This package is considered a duplicate. The official version of this package is found at:https://bmcclintock.r-universe.dev/momentuHMM

Package: momentuHMM 1.5.8

Brett McClintock

momentuHMM: Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models

Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, hierarchical HMMs, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, random effects, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.

Authors:Brett McClintock [aut, cre], Theo Michelot [aut]

momentuHMM_1.5.8.tar.gz
momentuHMM_1.5.8.zip(r-4.7)momentuHMM_1.5.8.zip(r-4.6)momentuHMM_1.5.8.zip(r-4.5)
momentuHMM_1.5.8.tgz(r-4.6-x86_64)momentuHMM_1.5.8.tgz(r-4.6-arm64)momentuHMM_1.5.8.tgz(r-4.5-x86_64)momentuHMM_1.5.8.tgz(r-4.5-arm64)
momentuHMM_1.5.8.tar.gz(r-4.7-arm64)momentuHMM_1.5.8.tar.gz(r-4.7-x86_64)momentuHMM_1.5.8.tar.gz(r-4.6-arm64)momentuHMM_1.5.8.tar.gz(r-4.6-x86_64)
momentuHMM_1.5.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
momentuHMM/json (API)

# Install 'momentuHMM' in R:

install.packages('momentuHMM', repos = c('https://ocean-tracking-network.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bmcclintock/momentuhmm/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

example - Example dataset
forest - Example dataset
miExample - Example dataset

On CRAN:

animal-movement hidden-markov-model hmm telemetry-data time-series-analysis openblas cpp

8.69 score 54 stars 301 scripts 684 downloads 6 mentions 33 exports 50 dependencies

Last updated from:49f4addec3. Checks:13 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	OK	353
linux-devel-x86_64	OK	495
source / vignettes	OK	2004
linux-release-arm64	OK	348
linux-release-x86_64	OK	440
macos-release-arm64	OK	215
macos-release-x86_64	OK	566
macos-oldrel-arm64	OK	233
macos-oldrel-x86_64	OK	381
windows-devel	OK	391
windows-release	OK	353
windows-oldrel	OK	354
wasm-release	OK	241

Exports:AICweights checkPar0 CIbeta circAngles CIreal crawlMerge crawlWrap fitHMM formatHierHMM getPar getPar0 getParDM getTrProbs MIfitHMM MIpool mixtureProbs plotPR plotSat plotSpatialCov plotStates plotStationary prepData pseudoRes randomEffects setModelName setStateNames simData simHierData simObsData stateProbs stationary timeInStates viterbi

Dependencies:boot Brobdingnag CircStats class classInt cli codetools cpp11 crawl DBI digest doParallel doRNG dplyr e1071 foreach generics glue iterators KernSmooth lattice lifecycle lubridate magrittr MASS Matrix mvtnorm numDeriv pillar pkgconfig proxy purrr R6 raster Rcpp RcppArmadillo rlang rngtools s2 sf sp terra tibble tidyselect timechange units utf8 vctrs withr wk

Guide to using momentuHMM

Introduction | momentuHMM overview | Examples | Discussion

Rendered frommomentuHMM.pdf.asisusingR.rsp::asis

Last update: 2019-12-17
Started: 2019-12-17

Help page	Topics
AIC	AIC.momentuHMM
Calculate Akaike information criterion model weights	AICweights
Matrix of all probabilities	allProbs
Check parameter length and order for a 'fitHMM' (or 'MIfitHMM') model	checkPar0 checkPar0.default checkPar0.hierarchical
Confidence intervals for working (i.e., beta) parameters	CIbeta
Convert standard direction angles (in radians relative to the x-axis) to turning angle covariates suitable for circular-circular regression on the angle mean	circAngles
Confidence intervals for the natural (i.e., real) parameters	CIreal CIreal.default CIreal.hierarchical
Merge crwData or crwHierData object with additional data streams and/or covariates	crawlMerge
Fit and predict tracks for using crawl	crawlWrap
Constructor of 'crwData' objects	crwData
Constructor of 'crwHierData' objects	crwHierData
Constructor of 'crwHierSim' objects	crwHierSim
Constructor of 'crwSim' objects	crwSim
Bernoulli density function	dbern_rcpp
Probability density function of the beta distribution (written in C++)	dbeta_rcpp
Categorical density function	dcat_rcpp
Exponential density function	dexp_rcpp
Gamma density function	dgamma_rcpp
Calculate distance between points y and z and turning angle between points x, y, and z	distAngle
Log-normal density function	dlnorm_rcpp
logistic density function	dlogis_rcpp
C++ implementation of multivariate Normal probability density function for multiple inputs	dmvnorm_rcpp
negative binomial density function	dnbinom_rcpp
Normal density function	dnorm_rcpp
Poisson density function	dpois_rcpp
student t density function	dt_rcpp
Von Mises density function	dvm_rcpp
Weibull density function	dweibull_rcpp
Wrapped Cauchy density function	dwrpcauchy_rcpp
Example dataset	example exampleData forest miExample
Expand vector of free working parameters to vector of all working parameters including any fixed parameters (used in fitHMM.R and nLogLike.R)	expandPar
Fit a multivariate HMM to the data	fitHMM fitHMM.momentuHierHMMData fitHMM.momentuHMMData
Convert hierarchical HMM structure to a conventional HMM	formatHierHMM
Get names of any covariates used in probability distribution parameters	getCovNames
Get design matrix	getDM_rcpp
Get starting values from momentuHMM, miHMM, or miSum object returned by fitHMM, MIfitHMM, or MIpool	getPar
Get starting values for new model from existing 'momentuHMM' or 'momentuHierHMM' model fit	getPar0 getPar0.default getPar0.hierarchical
Get starting values on working scale based on design matrix and other parameter constraints	getParDM getParDM.default getParDM.hierarchical
Transition probability matrix	getTrProbs getTrProbs.default getTrProbs.hierarchical
Constructor of 'HMMfits' objects	HMMfits
Is crwData	is.crwData
Is crwHierData	is.crwHierData
Is crwHierSim	is.crwHierSim
Is crwSim	is.crwSim
Is HMMfits	is.HMMfits
Is miHMM	is.miHMM
Is miSum	is.miSum
Is momentuHierHMM	is.momentuHierHMM
Is momentuHierHMMData	is.momentuHierHMMData
Is momentuHMM	is.momentuHMM
Is momentuHMMData	is.momentuHMMData
Forward log-probabilities	logAlpha
Backward log-probabilities	logBeta
Fit HMMs to multiple imputation data	MIfitHMM MIfitHMM.default MIfitHMM.hierarchical
Constructor of 'miHMM' objects	miHMM
Calculate pooled parameter estimates and states across multiple imputations	MIpool
Constructor of 'miSum' objects	miSum
Mixture probabilities	mixtureProbs
Constructor of 'momentuHierHMM' objects	momentuHierHMM
Constructor of 'momentuHierHMMData' objects	momentuHierHMMData
Constructor of 'momentuHMM' objects	momentuHMM
Constructor of 'momentuHMMData' objects	momentuHMMData
Scaling function: natural to working parameters.	n2w
Negative log-likelihood function	nLogLike
Negative log-likelihood	nLogLike_rcpp
Parameters definition	parDef
Plot 'crwData'	plot.crwData plot.crwHierData
Plot 'miHMM'	plot.miHMM
Plot 'miSum'	plot.miSum
Plot 'momentuHMM'	plot.momentuHMM
Plot 'momentuHMMData' or 'momentuHierHMMData'	plot.momentuHierHMMData plot.momentuHMMData
Plot pseudo-residuals	plotPR
Plot observations on satellite image	plotSat
Plot observations on raster image	plotSpatialCov
Plot states	plotStates
Plot stationary state probabilities	plotStationary
Preprocessing of the data streams and covariates	prepData prepData.default prepData.hierarchical
Print 'miHMM'	print.miHMM
Print 'miSum'	print.miSum
Print 'momentuHMM'	print.momentuHierHMM print.momentuHMM
Pseudo-residuals	pseudoRes
Random effects estimation	randomEffects
Set 'modelName' for a 'momentuHMM', 'miHMM', 'HMMfits', or 'miSum' object	setModelName
Set 'stateNames' for a 'momentuHMM', 'miHMM', 'HMMfits', or 'miSum' object	setStateNames
Simulation tool	simData simHierData
Observation error simulation tool	simObsData simObsData.momentuHierHMMData simObsData.momentuHMMData
State probabilities	stateProbs
Stationary state probabilities	stationary
Summary 'momentuHMMData'	summary.momentuHierHMMData summary.momentuHMMData
Calculate proportion of time steps assigned to each state (i.e. "activity budgets")	timeInStates timeInStates.HMMfits timeInStates.miHMM timeInStates.momentuHMM
Transition probability matrix	trMatrix_rcpp
Turning angle	turnAngle
Viterbi algorithm	viterbi
Scaling function: working to natural parameters	w2n
Get XB	XBloop_rcpp

Package: momentuHMM 1.5.8

momentuHMM: Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models

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