HMM: Create a HMM object

In STAN: The Genomic STate ANnotation Package

Description

This function creates a HMM object.

Usage

HMM(initProb = numeric(), transMat = matrix(numeric(), ncol = 1, nrow = 1),
  emission, nStates = numeric(), status = character(),
  stateNames = character(), dimNames = character(), LogLik = numeric())

Arguments

initProb	Initial state probabilities.
transMat	Transition probabilities
emission	Emission parameters as an HMMEmission object.
nStates	Number of states.
status	of the HMM. On of c('initial', 'EM').
stateNames	State names.
dimNames	Names of data tracks.
LogLik	Log likelihood of a fitted HMM.

Value

HMM

See Also

HMMEmission

Examples

nStates = 5
means = list(4,11,4,11,-1)
Sigma = lapply(list(4,4,4,4,4), as.matrix)
transMat = matrix(1/nStates, nrow=nStates, ncol=nStates)
initProb = rep(1/nStates, nStates)
HMM(initProb=initProb, transMat=transMat, emission=HMMEmission(type='Gaussian', parameters=list(mu=means, cov=Sigma), nStates=length(means)), nStates=nStates, status='initial')

STAN documentation built on Nov. 8, 2020, 11:11 p.m.