An Introduction to Animal Movement Modeling with Hidden Markov Models using Stan for Bayesian Inference

06/27/2018

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Hidden Markov models (HMMs) are popular time series model in many fields including ecology, economics and genetics. HMMs can be defined over discrete or continuous time, though here we only cover the former. In the field of movement ecology in particular, HMMs have become a popular tool for the analysis of movement data because of their ability to connect observed movement data to an underlying latent process, generally interpreted as the animal's unobserved behavior. Further, we model the tendency to persist in a given behavior over time. Notation presented here will generally follow the format of Zucchini et al. (2016) and cover HMMs applied in an unsupervised case to animal movement data, specifically positional data. We provide Stan code to analyze movement data of the wild haggis as presented first in Michelot et al. (2016).

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An Introduction to Animal Movement Modeling with Hidden Markov Models using Stan for Bayesian Inference

Integrated Continuous-time Hidden Markov Models

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

Inference of Dynamic Regimes in the Microbiome

A gentle tutorial on accelerated parameter and confidence interval estimation for hidden Markov models using Template Model Builder

momentuHMM: R package for generalized hidden Markov models of animal movement

Modeling animal movement with directional persistence and attractive points

Comment on "Under-reported data analysis with INAR-hidden Markov chains"

An Introduction to Animal Movement Modeling with Hidden Markov Models using Stan for Bayesian Inference

Related Research

Integrated Continuous-time Hidden Markov Models

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

Inference of Dynamic Regimes in the Microbiome

A gentle tutorial on accelerated parameter and confidence interval estimation for hidden Markov models using Template Model Builder

momentuHMM: R package for generalized hidden Markov models of animal movement

Modeling animal movement with directional persistence and attractive points

Comment on "Under-reported data analysis with INAR-hidden Markov chains"