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, bool identical_pi=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, bool identical_pi=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, bool identical_pi)
	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,
		bool	identical_pi = 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

References estimate().

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,
		bool	identical_pi = 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

References estimate().

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

• PhasedMTDMarkov.h