[R] R package for computing state path using Viterbi algorithm

Ingmar Visser I.Visser at uva.nl
Wed Mar 22 16:40:54 CET 2006

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

More information about the R-help mailing list