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

Documentation for package ‘momentuHMM’ version 1.5.5

Help Pages

-- 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 --

Constructor of 'HMMfits' objects

-- I --

-- 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 --

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 algorithm

-- W --

w2n	Scaling function: working to natural parameters

-- X --

Get XB