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momentuHMM

An 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 on CRAN. To install it:

install.packages("momentuHMM")

Install from Github

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

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

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

library(devtools)
install_github("bmcclintock/momentuHMM", ref="develop")

References

McClintock, B.T., Michelot, T. (2017) momentuHMM: R package for generalized hidden Markov models of animal movement. arXiv:1710.03786.

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

625

Version

1.2.0

License

GPL-3

Maintainer

Brett T McClintock

Last Published

October 20th, 2017

Functions in momentuHMM (1.2.0)

Merge crwData object with additional data streams and/or covariates

Fit and predict tracks for using crawl

Calculate pooled parameter estimates and states across multiple imputations

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

Fit HMMs to multiple imputation data

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

Matrix of all probabilities

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

Constructor of crwSim objects

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

Log-normal density function

Example dataset

Fit a multivariate HMM to the data

dwrpcauchy_rcpp

Wrapped Cauchy density function

Example data simulation

Backward log-probabilities

Constructor of miHMM objects

Normal density function

Poisson density function

Von Mises density function

Exponential density function

Gamma density function

Get names of any covariates used in probability distribution parameters

Get design matrix

is.momentuHMMData

Is momentuHMMData

Bernoulli density function

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

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

Get starting values for new model from existing momentuHMM model fit

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

Parameters definition

Constructor of momentuHMMData objects

Scaling function: natural to working parameters.

Preprocessing of the data streams and covariates

Forward log-probabilities

Constructor of miSum objects

Constructor of momentuHMM objects

Plot pseudo-residuals

Plot observations on satellite image

Transition probability matrix

Weibull density function

Negative log-likelihood function

Negative log-likelihood

Plot observations on raster image

plot.momentuHMM

Plot momentuHMM

plot.momentuHMMData

Plot momentuHMMData

Observation error simulation tool

State probabilities

Viterbi algorithm

Scaling function: working to natural parameters

Pseudo-residuals

Simulation tool

print.momentuHMM

Print momentuHMM