Learn R Programming

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.

Copy Link

Version

Install

install.packages('momentuHMM')

Monthly Downloads

647

Version

1.5.6

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

July 21st, 2025

Functions in momentuHMM (1.5.6)

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 crwSim objects

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

Constructor of crwHierData objects

Fit and predict tracks for using crawl

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

Constructor of crwHierSim objects

Constructor of crwData objects

Normal density function

Categorical density function

negative binomial density function

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

Log-normal density function

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

logistic density function

Exponential density function

Gamma density function

Von Mises density function

Get design matrix

student t density function

Convert hierarchical HMM structure to a conventional HMM

Bernoulli density function

Poisson density function

dwrpcauchy_rcpp

Wrapped Cauchy density function

Example dataset

Weibull density function

Get names of any covariates used in probability distribution parameters

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

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

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

is.momentuHierHMM

Is momentuHierHMM

Fit a multivariate HMM to the data

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

is.momentuHierHMMData

Is momentuHierHMMData

Mixture probabilities

is.momentuHMMData

Is momentuHMMData

Transition probability matrix

Constructor of miHMM objects

momentuHierHMMData

Constructor of momentuHierHMMData objects

Backward log-probabilities

Forward log-probabilities

Constructor of momentuHMMData objects

Constructor of momentuHierHMM objects

Preprocessing of the data streams and covariates

Plot stationary state probabilities

Scaling function: natural to working parameters.

Plot pseudo-residuals

Parameters definition

Plot observations on satellite image

Constructor of momentuHMM objects

Negative log-likelihood function

Negative log-likelihood

plot.momentuHMM

Plot momentuHMM

plot.momentuHMMData

Plot momentuHMMData or momentuHierHMMData

Constructor of miSum objects

Plot observations on raster image

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

Stationary state probabilities

print.momentuHMM

Print momentuHMM

Simulation tool

Random effects estimation

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

Pseudo-residuals

State probabilities

Observation error simulation tool

Scaling function: working to natural parameters

summary.momentuHMMData

Summary momentuHMMData

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

Transition probability matrix

Viterbi algorithm

Calculate pooled parameter estimates and states across multiple imputations

Calculate Akaike information criterion model weights

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

Constructor of HMMfits objects

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

Matrix of all probabilities

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

Fit HMMs to multiple imputation data