The conditionally autoregressive hidden Markov model (CarHMM): inferring behavioural states from animal tracking data exhibiting conditional autocorrelation

DOI10.1007/S13253-019-00366-2zbMATH Open1428.62490arXiv1903.04999OpenAlexW2921931329MaRDI QIDQ2009135FDOQ2009135

Authors: Ethan Lawler, Kim Whoriskey, William H. Aeberhard, Chris Field, Joanna Mills Flemming 

Publication date: 27 November 2019

Published in: Journal of Agricultural, Biological and Environmental Statistics (Search for Journal in Brave)

Abstract: One of the central interests of animal movement ecology is relating movement characteristics to behavioural characteristics. The traditional discrete-time statistical tool for inferring unobserved behaviours from movement data is the hidden Markov model (HMM). While the HMM is an important and powerful tool, sometimes it is not flexible enough to appropriately fit the data. Data for marine animals often exhibit conditional autocorrelation, self-dependence of the step length process which cannot be explained solely by the behavioural state, which violates one of the main assumptions of the HMM. Using a grey seal track as an example, along with multiple simulation scenarios, we motivate and develop the conditionally autoregressive hidden Markov model (CarHMM), which is a generalization of the HMM designed specifically to handle conditional autocorrelation. In addition to introducing and examining the new CarHMM, we provide guidelines for all stages of an analysis using either an HMM or CarHMM. These include guidelines for pre-processing location data to obtain deflection angles and step lengths, model selection, and model checking. In addition to these practical guidelines, we link estimated model parameters to biologically meaningful quantities such as activity budget and residency time. We also provide interpretations of traditional "foraging" and "transiting" behaviours in the context of the new CarHMM parameters.

Full work available at URL: https://arxiv.org/abs/1903.04999

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zbMATH Keywords

hidden Markov modelmodel checkingdiscrete timeautoregressive processmovement ecologymarine animal movement

Mathematics Subject Classification ID

Markov processes: estimation; hidden Markov models (62M05) Time series, auto-correlation, regression, etc. in statistics (GARCH) (62M10) Applications of statistics to environmental and related topics (62P12) Animal behavior (92D50)

Cites Work

• Incorporating telemetry error into hidden Markov models of animal movement using multiple imputation
• Hidden Markov models for time series. An introduction using R
• Selecting the number of states in hidden Markov models: pragmatic solutions illustrated using animal movement
• Statistical modelling of individual animal movement: an overview of key methods and a discussion of practical challenges
• Multi-scale modeling of animal movement and general behavior data using hidden Markov models with hierarchical structures
• Asymptotic properties of the maximum likelihood estimator in autoregressive models with Markov regime
• Guest editor's introduction to the special issue on ``Animal movement modeling
• Imputation approaches for animal movement modeling
• Some theoretical results on Markov-switching autoregressive models with gamma innovations
• Probability-scale residuals for continuous, discrete, and censored data

Cited In (6)

• A general hidden state random walk model for animal movement
• Modeling the diving behavior of whales: a latent-variable approach with feedback and semi-Markovian components
• New formulation of the logistic-Gaussian process to analyze trajectory tracking data
• Multi-scale modeling of animal movement and general behavior data using hidden Markov models with hierarchical structures
• Incorporating telemetry error into hidden Markov models of animal movement using multiple imputation
• Animal movement modelling: independent or dependent models?

Uses Software

• moveHMM
• TMB
• swim
• momentuHMM

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