Man pages for momentuHMM
Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models

AIC.momentuHMMAIC
AICweightsCalculate Akaike information criterion model weights
allProbsMatrix of all probabilities
checkPar0Check parameter length and order for a 'fitHMM' (or...
CIbetaConfidence intervals for working (i.e., beta) parameters
circAnglesConvert standard direction angles (in radians relative to the...
CIrealConfidence intervals for the natural (i.e., real) parameters
crawlMergeMerge crwData or crwHierData object with additional data...
crawlWrapFit and predict tracks for using crawl
crwDataConstructor of 'crwData' objects
crwHierDataConstructor of 'crwHierData' objects
crwHierSimConstructor of 'crwHierSim' objects
crwSimConstructor of 'crwSim' objects
dbern_rcppBernoulli density function
dbeta_rcppProbability density function of the beta distribution...
dcat_rcppCategorical density function
dexp_rcppExponential density function
dgamma_rcppGamma density function
distAngleCalculate distance between points y and z and turning angle...
dlnorm_rcppLog-normal density function
dlogis_rcpplogistic density function
dmvnorm_rcppC++ implementation of multivariate Normal probability density...
dnbinom_rcppnegative binomial density function
dnorm_rcppNormal density function
dpois_rcppPoisson density function
dt_rcppstudent t density function
dvm_rcppVon Mises density function
dweibull_rcppWeibull density function
dwrpcauchy_rcppWrapped Cauchy density function
exampleDataExample dataset
expandParExpand vector of free working parameters to vector of all...
fitHMMFit a multivariate HMM to the data
formatHierHMMConvert hierarchical HMM structure to a conventional HMM
getCovNamesGet names of any covariates used in probability distribution...
getDM_rcppGet design matrix
getParGet starting values from momentuHMM, miHMM, or miSum object...
getPar0Get starting values for new model from existing 'momentuHMM'...
getParDMGet starting values on working scale based on design matrix...
getTrProbsTransition probability matrix
HMMfitsConstructor of 'HMMfits' objects
is.crwDataIs crwData
is.crwHierDataIs crwHierData
is.crwHierSimIs crwHierSim
is.crwSimIs crwSim
is.HMMfitsIs HMMfits
is.miHMMIs miHMM
is.miSumIs miSum
is.momentuHierHMMIs momentuHierHMM
is.momentuHierHMMDataIs momentuHierHMMData
is.momentuHMMIs momentuHMM
is.momentuHMMDataIs momentuHMMData
logAlphaForward log-probabilities
logBetaBackward log-probabilities
MIfitHMMFit HMMs to multiple imputation data
miHMMConstructor of 'miHMM' objects
MIpoolCalculate pooled parameter estimates and states across...
miSumConstructor of 'miSum' objects
mixtureProbsMixture probabilities
momentuHierHMMConstructor of 'momentuHierHMM' objects
momentuHierHMMDataConstructor of 'momentuHierHMMData' objects
momentuHMMConstructor of 'momentuHMM' objects
momentuHMMDataConstructor of 'momentuHMMData' objects
n2wScaling function: natural to working parameters.
nLogLikeNegative log-likelihood function
nLogLike_rcppNegative log-likelihood
parDefParameters definition
plot.crwDataPlot 'crwData'
plot.miHMMPlot 'miHMM'
plot.miSumPlot 'miSum'
plot.momentuHMMPlot 'momentuHMM'
plot.momentuHMMDataPlot 'momentuHMMData' or 'momentuHierHMMData'
plotPRPlot pseudo-residuals
plotSatPlot observations on satellite image
plotSpatialCovPlot observations on raster image
plotStatesPlot states
plotStationaryPlot stationary state probabilities
prepDataPreprocessing of the data streams and covariates
print.miHMMPrint 'miHMM'
print.miSumPrint 'miSum'
print.momentuHMMPrint 'momentuHMM'
pseudoResPseudo-residuals
randomEffectsRandom effects estimation
setModelNameSet 'modelName' for a 'momentuHMM', 'miHMM', 'HMMfits', or...
setStateNamesSet 'stateNames' for a 'momentuHMM', 'miHMM', 'HMMfits', or...
simDataSimulation tool
simObsDataObservation error simulation tool
stateProbsState probabilities
stationaryStationary state probabilities
summary.momentuHMMDataSummary 'momentuHMMData'
timeInStatesCalculate proportion of time steps assigned to each state...
trMatrix_rcppTransition probability matrix
turnAngleTurning angle
viterbiViterbi algorithm
w2nScaling function: working to natural parameters
XBloop_rcppGet XB
momentuHMM documentation built on July 7, 2021, 9:06 a.m.