020
Type: article
Abstract: 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.
Source: Ecology Letters
DOI: 10.1111/ele.13610
Institutions: NOAA National Marine Fisheries Service, National Oceanic and Atmospheric Administration, NOAA National Marine Fisheries Service Northwest Fisheries Science Center, Bielefeld University, Centre National de la Recherche Scientifique, Centre d'Écologie Fonctionnelle et Évolutive, Ifremer, Institut Universitaire Européen de la Mer, Laboratoire des Sciences de l'Environnement Marin, Institut de Recherche pour le Développement, University of St Andrews, CSIRO Oceans and Atmosphere
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Open Access status: hybrid
Estimated APC paid: $4,500
OpenAlex ID: W3008308101