# Animal Movement Modelling using Hidden Markov Models

## 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