| Add smoothed gradient terms to data | addSmoothGradient |
| AIC | AIC.momentuHMM |
| Calculate Akaike information criterion model weights | AICweights |
| Matrix of all probabilities | allProbs |
| Check parameter length and order for a 'fitHMM' (or 'MIfitHMM') model | checkPar0 checkPar0.default checkPar0.hierarchical |
| Confidence intervals for working (i.e., beta) parameters | CIbeta |
| Convert standard direction angles (in radians relative to the x-axis) to turning angle covariates suitable for circular-circular regression on the angle mean | circAngles |
| Confidence intervals for the natural (i.e., real) parameters | CIreal CIreal.default CIreal.hierarchical |
| Transform a raster into a (x,y,z) list | collapseRaster |
| Merge crwData or crwHierData object with additional data streams and/or covariates | crawlMerge |
| Fit and predict tracks for using crawl | crawlWrap |
| Constructor of 'crwData' objects | crwData |
| Constructor of 'crwHierData' objects | crwHierData |
| Constructor of 'crwHierSim' objects | crwHierSim |
| Constructor of 'crwSim' objects | crwSim |
| Calculate and plot the (state-dependent) stationary (or utilization) distribution from a 'ctds' fitted model object | ctdsUD |
| Bernoulli density function | dbern_rcpp |
| Probability density function of the beta distribution (written in C++) | dbeta_rcpp |
| Categorical density function | dcat_rcpp |
| Correlated random walk Rice distribution | dcrwrice_rcpp |
| Correlated random walk von Mises density function | dcrwvm_rcpp |
| Exponential density function | dexp_rcpp |
| Gamma density function | dgamma_rcpp |
| Calculate distance between points y and z and turning angle between points x, y, and z | distAngle |
| Log-normal density function | dlnorm_rcpp |
| logistic density function | dlogis_rcpp |
| C++ implementation of multivariate Normal probability density function for multiple inputs | dmvnorm_rcpp |
| negative binomial density function | dnbinom_rcpp |
| Normal density function | dnorm_rcpp |
| Poisson density function | dpois_rcpp |
| student t density function | dt_rcpp |
| Von Mises density function | dvm_rcpp |
| Weibull density function | dweibull_rcpp |
| Wrapped Cauchy density function | dwrpcauchy_rcpp |
| Example dataset | example exampleData forest miExample |
| Expand vector of free working parameters to vector of all working parameters including any fixed parameters (used in fitHMM.R and nLogLike.R) | expandPar |
| Matrix Exponential | expmatrix_rcpp |
| Fit a continuous-time multivariate HMM to the data | fitCTHMM fitCTHMM.momentuHierHMMData fitCTHMM.momentuHMMData |
| Fit a multivariate HMM to the data | fitHMM fitHMM.momentuHierHMMData fitHMM.momentuHMMData |
| Convert hierarchical HMM structure to a conventional HMM | formatHierHMM |
| Get names of any covariates used in probability distribution parameters | getCovNames |
| Get design matrix | getDM_rcpp |
| Calculate gradient of spatial covariates using bilinear interpolation | getGradients |
| Get starting values from momentuHMM, miHMM, or miSum object returned by fitHMM, MIfitHMM, or MIpool | getPar |
| Get starting values for new model from existing 'momentuHMM' or 'momentuHierHMM' model fit | getPar0 getPar0.default getPar0.hierarchical |
| Get starting values on working scale based on design matrix and other parameter constraints | getParDM getParDM.default getParDM.hierarchical |
| Transition probability matrix | getTrProbs getTrProbs.default getTrProbs.hierarchical |
| Constructor of 'HMMfits' objects | HMMfits |
| 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 |
| Forward log-probabilities | logAlpha |
| Backward log-probabilities | logBeta |
| Fit continuous-time multivariate HMMs to multiple imputation data | MIfitCTHMM MIfitCTHMM.default MIfitCTHMM.hierarchical |
| Fit HMMs to multiple imputation data | MIfitHMM MIfitHMM.default MIfitHMM.hierarchical |
| Constructor of 'miHMM' objects | miHMM |
| Calculate pooled parameter estimates and states across multiple imputations | MIpool |
| Constructor of 'miSum' objects | miSum |
| Mixture probabilities | mixtureProbs |
| Constructor of 'momentuHierHMM' objects | momentuHierHMM |
| Constructor of 'momentuHierHMMData' objects | momentuHierHMMData |
| Constructor of 'momentuHMM' objects | momentuHMM |
| Constructor of 'momentuHMMData' objects | momentuHMMData |
| Scaling function: natural to working parameters. | n2w |
| Negative log-likelihood function | nLogLike |
| Negative log-likelihood | nLogLike_rcpp |
| Parameters definition | parDef |
| Plot 'crwData' | plot.crwData plot.crwHierData |
| Plot 'miHMM' | plot.miHMM |
| Plot 'miSum' | plot.miSum |
| Plot 'momentuHMM' | plot.momentuHMM |
| Plot 'momentuHMMData' or 'momentuHierHMMData' | plot.momentuHierHMMData plot.momentuHMMData |
| Plot pseudo-residuals | plotPR |
| Plot observations on satellite image | plotSat |
| Plot observations on raster image | plotSpatialCov |
| Plot states | plotStates |
| Plot stationary state probabilities | plotStationary |
| Preprocessing of continuous-time discrete-space (CTDS) movement HMMs using ctmcmove | prepCTDS prepCTDS.default prepCTDS.hierarchical |
| Preprocessing of the data streams and covariates | prepData prepData.default prepData.hierarchical |
| Print 'miHMM' | print.miHMM |
| Print 'miSum' | print.miSum |
| Print 'momentuHMM' | print.momentuHierHMM print.momentuHMM |
| Pseudo-residuals | pseudoRes |
| Random effects estimation | randomEffects |
| Set 'modelName' for a 'momentuHMM', 'miHMM', 'HMMfits', or 'miSum' object | setModelName |
| Set 'stateNames' for a 'momentuHMM', 'miHMM', 'HMMfits', or 'miSum' object | setStateNames |
| Simulation tool | simCTDS |
| Simulation tool | simCTHMM |
| Simulation tool | simData simHierData |
| Simulation tool | simHierCTDS |
| Simulation tool | simHierCTHMM |
| Observation error simulation tool | simObsData simObsData.momentuHierHMMData simObsData.momentuHMMData |
| State probabilities | stateProbs |
| Stationary state probabilities | stationary |
| Stationary distribution for a continuous-time Markov chain | stationary_rcpp |
| Summary 'momentuHMMData' | summary.momentuHierHMMData summary.momentuHMMData |
| Calculate proportion of time steps assigned to each state (i.e. "activity budgets") | timeInStates timeInStates.HMMfits timeInStates.miHMM timeInStates.momentuHMM |
| Transition probability matrix | trMatrix_rcpp |
| Turning angle | turnAngle |
| Viterbi algorithm | viterbi |
| Scaling function: working to natural parameters | w2n |
| Get XB | XBloop_rcpp |
