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

## Documentation for package ‘momentuHMM’ version 1.5.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G H I L M N P R S T V W X

## -- A --

AIC.momentuHMM | AIC
AICweights | Calculate Akaike information criterion model weights
allProbs | Matrix of all probabilities

## -- C --

checkPar0 | Check parameter length and order for a 'fitHMM' (or 'MIfitHMM') model
checkPar0.default | Check parameter length and order for a 'fitHMM' (or 'MIfitHMM') model
checkPar0.hierarchical | 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
CIreal.default | Confidence intervals for the natural (i.e., real) parameters
CIreal.hierarchical | Confidence intervals for the natural (i.e., real) parameters
crawlMerge | Merge crwData or crwHierData object with additional data streams and/or covariates
crawlWrap | Fit and predict tracks for using crawl
crwData | Constructor of 'crwData' objects
crwHierData | Constructor of 'crwHierData' objects
crwHierSim | Constructor of 'crwHierSim' objects
crwSim | Constructor of 'crwSim' objects

## -- D --

dbern_rcpp | Bernoulli density function
dbeta_rcpp | Probability density function of the beta distribution (written in C++)
dcat_rcpp | Categorical density function
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
dlogis_rcpp | logistic density function
dmvnorm_rcpp | C++ implementation of multivariate Normal probability density function for multiple inputs
dnbinom_rcpp | negative binomial density function
dnorm_rcpp | Normal density function
dpois_rcpp | Poisson density function
dt_rcpp | student t density function
dvm_rcpp | Von Mises density function
dweibull_rcpp | Weibull density function
dwrpcauchy_rcpp | Wrapped Cauchy density function

## -- E --

example | Example dataset
exampleData | Example dataset
expandPar | Expand vector of free working parameters to vector of all working parameters including any fixed parameters (used in fitHMM.R and nLogLike.R)

## -- F --

fitHMM | Fit a multivariate HMM to the data
fitHMM.momentuHierHMMData | Fit a multivariate HMM to the data
fitHMM.momentuHMMData | Fit a multivariate HMM to the data
forest | Example dataset
formatHierHMM | Convert hierarchical HMM structure to a conventional HMM

## -- G --

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' or 'momentuHierHMM' model fit
getPar0.default | Get starting values for new model from existing 'momentuHMM' or 'momentuHierHMM' model fit
getPar0.hierarchical | Get starting values for new model from existing 'momentuHMM' or 'momentuHierHMM' model fit
getParDM | Get starting values on working scale based on design matrix and other parameter constraints
getParDM.default | Get starting values on working scale based on design matrix and other parameter constraints
getParDM.hierarchical | Get starting values on working scale based on design matrix and other parameter constraints
getTrProbs | Transition probability matrix
getTrProbs.default | Transition probability matrix
getTrProbs.hierarchical | Transition probability matrix

## -- H --

HMMfits | Constructor of 'HMMfits' objects

## -- I --

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

## -- L --

logAlpha | Forward log-probabilities
logBeta | Backward log-probabilities

## -- M --

miExample | Example dataset
MIfitHMM | Fit HMMs to multiple imputation data
MIfitHMM.default | Fit HMMs to multiple imputation data
MIfitHMM.hierarchical | 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
mixtureProbs | Mixture probabilities
momentuHierHMM | Constructor of 'momentuHierHMM' objects
momentuHierHMMData | Constructor of 'momentuHierHMMData' objects
momentuHMM | Constructor of 'momentuHMM' objects
momentuHMMData | Constructor of 'momentuHMMData' objects

## -- N --

n2w | Scaling function: natural to working parameters.
nLogLike | Negative log-likelihood function
nLogLike_rcpp | Negative log-likelihood

## -- P --

parDef | Parameters definition
plot.crwData | Plot 'crwData'
plot.crwHierData | Plot 'crwData'
plot.miHMM | Plot 'miHMM'
plot.miSum | Plot 'miSum'
plot.momentuHierHMMData | Plot 'momentuHMMData' or 'momentuHierHMMData'
plot.momentuHMM | Plot 'momentuHMM'
plot.momentuHMMData | Plot 'momentuHMMData' or 'momentuHierHMMData'
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
prepData.default | Preprocessing of the data streams and covariates
prepData.hierarchical | Preprocessing of the data streams and covariates
print.miHMM | Print 'miHMM'
print.miSum | Print 'miSum'
print.momentuHierHMM | Print 'momentuHMM'
print.momentuHMM | Print 'momentuHMM'
pseudoRes | Pseudo-residuals

## -- R --

randomEffects | Random effects estimation

## -- S --

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
simHierData | Simulation tool
simObsData | Observation error simulation tool
simObsData.momentuHierHMMData | Observation error simulation tool
simObsData.momentuHMMData | Observation error simulation tool
stateProbs | State probabilities
stationary | Stationary state probabilities
summary.momentuHierHMMData | Summary 'momentuHMMData'
summary.momentuHMMData | Summary 'momentuHMMData'

## -- T --

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

## -- V --

viterbi | Viterbi algorithm

## -- W --

w2n | Scaling function: working to natural parameters

## -- X --

XBloop_rcpp | Get XB