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Viterbi algorithm for state decoding in inhomogeneous HMMs

viterbi_g.Rd

The Viterbi algorithm decodes the most probable state sequence of an HMM.

Usage

viterbi_g(delta, Gamma, allprobs, trackID = NULL, mod = NULL)

Arguments

delta

initial distribution; either

  • a vector of length nStates, or

  • a matrix of dimension c(nTracks, nStates) if trackID is provided

Gamma

array of transition probability matrices of dimension c(nStates, nStates, nObs), where the first slice of each track is ignored as there is no transition into the start of a track. For a single track, an array of dimension c(nStates, nStates, nObs-1) is also accepted.

allprobs

matrix of state-dependent probabilities or density values of dimension c(nObs, nStates)

trackID

optional vector of length nObs containing nTracks unique IDs that separate tracks

mod

optional model object containing delta, Gamma, allprobs, and optionally trackID. When using RTMB::MakeADFun or qreml with forward_g in the likelihood, these are reported automatically after model fitting and the object returned by RTMB::report() or qreml can be passed directly.

Value

vector of decoded states of length nObs

See also

Other decoding functions: stateprobs(), stateprobs_g(), stateprobs_p(), viterbi(), viterbi_p()

Examples

delta = c(0.5, 0.5)
Gamma = tpm_g(runif(10), matrix(c(-2,-2,1,-1), nrow = 2))
allprobs = matrix(runif(20), nrow = 10, ncol = 2)
states = viterbi_g(delta, Gamma[,,-1], allprobs)