R package for computing state path using Viterbi algorithm

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R package for computing state path using Viterbi algorithm

Wuming Gong
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

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Re: R package for computing state path using Viterbi algorithm

Ingmar Visser
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 <[hidden email]>
> Date: Wed, 22 Mar 2006 23:18:54 +0800
> To: <[hidden email]>
> 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
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

______________________________________________
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Re: R package for computing state path using Viterbi algorithm

Spencer Graves
In reply to this post by Wuming Gong
          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
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html