viterbi: Most probable state sequence.

Description Usage Arguments Details Value Warning Thanks Author(s) References See Also Examples

View source: R/viterbi.R


Calculates “the” most probable state sequence underlying each of one or more replicate observation sequences.


viterbi(y, model = NULL, tpm, Rho, ispd=NULL,log=FALSE, warn=TRUE)



The observations for which the underlying most probable hidden states are required. May be a sequence of observations, or a list each entry of which constitutes an independent sequence of observations. If y is missing (and if model is not NULL) then y is extracted from model, provided that the y component of model is present. Otherwise an error is given.


An object describing a hidden Markov model, as fitted to the data set y by hmm().


The transition probability matrix for a hidden Markov model; ignored if model is non-null.


An object specifying the probability distributions of the observations for a hidden Markov model. See hmm(). Ignored if model is non-null. Should bear some reasonable relationship to y.

If Rho has dimension names (or if its entries have dimension names in the case where Rho is a list) then the appropriate dimension names must include all corresponding values of the observations. If a relevant vector of dimension names is NULL then it is formed as the sort unique values of the approprate columns of the observation matrices. In this case the corresponding dimensions must match the number of unique values.


The initial state probability distribution for a hidden Markov model; ignored if model is non-null. Should bear some reasonable relationship to y. If model and ispd are both NULL then ispd is set equal to the stationary distribution calculated from tpm.


Logical scalar. Should logarithms be used in the recursive calculations of the probabilities involved in the Viterbi algorithm, so as to avoid underflow? If log is FALSE then underflow is avoided instead by a normalization procedure. The quantity delta (see Rabiner 1989, page 264) is replaced by delta/sum(delta) at each step. It should actually make no difference whether log is set to TRUE. I just included the option because I could. Also the HMM package uses the logarithm approach so setting log=TRUE might be of interest if comparisons are to be made between the results of the two packages.


Logical scalar; should a warning be issued if Rho hasn't got relevant dimension names? (Note that if this is so, then the corresponding dimension names are formed from the sorted unique values of y or of the appropriate column(s) of y. And if this is so, then the user should be sure that the ordering of the entries of Rho corresponds properly to the the sorted unique values of y.) This argument is passed to the utility function check.yval() which actually issues the warning if warn=TRUE.


Applies the Viterbi algorithm to calculate “the” most probable robable state sequence underlying each observation sequences.


If y consists of a single observation sequence, the value is the underlying most probable observation sequence, or a matrix whose columns consist of such sequences if there is more than one (equally) most probable sequence.

If y consists of a list of observation sequences, the value is a list each entry of which is of the form described above.


There may be more than one equally most probable state sequence underlying a given observation sequence. This phenomenon can occur but appears to be unlikely to do so in practice.


The correction made to the code so as to avoid underflow problems was made due to an inquiry and suggestion from Owen Marshall.


Rolf Turner [email protected]


Rabiner, L. R., "A tutorial on hidden Markov models and selected applications in speech recognition," Proc. IEEE vol. 77, pp. 257 – 286, 1989.

See Also

hmm(), rhmm(), mps(), pr(), viterbi()


# See the help for rhmm() for how to generate y.num and y.let.
## Not run: 
fit.num <- hmm(y.num,K=2,verb=TRUE)
v.1 <- viterbi(model=fit.num)
v.2 <- viterbi(y.num,tpm=P,Rho=R) # P and R as in the
                                  # help for rhmm().
# The order of the states has gotten swapped; 3-v.1[[1]] is much
# more similar to v.2[[1]] than is v.1[[1]].

fit.let <- hmm(y.let,K=2,verb=TRUE)
v.3 <- viterbi(model=fit.let)    # Works.
v.4 <- viterbi(y.let,tpm=P,Rho=R) # Throws an error (R has no row names.)

## End(Not run)

hmm.discnp documentation built on Nov. 12, 2018, 1:04 a.m.