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


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Documentation for package ‘momentuHMM’ version 1.4.3

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AIC.momentuHMM AIC
AICweights Calculate Akaike information criterion model weights
allProbs Matrix of all probabilities
checkPar0 Check parameter length and order for a 'fitHMM' (or 'MIfitHMM') model
CIbeta Confidence intervals for working (i.e., beta) parameters
circAngles Convert standard direction angles (in radians relative to the x-axis) to turning angle covariates suitable for circular-circular regression on the angle mean
CIreal Confidence intervals for the natural (i.e., real) parameters
crawlMerge Merge crwData object with additional data streams and/or covariates
crawlWrap Fit and predict tracks for using crawl
crwData Constructor of 'crwData' objects
crwSim Constructor of 'crwSim' objects
dbern_rcpp Bernoulli density function
dbeta_rcpp Probability density function of the beta distribution (written in C++)
dexp_rcpp Exponential density function
dgamma_rcpp Gamma density function
distAngle Calculate distance between points y and z and turning angle between points x, y, and z
dlnorm_rcpp Log-normal density function
dnorm_rcpp Normal density function
dpois_rcpp Poisson density function
dvm_rcpp Von Mises density function
dweibull_rcpp Weibull density function
dwrpcauchy_rcpp Wrapped Cauchy density function
example Example dataset
exGen Example data simulation
expandPar Expand vector of free working parameters to vector of all working parameters including any fixed parameters (used in fitHMM.R and nLogLike.R)
fitHMM Fit a multivariate HMM to the data
forest Example dataset
getCovNames Get names of any covariates used in probability distribution parameters
getDM_rcpp Get design matrix
getPar Get starting values from momentuHMM, miHMM, or miSum object returned by fitHMM, MIfitHMM, or MIpool
getPar0 Get starting values for new model from existing 'momentuHMM' model fit
getParDM Get starting values on working scale based on design matrix and other parameter constraints
HMMfits Constructor of 'HMMfits' objects
is.crwData Is crwData
is.crwSim Is crwSim
is.HMMfits Is HMMfits
is.miHMM Is miHMM
is.miSum Is miSum
is.momentuHMM Is momentuHMM
is.momentuHMMData Is momentuHMMData
logAlpha Forward log-probabilities
logBeta Backward log-probabilities
miExample Example dataset
MIfitHMM Fit HMMs to multiple imputation data
miHMM Constructor of 'miHMM' objects
MIpool Calculate pooled parameter estimates and states across multiple imputations
miSum Constructor of 'miSum' objects
momentuHMM Constructor of 'momentuHMM' objects
momentuHMMData Constructor of 'momentuHMMData' objects
n2w Scaling function: natural to working parameters.
nLogLike Negative log-likelihood function
nLogLike_rcpp Negative log-likelihood
parDef Parameters definition
plot.crwData Plot 'crwData'
plot.miHMM Plot 'miHMM'
plot.miSum Plot 'miSum'
plot.momentuHMM Plot 'momentuHMM'
plot.momentuHMMData Plot 'momentuHMMData'
plotPR Plot pseudo-residuals
plotSat Plot observations on satellite image
plotSpatialCov Plot observations on raster image
plotStates Plot states
plotStationary Plot stationary state probabilities
prepData Preprocessing of the data streams and covariates
print.miHMM Print 'miHMM'
print.miSum Print 'miSum'
print.momentuHMM Print 'momentuHMM'
pseudoRes Pseudo-residuals
setModelName Set 'modelName' for a 'momentuHMM', 'miHMM', 'HMMfits', or 'miSum' object
setStateNames Set 'stateNames' for a 'momentuHMM', 'miHMM', 'HMMfits', or 'miSum' object
simData Simulation tool
simObsData Observation error simulation tool
stateProbs State probabilities
stationary Stationary state probabilities
summary.momentuHMMData Summary 'momentuHMMData'
timeInStates Calculate proportion of time steps assigned to each state (i.e. "activity budgets")
timeInStates.HMMfits Calculate proportion of time steps assigned to each state (i.e. "activity budgets")
timeInStates.miHMM Calculate proportion of time steps assigned to each state (i.e. "activity budgets")
timeInStates.momentuHMM Calculate proportion of time steps assigned to each state (i.e. "activity budgets")
trMatrix_rcpp Transition probability matrix
turnAngle Turning angle
viterbi Viterbi algorithm
w2n Scaling function: working to natural parameters
XBloop_rcpp Get XB