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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

514

Version

1.5.5

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

October 18th, 2022

Functions in momentuHMM (1.5.5)

Calculate pooled parameter estimates and states across multiple imputations

Constructor of HMMfits objects

Fit HMMs to multiple imputation data

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

Matrix of all probabilities

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

Calculate Akaike information criterion model weights

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

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

Constructor of crwHierData objects

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

Bernoulli density function

Constructor of crwSim objects

Constructor of crwHierSim objects

Log-normal density function

Exponential density function

Gamma density function

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

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

negative binomial density function

Poisson density function

Normal density function

Categorical density function

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

Constructor of crwData objects

Fit and predict tracks for using crawl

student t density function

logistic density function

dwrpcauchy_rcpp

Wrapped Cauchy density function

Get design matrix

Get names of any covariates used in probability distribution parameters

Fit a multivariate HMM to the data

Example dataset

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

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

Convert hierarchical HMM structure to a conventional HMM

Von Mises density function

Weibull density function

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

Transition probability matrix

Constructor of momentuHMM objects

Constructor of miSum objects

is.momentuHierHMM

Is momentuHierHMM

is.momentuHMMData

Is momentuHMMData

Constructor of miHMM objects

Mixture probabilities

is.momentuHierHMMData

Is momentuHierHMMData

Backward log-probabilities

Forward log-probabilities

Constructor of momentuHMMData objects

Parameters definition

momentuHierHMMData

Constructor of momentuHierHMMData objects

Negative log-likelihood

Constructor of momentuHierHMM objects

Negative log-likelihood function

Scaling function: natural to working parameters.

Plot stationary state probabilities

Preprocessing of the data streams and covariates

Plot pseudo-residuals

plot.momentuHMMData

Plot momentuHMMData or momentuHierHMMData

plot.momentuHMM

Plot momentuHMM

Plot observations on raster image

Plot observations on satellite image

Random effects estimation

Observation error simulation tool

summary.momentuHMMData

Summary momentuHMMData

print.momentuHMM

Print momentuHMM

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

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

Stationary state probabilities

State probabilities

Simulation tool

Pseudo-residuals

Transition probability matrix

Scaling function: working to natural parameters

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

Viterbi algorithm