A scaled Viterbi algorithm for allocating clones to one of two underlying states.
A work horse of the fit.model function. It uses a scaled version of the Viterbi algorithm to allocate clones to one of three underlying states as fitted using a heterogeneous HMM.
Viterbi.three(y, BFGS.output, BFGS.trans)
the data to be allocated to states
The output obtained from the find.param.three function
A list of the heterogeneous transition matrices
A vector of numbers indicating to which state clones are allocated to.
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