R help - Mar 2006 - R package for computing state path using Viterbi algorithm

Dear list,

This question is about Hidden Markov Model.  Given a transition
matrix, an emission matrix and a sequence of observed symbols
(actually, nucleotide sequences, A, T, C and G), I hope to predict the
sequence of state by Viterbi algorithm.  I searched R repository for
related packages.  msm package has function viterbi.msm (as well as
very good document), but it only works for continuous-time condition. 
Other two HMM related packages, hmm.discnp and repeats, however, does
not have such a function (similar to "hmmviterbi()" function in
MatLab).

Is there an R package that implements such a function?

Thanks,

Wuming

Wuming,
Have a look at the depmix package that implements the viterbi algorithm for
hidden markov models (in discrete time). The function to use is
posterior(...). The package includes a manual with a number of examples.
Hth, Ingmar

> From: Wuming Gong <wuming.gong at gmail.com>
> Date: Wed, 22 Mar 2006 23:18:54 +0800
> To: <r-help at stat.math.ethz.ch>
> Subject: [R] R package for computing state path using Viterbi algorithm
> 
> Dear list,
> 
> This question is about Hidden Markov Model.  Given a transition
> matrix, an emission matrix and a sequence of observed symbols
> (actually, nucleotide sequences, A, T, C and G), I hope to predict the
> sequence of state by Viterbi algorithm.  I searched R repository for
> related packages.  msm package has function viterbi.msm (as well as
> very good document), but it only works for continuous-time condition.
> Other two HMM related packages, hmm.discnp and repeats, however, does
> not have such a function (similar to "hmmviterbi()" function in
> MatLab).
> 
> Is there an R package that implements such a function?
> 
> Thanks,
> 
> Wuming
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html

Have you tried www.bioconductor.org?

	  If you are studying nucleatide sequences, I would think you might get 
better help from Bioconductor.  If you've already tried that (and you 
haven't received replies I've missed), it looks like you've found an
opportunity to develop new code.

	  I hope that this relatively negative reply is better than the none 
that I've seen.

	  best wishes,
	  spencer graves

Wuming Gong wrote:
> Dear list,
> 
> This question is about Hidden Markov Model.  Given a transition
> matrix, an emission matrix and a sequence of observed symbols
> (actually, nucleotide sequences, A, T, C and G), I hope to predict the
> sequence of state by Viterbi algorithm.  I searched R repository for
> related packages.  msm package has function viterbi.msm (as well as
> very good document), but it only works for continuous-time condition. 
> Other two HMM related packages, hmm.discnp and repeats, however, does
> not have such a function (similar to "hmmviterbi()" function in
> MatLab).
> 
> Is there an R package that implements such a function?
> 
> Thanks,
> 
> Wuming
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html