Analytical reward using the eigen decomposition method. More...

#include <Bpp/Phyl/Mapping/DecompositionReward.h>

Inheritance diagram for bpp::DecompositionReward:

Collaboration diagram for bpp::DecompositionReward:

Public Member Functions
	DecompositionReward (const SubstitutionModel model, AlphabetIndex1 alphIndex)

	DecompositionReward (const DecompositionReward &dr)

DecompositionReward &	operator= (const DecompositionReward &dr)

virtual	~DecompositionReward ()

DecompositionReward *	clone () const

double	getReward (size_t initialState, size_t finalState, double length) const
	Get the reward of susbstitutions on a branch, given the initial and final states, and the branch length. More...

Matrix< double > *	getAllRewards (double length) const
	Get the rewards on a branch, for each initial and final states, and given the branch length. More...

void	setSubstitutionModel (const SubstitutionModel *model)
	Set the substitution model. More...

bool	hasAlphabetIndex () const

void	setAlphabetIndex (AlphabetIndex1 *alphIndex)

const AlphabetIndex1 *	getAlphabetIndex () const

AlphabetIndex1 *	getAlphabetIndex ()

virtual const Alphabet *	getAlphabet () const
	Short cut function, equivalent to getSubstitutionRegister()->getAlphabet(). More...

virtual size_t	getNumberOfStates () const
	Short cut function, equivalent to getSubstitutionRegister()->getAlphabet()->getSize(). More...

Protected Member Functions
void	computeRewards_ (double length) const

void	jFunction_ (const std::vector< double > &lambda, double t, RowMatrix< double > &result) const

void	alphabetIndexHasChanged () throw (Exception)

Protected Attributes
AlphabetIndex1 *	alphIndex_

Private Member Functions
void	resetStates_ ()

void	computeBMatrice_ ()

void	computeEigen_ ()

void	computeProducts_ ()

Private Attributes
const ReversibleSubstitutionModel *	model_

size_t	nbStates_

RowMatrix< double >	jMat_

RowMatrix< double >	v_

RowMatrix< double >	vInv_

std::vector< double >	lambda_

RowMatrix< double >	bMatrice_

RowMatrix< double >	insideProduct_

RowMatrix< double >	rewards_

double	currentLength_

Detailed Description

Analytical reward using the eigen decomposition method.

The codes is adapted from the original R code by Paula Tataru and Asger Hobolth to the formula in the article of Minin & Suchard.

Minin, V.N. and Suchard, M.A., Fast, accurate and simulation-free stochastic mapping Philosophical Transactions of the Royal Society B 2008 363:3985-95.

Only reversible models are supported for now.

Author: Laurent Guéguen

Definition at line 65 of file DecompositionReward.h.

Constructor & Destructor Documentation

◆ DecompositionReward() [1/2]

DecompositionReward::DecompositionReward	(	const SubstitutionModel *	model,
		AlphabetIndex1 *	alphIndex
	)

Definition at line 50 of file DecompositionReward.cpp.

References bpp::AbstractReward::alphIndex_, computeBMatrice_(), computeEigen_(), computeProducts_(), and bpp::SubstitutionModel::getAlphabet().

Referenced by clone().

◆ DecompositionReward() [2/2]

bpp::DecompositionReward::DecompositionReward ( const DecompositionReward & dr )

inline

Definition at line 80 of file DecompositionReward.h.

◆ ~DecompositionReward()

virtual bpp::DecompositionReward::~DecompositionReward ( )

inlinevirtual

Definition at line 110 of file DecompositionReward.h.

Member Function Documentation

◆ alphabetIndexHasChanged()

void DecompositionReward::alphabetIndexHasChanged	(		)
throw	(	Exception
	)

protectedvirtual

Implements bpp::AbstractReward.

Definition at line 200 of file DecompositionReward.cpp.

References bpp::AbstractReward::alphIndex_, computeBMatrice_(), computeProducts_(), computeRewards_(), currentLength_, bpp::SubstitutionModel::getAlphabet(), and model_.

◆ clone()

DecompositionReward* bpp::DecompositionReward::clone ( ) const

inlinevirtual

Implements bpp::Reward.

Definition at line 112 of file DecompositionReward.h.

References DecompositionReward().

◆ computeBMatrice_()

void DecompositionReward::computeBMatrice_ ( )

private

Definition at line 78 of file DecompositionReward.cpp.

References bMatrice_, bpp::AbstractReward::getAlphabetIndex(), bpp::SubstitutionModel::getAlphabetStates(), model_, and nbStates_.

Referenced by alphabetIndexHasChanged(), and DecompositionReward().

◆ computeEigen_()

void DecompositionReward::computeEigen_ ( )

private

Definition at line 85 of file DecompositionReward.cpp.

References bpp::SubstitutionModel::getColumnRightEigenVectors(), bpp::SubstitutionModel::getEigenValues(), bpp::SubstitutionModel::getRowLeftEigenVectors(), lambda_, model_, v_, and vInv_.

Referenced by DecompositionReward(), and setSubstitutionModel().

◆ computeProducts_()

void DecompositionReward::computeProducts_ ( )

private

Definition at line 92 of file DecompositionReward.cpp.

References bMatrice_, insideProduct_, nbStates_, v_, and vInv_.

Referenced by alphabetIndexHasChanged(), DecompositionReward(), and setSubstitutionModel().

◆ computeRewards_()

void DecompositionReward::computeRewards_ ( double length ) const

protected

Definition at line 127 of file DecompositionReward.cpp.

References bpp::SubstitutionModel::getPij_t(), insideProduct_, jFunction_(), jMat_, lambda_, model_, nbStates_, rewards_, v_, and vInv_.

Referenced by alphabetIndexHasChanged(), getAllRewards(), getReward(), and setSubstitutionModel().

◆ getAllRewards()

Matrix< double > * DecompositionReward::getAllRewards ( double length ) const

virtual

Get the rewards on a branch, for each initial and final states, and given the branch length.

Parameters

length The length of the branch.

Returns: A matrix with all rewards for each initial and final states.

Implements bpp::Reward.

Definition at line 148 of file DecompositionReward.cpp.

References computeRewards_(), currentLength_, and rewards_.

◆ getAlphabet()

virtual const Alphabet* bpp::Reward::getAlphabet ( ) const

inlinevirtualinherited

Short cut function, equivalent to getSubstitutionRegister()->getAlphabet().

Returns: The alphabet associated to this substitution count.

Definition at line 108 of file Reward.h.

References bpp::Reward::getAlphabetIndex().

Referenced by bpp::Reward::getNumberOfStates().

◆ getAlphabetIndex() [1/2]

const AlphabetIndex1* bpp::AbstractReward::getAlphabetIndex ( ) const

inlinevirtualinherited

Returns: The AlphabetIndex1 object associated to this instance. The alphabet index contains the value associated to each state.

Implements bpp::Reward.

Definition at line 194 of file Reward.h.

References bpp::AbstractReward::alphIndex_.

Referenced by computeBMatrice_().

◆ getAlphabetIndex() [2/2]

AlphabetIndex1* bpp::AbstractReward::getAlphabetIndex ( )

inlinevirtualinherited

Returns: The AlphabetIndex1 object associated to this instance. The alphabet index contains the value associated to each state.

Implements bpp::Reward.

Definition at line 196 of file Reward.h.

References bpp::AbstractReward::alphIndex_.

◆ getNumberOfStates()

virtual size_t bpp::Reward::getNumberOfStates ( ) const

inlinevirtualinherited

Short cut function, equivalent to getSubstitutionRegister()->getAlphabet()->getSize().

Returns: The number of states in the model/alphabet.

Definition at line 115 of file Reward.h.

References bpp::Reward::getAlphabet().

◆ getReward()

double DecompositionReward::getReward	(	size_t	initialState,
		size_t	finalState,
		double	length
	)		const

virtual

Get the reward of susbstitutions on a branch, given the initial and final states, and the branch length.

Parameters

initialState	The initial state.
finalState	The final state.
length	The length of the branch.

Returns: The reward of the function on a branch of specified length and according to initial and final states.

Implements bpp::Reward.

Definition at line 162 of file DecompositionReward.cpp.

References computeRewards_(), currentLength_, and rewards_.

◆ hasAlphabetIndex()

bool bpp::AbstractReward::hasAlphabetIndex ( ) const

inlinevirtualinherited

Returns: Tell if an alphabet index has been attached to this class.

Implements bpp::Reward.

Definition at line 179 of file Reward.h.

References bpp::AbstractReward::alphIndex_.

◆ jFunction_()

void DecompositionReward::jFunction_	(	const std::vector< double > &	lambda,
		double	t,
		RowMatrix< double > &	result
	)		const

protected

Definition at line 110 of file DecompositionReward.cpp.

References nbStates_.

Referenced by computeRewards_().

◆ operator=()

DecompositionReward& bpp::DecompositionReward::operator= ( const DecompositionReward & dr )

inline

Definition at line 94 of file DecompositionReward.h.

References bMatrice_, currentLength_, insideProduct_, jMat_, lambda_, model_, nbStates_, bpp::AbstractReward::operator=(), rewards_, v_, and vInv_.

◆ resetStates_()

void DecompositionReward::resetStates_ ( )

private

Definition at line 99 of file DecompositionReward.cpp.

References bMatrice_, insideProduct_, jMat_, lambda_, nbStates_, rewards_, v_, and vInv_.

Referenced by setSubstitutionModel().

◆ setAlphabetIndex()

void bpp::AbstractReward::setAlphabetIndex ( AlphabetIndex1 * alphind )

inlinevirtualinherited

Parameters

alphind The new AlphabetIndex1 object to be associated to this instance.

Implements bpp::Reward.

Definition at line 188 of file Reward.h.

References bpp::AbstractReward::alphabetIndexHasChanged(), and bpp::AbstractReward::alphIndex_.

◆ setSubstitutionModel()

void DecompositionReward::setSubstitutionModel ( const SubstitutionModel * model )

virtual

Set the substitution model.

Parameters

model A pointer toward the substitution model to use. Only reversible models are currently supported. Setting a non-reversible model will throw an exception.

Implements bpp::Reward.

Definition at line 176 of file DecompositionReward.cpp.

References bpp::AbstractReward::alphIndex_, computeEigen_(), computeProducts_(), computeRewards_(), currentLength_, bpp::SubstitutionModel::getAlphabet(), model_, nbStates_, and resetStates_().

Member Data Documentation

◆ alphIndex_

AlphabetIndex1* bpp::AbstractReward::alphIndex_

protectedinherited

Definition at line 155 of file Reward.h.

Referenced by alphabetIndexHasChanged(), DecompositionReward(), bpp::AbstractReward::getAlphabetIndex(), bpp::AbstractReward::hasAlphabetIndex(), bpp::AbstractReward::operator=(), bpp::AbstractReward::setAlphabetIndex(), and setSubstitutionModel().

◆ bMatrice_

RowMatrix<double> bpp::DecompositionReward::bMatrice_

private

Definition at line 73 of file DecompositionReward.h.

Referenced by computeBMatrice_(), computeProducts_(), operator=(), and resetStates_().

◆ currentLength_

double bpp::DecompositionReward::currentLength_

mutableprivate

Definition at line 75 of file DecompositionReward.h.

Referenced by alphabetIndexHasChanged(), getAllRewards(), getReward(), operator=(), and setSubstitutionModel().

◆ insideProduct_

RowMatrix<double> bpp::DecompositionReward::insideProduct_

private

Definition at line 73 of file DecompositionReward.h.

Referenced by computeProducts_(), computeRewards_(), operator=(), and resetStates_().

◆ jMat_

RowMatrix<double> bpp::DecompositionReward::jMat_

mutableprivate

Definition at line 71 of file DecompositionReward.h.

Referenced by computeRewards_(), operator=(), and resetStates_().

◆ lambda_

std::vector<double> bpp::DecompositionReward::lambda_

mutableprivate

Definition at line 72 of file DecompositionReward.h.

Referenced by computeEigen_(), computeRewards_(), operator=(), and resetStates_().

◆ model_

const ReversibleSubstitutionModel* bpp::DecompositionReward::model_

private

Definition at line 69 of file DecompositionReward.h.

Referenced by alphabetIndexHasChanged(), computeBMatrice_(), computeEigen_(), computeRewards_(), operator=(), and setSubstitutionModel().

◆ nbStates_

size_t bpp::DecompositionReward::nbStates_

private

Definition at line 70 of file DecompositionReward.h.

Referenced by computeBMatrice_(), computeProducts_(), computeRewards_(), jFunction_(), operator=(), resetStates_(), and setSubstitutionModel().

◆ rewards_

RowMatrix<double> bpp::DecompositionReward::rewards_

mutableprivate

Definition at line 74 of file DecompositionReward.h.

Referenced by computeRewards_(), getAllRewards(), getReward(), operator=(), and resetStates_().

◆ v_

RowMatrix<double> bpp::DecompositionReward::v_

mutableprivate

Definition at line 71 of file DecompositionReward.h.

Referenced by computeEigen_(), computeProducts_(), computeRewards_(), operator=(), and resetStates_().

◆ vInv_

RowMatrix<double> bpp::DecompositionReward::vInv_

mutableprivate

Definition at line 71 of file DecompositionReward.h.

Referenced by computeEigen_(), computeProducts_(), computeRewards_(), operator=(), and resetStates_().

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

Bpp/Phyl/Mapping/DecompositionReward.h
Bpp/Phyl/Mapping/DecompositionReward.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DecompositionReward() [1/2]

◆ DecompositionReward() [2/2]

◆ ~DecompositionReward()

Member Function Documentation

◆ alphabetIndexHasChanged()

◆ clone()

◆ computeBMatrice_()

◆ computeEigen_()

◆ computeProducts_()

◆ computeRewards_()

◆ getAllRewards()

◆ getAlphabet()

◆ getAlphabetIndex() [1/2]

◆ getAlphabetIndex() [2/2]

◆ getNumberOfStates()

◆ getReward()

◆ hasAlphabetIndex()

◆ jFunction_()

◆ operator=()

◆ resetStates_()

◆ setAlphabetIndex()

◆ setSubstitutionModel()

Member Data Documentation

◆ alphIndex_

◆ bMatrice_

◆ currentLength_

◆ insideProduct_

◆ jMat_

◆ lambda_

◆ model_

◆ nbStates_

◆ rewards_

◆ v_

◆ vInv_