AIC.momentuHMM |
AIC |
AICweights |
Calculate Akaike information criterion model weights |
allProbs |
Matrix of all probabilities |
checkPar0 |
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 |
crawlMerge |
Merge crwData object with additional data streams and/or covariates |
crawlWrap |
Fit and predict tracks for using crawl |
crwData |
Constructor of 'crwData' objects |
crwSim |
Constructor of 'crwSim' objects |
dbern_rcpp |
Bernoulli density function |
dbeta_rcpp |
Probability density function of the beta distribution (written in C++) |
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 |
dnorm_rcpp |
Normal density function |
dpois_rcpp |
Poisson density function |
dvm_rcpp |
Von Mises density function |
dweibull_rcpp |
Weibull density function |
dwrpcauchy_rcpp |
Wrapped Cauchy density function |
example |
Example dataset |
exGen |
Example data simulation |
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 |
forest |
Example dataset |
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' model fit |
getParDM |
Get starting values on working scale based on design matrix and other parameter constraints |
HMMfits |
Constructor of 'HMMfits' objects |
is.crwData |
Is crwData |
is.crwSim |
Is crwSim |
is.HMMfits |
Is HMMfits |
is.miHMM |
Is miHMM |
is.miSum |
Is miSum |
is.momentuHMM |
Is momentuHMM |
is.momentuHMMData |
Is momentuHMMData |
logAlpha |
Forward log-probabilities |
logBeta |
Backward log-probabilities |
miExample |
Example dataset |
MIfitHMM |
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 |
momentuHMM |
Constructor of 'momentuHMM' objects |
momentuHMMData |
Constructor of 'momentuHMMData' 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' |
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 |
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") |
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 |
viterbi |
Viterbi algorithm |
w2n |
Scaling function: working to natural parameters |
XBloop_rcpp |
Get XB |