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momentuHMM

R package for Maximum likelihood analysis Of animal MovemENT behavior Using multivariate Hidden Markov Models

Get started with the vignette: Guide to using momentuHMM

Installation instructions

CRAN release

The package is available at . To install it:

install.packages("momentuHMM")

Install from Github

To install the latest (stable) version of the package from Github:

library(remotes)
install_github("bmcclintock/momentuHMM")

To install the latest (unstable) version of the package from Github:

library(remotes)
install_github("bmcclintock/momentuHMM@develop")

References

McClintock, B.T., Michelot, T. (2018) momentuHMM: R package for generalized hidden Markov models of animal movement. Methods in Ecology and Evolution, 9(6), 1518-1530.

McClintock, B.T., King R., Thomas L., Matthiopoulos J., McConnell B.J., Morales J.M. (2012) A general discrete-time modeling framework for animal movement using multistate random walks. Ecological Monographs, 82(3), 335-349.

McClintock, B.T. (2017) Incorporating telemetry error into hidden Markov models of animal movement using multiple imputation. Journal of Agricultural, Biological, and Environmental Statistics, 22(3), 249-269.

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Version

Install

install.packages('momentuHMM')

Monthly Downloads

2,143

Version

1.5.8

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/bmcclintock/momentuHMM

Homepage

https://github.com/bmcclintock/momentuHMM/discussions

Maintainer

Brett T McClintock

Last Published

November 25th, 2025

Functions in momentuHMM (1.5.8)

student t density function

Poisson density function

Constructor of crwSim objects

Gamma density function

Exponential density function

Get design matrix

Normal density function

negative binomial density function

Get starting values from momentuHMM, miHMM, or miSum object returned by fitHMM, MIfitHMM, or MIpool

Von Mises density function

Transition probability matrix

Fit a multivariate HMM to the data

Bernoulli density function

Log-normal density function

Weibull density function

Calculate distance between points y and z and turning angle between points x, y, and z

Constructor of crwHierData objects

Expand vector of free working parameters to vector of all working parameters including any fixed parameters (used in fitHMM.R and nLogLike.R)

Probability density function of the beta distribution (written in C++)

Constructor of crwHierSim objects

Example dataset

dwrpcauchy_rcpp

Wrapped Cauchy density function

Forward log-probabilities

Categorical density function

is.momentuHMMData

Is momentuHMMData

Get starting values for new model from existing momentuHMM or momentuHierHMM model fit

is.momentuHierHMM

Is momentuHierHMM

is.momentuHierHMMData

Is momentuHierHMMData

Constructor of momentuHMMData objects

Constructor of momentuHierHMM objects

Plot pseudo-residuals

Backward log-probabilities

momentuHierHMMData

Constructor of momentuHierHMMData objects

Scaling function: natural to working parameters.

Plot stationary state probabilities

logistic density function

C++ implementation of multivariate Normal probability density function for multiple inputs

Plot observations on raster image

Parameters definition

Mixture probabilities

Get starting values on working scale based on design matrix and other parameter constraints

Constructor of momentuHMM objects

Plot observations on satellite image

Get names of any covariates used in probability distribution parameters

Convert hierarchical HMM structure to a conventional HMM

Preprocessing of the data streams and covariates

Negative log-likelihood

Negative log-likelihood function

plot.momentuHMM

Plot momentuHMM

Set modelName for a momentuHMM, miHMM, HMMfits, or miSum object

Random effects estimation

Stationary state probabilities

summary.momentuHMMData

Summary momentuHMMData

Viterbi algorithm

plot.momentuHMMData

Plot momentuHMMData or momentuHierHMMData

Constructor of miHMM objects

Constructor of miSum objects

Observation error simulation tool

State probabilities

Calculate proportion of time steps assigned to each state (i.e. “activity budgets”)

Transition probability matrix

Set stateNames for a momentuHMM, miHMM, HMMfits, or miSum object

Simulation tool

print.momentuHMM

Print momentuHMM

Scaling function: working to natural parameters

Pseudo-residuals

Matrix of all probabilities

Calculate pooled parameter estimates and states across multiple imputations

Confidence intervals for working (i.e., beta) parameters

Confidence intervals for the natural (i.e., real) parameters

Constructor of HMMfits objects

Check parameter length and order for a fitHMM (or MIfitHMM) model

Fit HMMs to multiple imputation data

Calculate Akaike information criterion model weights

Fit and predict tracks for using crawl

Convert standard direction angles (in radians relative to the x-axis) to turning angle covariates suitable for circular-circular regression on the angle mean

Constructor of crwData objects

Merge crwData or crwHierData object with additional data streams and/or covariates