Version 4.1.5

PhasedMTDMarkov Class Reference

Phased Mixture Transition Distribution Markov modelling, estimation and simulation. More...

#include <seqpp/PhasedMTDMarkov.h>

Inheritance diagram for PhasedMTDMarkov:

List of all members.

Public Member Functions
template<class TSeq>
	PhasedMTDMarkov (const TSeq &tseq, short mkv_order, short phase, short initial_phase=0, short nbseed=NBSEED, int nbiter_max=NBITERMAX, double eps=EPS, bool log=false)
	Constructor 1 from a SequenceSet or a Sequence.
	PhasedMTDMarkov (unsigned long **count, short size, short mtd_order, short mkv_order, short phase, short initial_phase=0, short nbseed=NBSEED, int nbiter_max=NBITERMAX, double eps=EPS, bool log=false)
	Constructor 2 from a coded-word count.
void	estimate (unsigned long **count, bool decal_required, short mkv_order, short phase, short initial_phase, short nbseed, int nbiter_max, double eps, bool log)
	performs the estimation [used by each constructor]
	~PhasedMTDMarkov ()
	Destructor.

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Detailed Description

Phased Mixture Transition Distribution Markov modelling, estimation and simulation.

PhasedMTDMarkov is a PhasedMarkov object with a different estimation step. This object performs the estimation with the Mixture Transition Distribution algorithm and then transfoms, once per phase, the MTD model in a markovian matrix.

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Constructor & Destructor Documentation

template<class TSeq> PhasedMTDMarkov::PhasedMTDMarkov (  const TSeq &  tseq, short  mkv_order, short  phase, short  initial_phase = 0, short  nbseed = NBSEED, int  nbiter_max = NBITERMAX, double  eps = EPS, bool  log = false )  [inline]

Constructor 1 from a SequenceSet or a Sequence. Parameters: tseq  a set of sequences or a sequence for estimation mkv_order  markovian order on the markovian matrix of the MTD phase  phase short initial_phase  phase of the first element of each sequence nbseed  number of seeds for the EM algorithm nbiter_max  maximum iterations number of the EM algorithm eps  value of the epsilon of the EM algorithm log  true to log the successive likelihood values

PhasedMTDMarkov::PhasedMTDMarkov (  unsigned long **  count, short  size, short  mtd_order, short  mkv_order, short  phase, short  initial_phase = 0, short  nbseed = NBSEED, int  nbiter_max = NBITERMAX, double  eps = EPS, bool  log = false )  [inline]

Constructor 2 from a coded-word count. Parameters: count  count of all the coded word(base size) of size order+1 for each phase, for estimation size  alphabet size mtd_order  markovian order for the resulting model mkv_order  markovian order on the markovian matrices used in the MTD phase  phase initial_phase  phase of the first element of each sequence nbseed  number of seeds for the EM algorithm nbiter_max  maximum iterations number of the EM algorithm eps  value of the epsilon of the EM algorithm log  true to log the successive likelihood values

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The documentation for this class was generated from the following file:

• PhasedMTDMarkov.h

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Contributors : M.Baudry, P.Y.Bourguignon, M.Hoebeke, V.Miele, P.Nicolas, G.Nuel, H.Richard, D.Robelin

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