For a given model, computes the probability of the process being in the different states at each time point.
Logical indicating whether or not to return a list of state probabilities for each level of a hierarchical HMM. Ignored unless
The matrix of state probabilities, with element [i,j] the probability of being in state j in observation i.
Zucchini, W. and MacDonald, I.L. 2009. Hidden Markov Models for Time Series: An Introduction Using R. Chapman & Hall (London).
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