AIC.momentuHMM          AIC
AICweights              Calculate Akaike information criterion model
                        weights
CIbeta                  Confidence intervals for working (i.e., beta)
                        parameters
CIreal                  Confidence intervals for the natural (i.e.,
                        real) parameters
HMMfits                 Constructor of 'HMMfits' objects
MIfitHMM                Fit HMMs to multiple imputation data
MIpool                  Calculate pooled parameter estimates and states
                        across multiple imputations
XBloop_rcpp             Get XB
allProbs                Matrix of all probabilities
checkPar0               Check parameter length and order for a 'fitHMM'
                        (or 'MIfitHMM') model
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
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
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
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)
fitHMM                  Fit a multivariate HMM to the data
formatHierHMM           Convert hierarchical HMM structure to a
                        conventional HMM
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
getParDM                Get starting values on working scale based on
                        design matrix and other parameter constraints
getTrProbs              Transition probability matrix
is.HMMfits              Is HMMfits
is.crwData              Is crwData
is.crwHierData          Is crwHierData
is.crwHierSim           Is crwHierSim
is.crwSim               Is crwSim
is.miHMM                Is miHMM
is.miSum                Is miSum
is.momentuHMM           Is momentuHMM
is.momentuHMMData       Is momentuHMMData
is.momentuHierHMM       Is momentuHierHMM
is.momentuHierHMMData   Is momentuHierHMMData
logAlpha                Forward log-probabilities
logBeta                 Backward log-probabilities
miHMM                   Constructor of 'miHMM' objects
miSum                   Constructor of 'miSum' objects
mixtureProbs            Mixture probabilities
momentuHMM              Constructor of 'momentuHMM' objects
momentuHMMData          Constructor of 'momentuHMMData' objects
momentuHierHMM          Constructor of 'momentuHierHMM' objects
momentuHierHMMData      Constructor of 'momentuHierHMMData' 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' 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
print.miHMM             Print 'miHMM'
print.miSum             Print 'miSum'
print.momentuHMM        Print 'momentuHMM'
pseudoRes               Pseudo-residuals
randomEffects           Random effects estimation
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")
trMatrix_rcpp           Transition probability matrix
turnAngle               Turning angle
viterbi                 Viterbi algorithm
w2n                     Scaling function: working to natural parameters
