Animal Movement Modelling using Hidden Markov Models

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Documentation for package ‘moveHMM’ version 1.9

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

AIC.moveHMM	AIC
angleCI	Confidence intervals for angle parameters
CI	Confidence intervals
dexp_rcpp	Exponential density function
dgamma_rcpp	Gamma density function
dlnorm_rcpp	Log-normal density function
dvm_rcpp	Von Mises density function
dweibull_rcpp	Weibull density function
dwrpcauchy_rcpp	Wrapped Cauchy density function
elk_data	Elk data set from Morales et al. (2004, Ecology)
example	Example dataset
exGen	Example data simulation
fitHMM	Fit an HMM to the data
getPalette	Discrete colour palette for states
getPlotData	Data to produce plots of fitted model
haggis_data	Wild haggis data set from Michelot et al. (2016, Methods Eco Evol)
is.moveData	Is moveData
is.moveHMM	Is moveHMM
logAlpha	Forward log-probabilities
logBeta	Backward log-probabilities
moveData	Constructor of 'moveData' objects
moveHMM	Constructor of 'moveHMM' objects
n2w	Scaling function: natural to working parameters.
nLogLike	Negative log-likelihood function
nLogLike_rcpp	Negative log-likelihood
parDef	Parameters definition
plot.moveData	Plot 'moveData'
plot.moveHMM	Plot 'moveHMM'
plotPR	Plot pseudo-residuals
plotSat	Plot observations on satellite image
plotStates	Plot states
plotStationary	Plot stationary state probabilities
predictStationary	Predict stationary state probabilities
predictTPM	Predict transition probabilities for new covariate values
prepData	Preprocessing of the tracking data
print.moveHMM	Print 'moveHMM'
pseudoRes	Pseudo-residuals
simData	Simulation tool
stateProbs	State probabilities
stationary	Stationary state probabilities
summary.moveData	Summary 'moveData'
trMatrix_rcpp	Transition probability matrix
turnAngle	Turning angle
viterbi	Viterbi algorithm
w2n	Scaling function: working to natural parameters