The general multiple substitution model for codons, from Zaheri & al, 2014. More...

#include <Bpp/Phyl/Model/Codon/KCM.h>

Inheritance diagram for bpp::KCM:

Collaboration diagram for bpp::KCM:

Public Member Functions
	KCM (std::shared_ptr< const GeneticCode > gc, bool oneModel)
	constructor. More...

	KCM (const KCM &kcm)

KCM &	operator= (const KCM &)

virtual	~KCM ()

KCM *	clone () const override

std::string	getName () const override
	Get the name of the model. More...

const SubstitutionModelInterface &	substitutionModel () const override

std::shared_ptr< const GeneticCode >	getGeneticCode () const override

double	getCodonsMulRate (size_t i, size_t j) const override
	Returns the multiplicative rate specific to two codons specified by their number. The respective generator rate is this rate multiplied by the rate defined by the model defined on nucleotides. More...

std::string	getParNameFromPmodel (const std::string &name) const
	get the name of a parameter from its name in a submodel More...

std::string	getPmodelParName (const std::string &name) const
	get the name of a parameter in the submodel from its apparent name More...

const FrequencySetInterface &	frequencySet () const override

const BranchModelInterface &	model () const override

bool	hasIndependentParameter (const std::string &name) const

const ParameterList &	getIndependentParameters () const

size_t	getNumberOfIndependentParameters () const

void	aliasParameters (const std::string &p1, const std::string &p2)

void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)

void	unaliasParameters (const std::string &p1, const std::string &p2)

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

virtual std::vector< std::string >	getAlias (const std::string &name) const

virtual std::map< std::string, std::string >	getAliases () const

std::string	getFrom (const std::string &name) const

bool	hasParameter (const std::string &name) const override

const ParameterList &	getParameters () const override

const Parameter &	parameter (const std::string &name) const override

const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const

double	getParameterValue (const std::string &name) const override

void	setAllParametersValues (const ParameterList &parameters) override

void	setParameterValue (const std::string &name, double value) override

void	setParametersValues (const ParameterList &parameters) override

bool	matchParametersValues (const ParameterList &parameters) override

void	removeConstraint (const std::string &name) override

void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override

size_t	getNumberOfParameters () const override

std::string	getNamespace () const override

std::string	getParameterNameWithoutNamespace (const std::string &name) const override

virtual const Eigen::VectorXd &	Lik_t (const Eigen::VectorXd &values, double t) const =0

const Eigen::VectorXd &	Lik_t (const Eigen::VectorXd &values, double t) const override

virtual const Eigen::VectorXd &	dLik_dt (const Eigen::VectorXd &values, double t) const =0

const Eigen::VectorXd &	dLik_dt (const Eigen::VectorXd &values, double t) const override

virtual const Eigen::VectorXd &	d2Lik_dt2 (const Eigen::VectorXd &values, double t) const =0

const Eigen::VectorXd &	d2Lik_dt2 (const Eigen::VectorXd &values, double t) const override

virtual const TransitionModelInterface &	transitionModel () const =0

const TransitionModelInterface &	transitionModel () const

bool	isScalable () const
	returns if model is scalable More...

void	setScalable (bool scalable)
	sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example. More...

void	normalize ()
	Normalize the generator. More...

void	setDiagonal ()
	set the diagonal of the generator such that sum on each line equals 0. More...

double	getScale () const
	Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale. More...

void	setScale (double scale)
	Multiplies the current generator by the given scale. More...


void	addRateParameter () override
	Methods to supersede TransitionModel methods. More...

void	setFreqFromData (const SequenceDataInterface &data, double pseudoCount=0) override
	Set equilibrium frequencies equal to the frequencies estimated from the data. More...

virtual void	fireParameterChanged (const ParameterList &parameters) override
	Methods to supersede AbstractTransitionModel methods. More...

void	setNamespace (const std::string &name) override


double	freq (size_t i) const override
	Methods to supersede TransitionModel methods. More...

double	Pij_t (size_t i, size_t j, double t) const override

double	dPij_dt (size_t i, size_t j, double t) const override

double	d2Pij_dt2 (size_t i, size_t j, double t) const override

const Vdouble &	getFrequencies () const override

const Matrix< double > &	getPij_t (double t) const override

const Matrix< double > &	getdPij_dt (double t) const override

const Matrix< double > &	getd2Pij_dt2 (double t) const override

double	getInitValue (size_t i, int state) const override

double	getRate () const override
	Get the rate. More...

void	setRate (double rate) override
	Set the rate of the model (must be positive). More...

bool	computeFrequencies () const override

void	computeFrequencies (bool yn) override


const std::vector< int > &	getAlphabetStates () const override

const StateMapInterface &	stateMap () const override

std::shared_ptr< const StateMapInterface >	getStateMap () const override

int	getAlphabetStateAsInt (size_t i) const override

std::string	getAlphabetStateAsChar (size_t i) const override

std::vector< size_t >	getModelStates (int code) const override
	Get the state in the model corresponding to a particular state in the alphabet. More...

std::vector< size_t >	getModelStates (const std::string &code) const override
	Get the state in the model corresponding to a particular state in the alphabet. More...

const Alphabet &	alphabet () const override

std::shared_ptr< const Alphabet >	getAlphabet () const override

size_t	getNumberOfStates () const override
	Get the number of states. More...


double	Qij (size_t i, size_t j) const
	Methods to supersede SubstitutionModel methods. More...

const Matrix< double > &	generator () const

const Matrix< double > &	exchangeabilityMatrix () const

double	Sij (size_t i, size_t j) const

void	enableEigenDecomposition (bool yn)
	Set if eigenValues and Vectors must be computed. More...

bool	enableEigenDecomposition ()
	Tell if eigenValues and Vectors must be computed. More...

bool	isDiagonalizable () const

bool	isNonSingular () const

const Vdouble &	getEigenValues () const

const Vdouble &	getIEigenValues () const

const Matrix< double > &	getRowLeftEigenVectors () const

const Matrix< double > &	getColumnRightEigenVectors () const

Protected Member Functions
SubstitutionModelInterface &	substitutionModel_ () override

const CodonFrequencySetInterface &	codonFrequencySet () const override

bool	hasCodonFrequencySet () const override

void	setFreq (std::map< int, double > &frequencies) override
	Set equilibrium frequencies. More...

void	updateMatrices_ () override

Vdouble &	getFrequencies_ () override

BranchModelInterface &	model_ ()

virtual TransitionModelInterface &	transitionModel_ ()=0

TransitionModelInterface &	transitionModel_ ()

const std::shared_ptr< Parameter > &	getParameter (size_t i) const

std::shared_ptr< Parameter > &	getParameter (size_t i)

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)

void	shareParameters_ (const ParameterList &parameters)

void	includeParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index)

void	deleteParameter_ (std::string &name)

void	deleteParameters_ (const std::vector< std::string > &names)

void	resetParameters_ ()

Parameter &	getParameter_ (const std::string &name)

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

Parameter &	getParameterWithNamespace_ (const std::string &name)

const Parameter &	getParameterWithNamespace_ (const std::string &name) const

ParameterList &	getParameters_ () override

Protected Attributes
std::map< std::string, std::string >	mapParNamesFromPmodel_
	Tools to make the link between the Parameters of the object and those of pmixmodel_. More...

ParameterList	lParPmodel_

Private Attributes
std::unique_ptr< KroneckerCodonDistanceSubstitutionModel >	pmodel_

bool	oneModel_

ParameterList	independentParameters_

std::map< std::string, std::shared_ptr< AliasParameterListener > >	aliasListenersRegister_

ParameterList	parameters_

std::string	prefix_

Eigen::VectorXd	lik_

Detailed Description

The general multiple substitution model for codons, from Zaheri & al, 2014.

Author: Laurent Guéguen

This model is built from one or several nucleotide substitution models. It also allows distinct equilibrium frequencies between codons. A multiplicative factor accounts for the selective restraints at the amino acid level, depending on the synonymy of the amino acids.

This model includes :

parameters of the nucleotide models,
$\omega$ for the ratio of non-synonymous vs synonymous substitution rates,
parameters of the equilibrium frequencies

The codon frequencies $\pi_j$ are either observed or inferred.

Reference:

Zaheri, M. and Dib, L. and Salamin, N. A Generalized Mechanistic Codon Model, Mol Biol Evol. 2014 Sep;31(9):2528-41. doi: 10.1093/molbev/msu196. Epub 2014 Jun 23.

Definition at line 41 of file KCM.h.

Constructor & Destructor Documentation

◆ KCM() [1/2]

KCM::KCM	(	std::shared_ptr< const GeneticCode >	gc,
		bool	oneModel
	)

constructor.

If onemod, a unique GTR model is used, otherwise three different GTR models are used.

Definition at line 17 of file KCM.cpp.

References bpp::ParameterList::addParameters(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::getParameter_(), bpp::ParameterList::getParameterNames(), bpp::ParameterAliasable::getParameterNameWithoutNamespace(), bpp::AbstractBiblioTransitionModel::lParPmodel_, bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_, pmodel_, bpp::Parameter::setName(), and bpp::AbstractBiblioSubstitutionModel::updateMatrices_().

Referenced by clone().

◆ KCM() [2/2]

KCM::KCM ( const KCM & kcm )

Definition at line 67 of file KCM.cpp.

◆ ~KCM()

virtual bpp::KCM::~KCM ( )

inlinevirtual

Definition at line 62 of file KCM.h.

Member Function Documentation

◆ addRateParameter()

void AbstractBiblioTransitionModel::addRateParameter ( )

overridevirtualinherited

Methods to supersede TransitionModel methods.

Implements bpp::BranchModelInterface.

Definition at line 76 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::ParameterList::addParameters(), bpp::BranchModelInterface::addRateParameter(), bpp::AbstractParameterAliasable::getNamespace(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractTotallyWrappedTransitionModel::getRate(), bpp::AbstractBiblioTransitionModel::lParPmodel_, bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_, bpp::AbstractWrappedTransitionModel::model(), bpp::AbstractWrappedTransitionModel::model_(), bpp::Parameter::R_PLUS_STAR, and bpp::ParameterList::reset().

◆ alphabet()

const Alphabet& bpp::AbstractWrappedModel::alphabet ( ) const

inlineoverridevirtualinherited

Returns: A reference to the alphabet associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 53 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::alphabet(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::alphabet(), and bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel().

◆ clone()

KCM* bpp::KCM::clone ( ) const

inlineoverridevirtual

Implements bpp::CodonReversibleSubstitutionModelInterface.

Definition at line 64 of file KCM.h.

References KCM().

◆ codonFrequencySet()

const CodonFrequencySetInterface& bpp::KCM::codonFrequencySet ( ) const

inlineoverrideprotectedvirtual

Implements bpp::CoreCodonSubstitutionModelInterface.

Definition at line 78 of file KCM.h.

◆ computeFrequencies() [1/2]

bool bpp::AbstractTotallyWrappedTransitionModel::computeFrequencies ( ) const

inlineoverridevirtualinherited

Returns: Says if equilibrium frequencies should be computed

Implements bpp::TransitionModelInterface.

Definition at line 162 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::computeFrequencies(), and bpp::WrappedTransitionModelInterface::transitionModel().

Referenced by bpp::DFP07::DFP07(), and bpp::YN98::YN98().

◆ computeFrequencies() [2/2]

void bpp::AbstractTotallyWrappedTransitionModel::computeFrequencies ( bool yn )

inlineoverridevirtualinherited

Returns: Set if equilibrium frequencies should be computed from the generator

Implements bpp::TransitionModelInterface.

Definition at line 171 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::computeFrequencies(), and bpp::AbstractWrappedTransitionModel::transitionModel_().

◆ d2Lik_dt2() [1/2]

virtual const Eigen::VectorXd& bpp::BranchModelInterface::d2Lik_dt2	(	const Eigen::VectorXd &	values,
		double	t
	)		const

pure virtualinherited

Implemented in bpp::AbstractLkTransitionModel, bpp::TransitionModelInterface, bpp::TransitionFromTransitionModel, and bpp::MultinomialFromTransitionModel.

◆ d2Lik_dt2() [2/2]

const Eigen::VectorXd& bpp::AbstractLkTransitionModel::d2Lik_dt2	(	const Eigen::VectorXd &	values,
		double	t
	)		const

inlineoverridevirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 64 of file AbstractSubstitutionModel.h.

References bpp::TransitionModelInterface::getd2Pij_dt2(), and bpp::AbstractLkTransitionModel::lik_.

◆ d2Pij_dt2()

double bpp::AbstractTotallyWrappedTransitionModel::d2Pij_dt2	(	size_t	i,
		size_t	j,
		double	t
	)		const

inlineoverridevirtualinherited

Returns: The second order derivative of the probability of change from state i to state j with respect to time t, at time t.

See also: getd2Pij_dt2(), getStates()

Implements bpp::TransitionModelInterface.

Definition at line 124 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::d2Pij_dt2(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ dLik_dt() [1/2]

virtual const Eigen::VectorXd& bpp::BranchModelInterface::dLik_dt	(	const Eigen::VectorXd &	values,
		double	t
	)		const

pure virtualinherited

Implemented in bpp::AbstractLkTransitionModel, bpp::TransitionModelInterface, bpp::TransitionFromTransitionModel, and bpp::MultinomialFromTransitionModel.

◆ dLik_dt() [2/2]

const Eigen::VectorXd& bpp::AbstractLkTransitionModel::dLik_dt	(	const Eigen::VectorXd &	values,
		double	t
	)		const

inlineoverridevirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 47 of file AbstractSubstitutionModel.h.

References bpp::TransitionModelInterface::getdPij_dt(), and bpp::AbstractLkTransitionModel::lik_.

◆ dPij_dt()

double bpp::AbstractTotallyWrappedTransitionModel::dPij_dt	(	size_t	i,
		size_t	j,
		double	t
	)		const

inlineoverridevirtualinherited

Returns: The first order derivative of the probability of change from state i to state j with respect to time t, at time t.

See also: getdPij_dt(), getStates()

Implements bpp::TransitionModelInterface.

Definition at line 123 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::dPij_dt(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ enableEigenDecomposition() [1/2]

bool bpp::AbstractTotallyWrappedSubstitutionModel::enableEigenDecomposition ( )

inlinevirtualinherited

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModelInterface.

Definition at line 240 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::enableEigenDecomposition(), and bpp::AbstractWrappedSubstitutionModel::substitutionModel_().

◆ enableEigenDecomposition() [2/2]

void bpp::AbstractTotallyWrappedSubstitutionModel::enableEigenDecomposition ( bool yn )

inlinevirtualinherited

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModelInterface.

Definition at line 238 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::enableEigenDecomposition(), and bpp::AbstractWrappedSubstitutionModel::substitutionModel_().

◆ exchangeabilityMatrix()

const Matrix<double>& bpp::AbstractTotallyWrappedSubstitutionModel::exchangeabilityMatrix ( ) const

inlinevirtualinherited

Returns: The matrix of exchangeability terms. It is recommended that exchangeability matrix be normalized so that the normalized generator be obtained directly by the dot product $S . \pi$ .

Implements bpp::SubstitutionModelInterface.

Definition at line 234 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::exchangeabilityMatrix(), and bpp::WrappedSubstitutionModelInterface::substitutionModel().

◆ fireParameterChanged()

virtual void bpp::AbstractBiblioTransitionModel::fireParameterChanged ( const ParameterList & parameters )

inlineoverridevirtualinherited

Methods to supersede AbstractTransitionModel methods.

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 86 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractParameterAliasable::getNamespace(), bpp::ParameterList::getParameterValue(), bpp::ParameterList::hasParameter(), bpp::AbstractWrappedTransitionModel::model_(), bpp::BranchModelInterface::setRate(), bpp::ParameterList::size(), and bpp::AbstractBiblioTransitionModel::updateMatrices_().

◆ freq()

double bpp::AbstractTotallyWrappedTransitionModel::freq ( size_t i ) const

inlineoverridevirtualinherited

Methods to supersede TransitionModel methods.

Implements bpp::TransitionModelInterface.

Definition at line 120 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::freq(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ frequencySet()

const FrequencySetInterface& bpp::AbstractWrappedTransitionModel::frequencySet ( ) const

inlineoverridevirtualinherited

Returns: Get the FrequencySet of equilibrium of this model.

Exceptions

Exception if no FrequenceSet is associated to this model.

Reimplemented from bpp::AbstractWrappedModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, and bpp::YN98.

Definition at line 93 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::frequencySet(), and bpp::WrappedTransitionModelInterface::transitionModel().

Referenced by bpp::RegisterRatesSubstitutionModel::frequencySet().

◆ generator()

const Matrix<double>& bpp::AbstractTotallyWrappedSubstitutionModel::generator ( ) const

inlinevirtualinherited

Returns: The normalized Markov generator matrix, i.e. all normalized rates of changes from state i to state j. The generator is normalized so that (i) $\forall i; \sum_j Q_{i,j} = 0$ , meaning that $ $\forall i; Q_{i,i} = -\sum_{j \neq i}Q_{i,j}$ , and (ii) $\sum_i Q_{i,i} \times \pi_i = -1$ . This means that, under normalization, the mean rate of replacement at equilibrium is 1 and that time are measured in units of expected number of changes per site. Additionally, the rate_ attribute provides the possibility to increase or decrease this mean rate.

See Kosiol and Goldman (2005), Molecular Biology And Evolution 22(2) 193-9.

See also: Qij()

Implements bpp::SubstitutionModelInterface.

Definition at line 232 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::generator(), and bpp::WrappedSubstitutionModelInterface::substitutionModel().

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::AbstractWrappedModel::getAlphabet ( ) const

inlineoverridevirtualinherited

Returns: A pointer toward the alphabet associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 55 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabet(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabet(), and bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel().

◆ getAlphabetStateAsChar()

std::string bpp::AbstractWrappedModel::getAlphabetStateAsChar ( size_t index ) const

inlineoverridevirtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 46 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStateAsChar(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStateAsChar().

◆ getAlphabetStateAsInt()

int bpp::AbstractWrappedModel::getAlphabetStateAsInt ( size_t index ) const

inlineoverridevirtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 44 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStateAsInt(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStateAsInt().

◆ getAlphabetStates()

const std::vector<int>& bpp::AbstractWrappedModel::getAlphabetStates ( ) const

inlineoverridevirtualinherited

@ brief Methods to supersede TransitionModel methods.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 38 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStates(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStates().

◆ getCodonsMulRate()

double bpp::KCM::getCodonsMulRate	(	size_t	,
		size_t
	)		const

inlineoverridevirtual

Returns the multiplicative rate specific to two codons specified by their number. The respective generator rate is this rate multiplied by the rate defined by the model defined on nucleotides.

Implements bpp::CoreCodonSubstitutionModelInterface.

Definition at line 73 of file KCM.h.

References pmodel_.

◆ getColumnRightEigenVectors()

const Matrix<double>& bpp::AbstractTotallyWrappedSubstitutionModel::getColumnRightEigenVectors ( ) const

inlinevirtualinherited

Returns: A matrix with right eigen vectors. Each column in the matrix stands for an eigen vector.

Implements bpp::SubstitutionModelInterface.

Definition at line 252 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::getColumnRightEigenVectors(), and bpp::WrappedSubstitutionModelInterface::substitutionModel().

◆ getd2Pij_dt2()

const Matrix<double>& bpp::AbstractTotallyWrappedTransitionModel::getd2Pij_dt2 ( double t ) const

inlineoverridevirtualinherited

Returns: All second order derivatives of the probability of change from state i to state j with respect to time t, at time t.

See also: d2Pij_dt2()

Implements bpp::TransitionModelInterface.

Definition at line 132 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getd2Pij_dt2(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ getdPij_dt()

const Matrix<double>& bpp::AbstractTotallyWrappedTransitionModel::getdPij_dt ( double t ) const

inlineoverridevirtualinherited

Returns: Get all first order derivatives of the probability of change from state i to state j with respect to time t, at time t.

See also: dPij_dt()

Implements bpp::TransitionModelInterface.

Definition at line 130 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getdPij_dt(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ getEigenValues()

const Vdouble& bpp::AbstractTotallyWrappedSubstitutionModel::getEigenValues ( ) const

inlinevirtualinherited

Returns: A vector with all real parts of the eigen values of the generator of this model;

Implements bpp::SubstitutionModelInterface.

Definition at line 246 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::getEigenValues(), and bpp::WrappedSubstitutionModelInterface::substitutionModel().

◆ getFrequencies()

const Vdouble& bpp::AbstractTotallyWrappedTransitionModel::getFrequencies ( ) const

inlineoverridevirtualinherited

Returns: A vector of all equilibrium frequencies.

See also: freq()

Implements bpp::TransitionModelInterface.

Definition at line 126 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getFrequencies(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ getFrequencies_()

Vdouble& bpp::AbstractTotallyWrappedTransitionModel::getFrequencies_ ( )

inlineoverrideprotectedvirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 181 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getFrequencies_(), and bpp::AbstractWrappedTransitionModel::transitionModel_().

◆ getGeneticCode()

std::shared_ptr<const GeneticCode> bpp::KCM::getGeneticCode ( ) const

inlineoverridevirtual

Implements bpp::CodonSubstitutionModelInterface.

Definition at line 71 of file KCM.h.

References pmodel_.

◆ getIEigenValues()

const Vdouble& bpp::AbstractTotallyWrappedSubstitutionModel::getIEigenValues ( ) const

inlinevirtualinherited

Returns: A vector with all imaginary parts of the eigen values of the generator of this model;

Implements bpp::SubstitutionModelInterface.

Definition at line 248 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::getIEigenValues(), and bpp::WrappedSubstitutionModelInterface::substitutionModel().

◆ getInitValue()

double bpp::AbstractTotallyWrappedTransitionModel::getInitValue	(	size_t	i,
		int	state
	)		const

inlineoverridevirtualinherited

This method is used to initialize likelihoods in recursions. It typically sends 1 if i = state, 0 otherwise, where i is one of the possible states of the alphabet allowed in the model and state is the observed state in the considered sequence/site.

Parameters

i	the index of the state in the model.
state	An observed state in the sequence/site.

Returns: 1 or 0 depending if the two states are compatible.

Exceptions

IndexOutOfBoundsException	if array position is out of range.
BadIntException	if states are not allowed in the associated alphabet.

See also: getStates();

Implements bpp::BranchModelInterface.

Definition at line 134 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getInitValue(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ getModelStates() [1/2]

std::vector<size_t> bpp::AbstractWrappedModel::getModelStates ( const std::string & code ) const

inlineoverridevirtualinherited

Get the state in the model corresponding to a particular state in the alphabet.

Parameters

code	The alphabet state to check.

Returns: A vector of indices of model states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 50 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getModelStates(), and bpp::WrappedModelInterface::model().

◆ getModelStates() [2/2]

std::vector<size_t> bpp::AbstractWrappedModel::getModelStates ( int code ) const

inlineoverridevirtualinherited

Get the state in the model corresponding to a particular state in the alphabet.

Parameters

code	The alphabet state to check.

Returns: A vector of indices of model states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 48 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getModelStates(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getModelStates().

◆ getName()

std::string bpp::KCM::getName ( ) const

inlineoverridevirtual

Get the name of the model.

Returns: The name of this model.

Reimplemented from bpp::AbstractWrappedModel.

Definition at line 67 of file KCM.h.

References oneModel_.

◆ getNumberOfStates()

size_t bpp::AbstractWrappedModel::getNumberOfStates ( ) const

inlineoverridevirtualinherited

Get the number of states.

For most models, this equals the size of the alphabet.

See also: getAlphabetChars for the list of supported states.

Returns: The number of different states in the model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 57 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getNumberOfStates(), and bpp::WrappedModelInterface::model().

◆ getParNameFromPmodel()

std::string AbstractBiblioTransitionModel::getParNameFromPmodel ( const std::string & name ) const

inherited

get the name of a parameter from its name in a submodel

Parameters

name	the name of the parameter in the submodel

Definition at line 37 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_.

◆ getPij_t()

const Matrix<double>& bpp::AbstractTotallyWrappedTransitionModel::getPij_t ( double t ) const

inlineoverridevirtualinherited

Returns: All probabilities of change from state i to state j during time t.

See also: Pij_t()

Implements bpp::TransitionModelInterface.

Definition at line 128 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getPij_t(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ getPmodelParName()

std::string AbstractBiblioTransitionModel::getPmodelParName ( const std::string & name ) const

inherited

get the name of a parameter in the submodel from its apparent name

Parameters

name	the name of the parameter

Definition at line 47 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_.

◆ getRate()

double bpp::AbstractTotallyWrappedTransitionModel::getRate ( ) const

inlineoverridevirtualinherited

Get the rate.

Implements bpp::BranchModelInterface.

Definition at line 139 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getRate(), and bpp::WrappedTransitionModelInterface::transitionModel().

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), and bpp::FromMixtureSubstitutionModel::addRateParameter().

◆ getRowLeftEigenVectors()

const Matrix<double>& bpp::AbstractTotallyWrappedSubstitutionModel::getRowLeftEigenVectors ( ) const

inlinevirtualinherited

Returns: A matrix with left eigen vectors. Each row in the matrix stands for an eigen vector.

Implements bpp::SubstitutionModelInterface.

Definition at line 250 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::getRowLeftEigenVectors(), and bpp::WrappedSubstitutionModelInterface::substitutionModel().

◆ getScale()

double bpp::AbstractTotallyWrappedSubstitutionModel::getScale ( ) const

inlinevirtualinherited

Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.

Returns: Minus the scalar product of diagonal elements and the frequencies vector.

Implements bpp::SubstitutionModelInterface.

Definition at line 278 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::getScale(), and bpp::WrappedSubstitutionModelInterface::substitutionModel().

◆ getStateMap()

std::shared_ptr<const StateMapInterface> bpp::AbstractWrappedModel::getStateMap ( ) const

inlineoverridevirtualinherited

Returns: A shared_ptr to the mapping of model states with alphabet states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 42 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getStateMap(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getStateMap().

◆ hasCodonFrequencySet()

bool bpp::KCM::hasCodonFrequencySet ( ) const

inlineoverrideprotectedvirtual

Implements bpp::CoreCodonSubstitutionModelInterface.

Definition at line 83 of file KCM.h.

◆ isDiagonalizable()

bool bpp::AbstractTotallyWrappedSubstitutionModel::isDiagonalizable ( ) const

inlinevirtualinherited

Returns: True if the model is diagonalizable in R.

Implements bpp::SubstitutionModelInterface.

Definition at line 242 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::isDiagonalizable(), and bpp::WrappedSubstitutionModelInterface::substitutionModel().

◆ isNonSingular()

bool bpp::AbstractTotallyWrappedSubstitutionModel::isNonSingular ( ) const

inlinevirtualinherited

Returns: True is the model is non-singular.

Implements bpp::SubstitutionModelInterface.

Definition at line 244 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::isNonSingular(), and bpp::WrappedSubstitutionModelInterface::substitutionModel().

◆ isScalable()

bool bpp::AbstractTotallyWrappedSubstitutionModel::isScalable ( ) const

inlinevirtualinherited

returns if model is scalable

Implements bpp::SubstitutionModelInterface.

Definition at line 258 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::isScalable(), and bpp::WrappedSubstitutionModelInterface::substitutionModel().

◆ Lik_t() [1/2]

virtual const Eigen::VectorXd& bpp::BranchModelInterface::Lik_t	(	const Eigen::VectorXd &	values,
		double	t
	)		const

pure virtualinherited

This method is used to compute likelihoods in recursions. It computes the probability of a vector given a start state.

Parameters

values	An vector of states on the site.
t	time

Exceptions

IndexOutOfBoundsException	if array position is out of range.
BadIntException	if states are not allowed in the associated alphabet.

Implemented in bpp::AbstractLkTransitionModel, bpp::TransitionModelInterface, bpp::TransitionFromTransitionModel, and bpp::MultinomialFromTransitionModel.

◆ Lik_t() [2/2]

const Eigen::VectorXd& bpp::AbstractLkTransitionModel::Lik_t	(	const Eigen::VectorXd &	values,
		double	t
	)		const

inlineoverridevirtualinherited

This method is used to compute likelihoods in recursions. It computes the probability of a vector given a start state.

Parameters

values	An vector of states on the site.
t	the branch length

Implements bpp::TransitionModelInterface.

Definition at line 30 of file AbstractSubstitutionModel.h.

References bpp::TransitionModelInterface::getPij_t(), and bpp::AbstractLkTransitionModel::lik_.

◆ model()

const BranchModelInterface& bpp::AbstractWrappedTransitionModel::model ( ) const

inlineoverridevirtualinherited

Implements bpp::WrappedModelInterface.

Definition at line 98 of file AbstractWrappedModel.h.

References bpp::WrappedTransitionModelInterface::transitionModel().

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), bpp::InMixedSubstitutionModel::getInitValue(), bpp::FromMixtureSubstitutionModel::getName(), bpp::RegisterRatesSubstitutionModel::getRate(), bpp::AbstractBiblioSubstitutionModel::operator=(), bpp::AbstractBiblioTransitionModel::operator=(), bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel(), bpp::AbstractBiblioTransitionModel::setFreq(), bpp::AbstractBiblioTransitionModel::setNamespace(), and bpp::BppOSubstitutionModelFormat::write().

◆ model_()

BranchModelInterface& bpp::AbstractWrappedTransitionModel::model_ ( )

inlineprotectedinherited

Definition at line 85 of file AbstractWrappedModel.h.

References bpp::AbstractWrappedTransitionModel::transitionModel_().

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), bpp::AbstractBiblioTransitionModel::fireParameterChanged(), bpp::FromMixtureSubstitutionModel::fireParameterChanged(), bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel(), bpp::AbstractBiblioTransitionModel::setNamespace(), bpp::FromMixtureSubstitutionModel::setNamespace(), bpp::RegisterRatesSubstitutionModel::setRate(), and bpp::AbstractBiblioTransitionModel::updateMatrices_().

◆ normalize()

void bpp::AbstractTotallyWrappedSubstitutionModel::normalize ( )

inlinevirtualinherited

Normalize the generator.

Implements bpp::SubstitutionModelInterface.

Definition at line 268 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::normalize(), and bpp::AbstractWrappedSubstitutionModel::substitutionModel_().

◆ operator=()

KCM & KCM::operator= ( const KCM & kcm )

Definition at line 80 of file KCM.cpp.

References oneModel_, bpp::AbstractBiblioSubstitutionModel::operator=(), and pmodel_.

◆ Pij_t()

double bpp::AbstractTotallyWrappedTransitionModel::Pij_t	(	size_t	i,
		size_t	j,
		double	t
	)		const

inlineoverridevirtualinherited

Returns: The probability of change from state i to state j during time t.

See also: getPij_t(), getStates()

Implements bpp::TransitionModelInterface.

Definition at line 122 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::Pij_t(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ Qij()

double bpp::AbstractTotallyWrappedSubstitutionModel::Qij	(	size_t	i,
		size_t	j
	)		const

inlinevirtualinherited

Methods to supersede SubstitutionModel methods.

Implements bpp::SubstitutionModelInterface.

Definition at line 230 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::Qij(), and bpp::WrappedSubstitutionModelInterface::substitutionModel().

◆ setDiagonal()

void bpp::AbstractTotallyWrappedSubstitutionModel::setDiagonal ( )

inlinevirtualinherited

set the diagonal of the generator such that sum on each line equals 0.

Implements bpp::SubstitutionModelInterface.

Definition at line 273 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::setDiagonal(), and bpp::AbstractWrappedSubstitutionModel::substitutionModel_().

◆ setFreq()

void bpp::KCM::setFreq ( std::map< int, double > & frequencies )

inlineoverrideprotectedvirtual

Set equilibrium frequencies.

Parameters

frequencies The map of the frequencies to use.

Reimplemented from bpp::AbstractBiblioTransitionModel.

Definition at line 88 of file KCM.h.

References bpp::AbstractBiblioTransitionModel::setFreq().

◆ setFreqFromData()

void AbstractBiblioTransitionModel::setFreqFromData	(	const SequenceDataInterface &	data,
		double	pseudoCount = `0`
	)

overridevirtualinherited

Set equilibrium frequencies equal to the frequencies estimated from the data.

Parameters

data	The sequences to use.
pseudoCount	A quantity $\psi$ to add to adjust the observed values in order to prevent issues due to missing states on small data set. The corrected frequencies shall be computed as $\pi_i = \frac{n_i+\psi}{\sum_j (f_j+\psi)}$

Implements bpp::TransitionModelInterface.

Definition at line 125 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::SequenceContainerTools::getFrequencies(), and bpp::AbstractBiblioTransitionModel::setFreq().

◆ setNamespace()

void AbstractBiblioTransitionModel::setNamespace ( const std::string & name )

overridevirtualinherited

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 88 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::ParameterList::addParameters(), bpp::ParameterAliasable::getParameterNameWithoutNamespace(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractBiblioTransitionModel::lParPmodel_, bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_, bpp::AbstractWrappedTransitionModel::model(), bpp::AbstractWrappedTransitionModel::model_(), bpp::ParameterList::reset(), bpp::AbstractParameterAliasable::setNamespace(), and bpp::ParameterAliasable::setNamespace().

◆ setRate()

void bpp::AbstractTotallyWrappedTransitionModel::setRate ( double rate )

inlineoverridevirtualinherited

Set the rate of the model (must be positive).

Parameters

rate	must be positive.

Implements bpp::BranchModelInterface.

Definition at line 144 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::setRate(), and bpp::AbstractWrappedTransitionModel::transitionModel_().

◆ setScalable()

void bpp::AbstractTotallyWrappedSubstitutionModel::setScalable ( bool scalable )

inlinevirtualinherited

sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example.

Implements bpp::SubstitutionModelInterface.

Definition at line 263 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::setScalable(), and bpp::AbstractWrappedSubstitutionModel::substitutionModel_().

◆ setScale()

void bpp::AbstractTotallyWrappedSubstitutionModel::setScale ( double scale )

inlinevirtualinherited

Multiplies the current generator by the given scale.

Parameters

scale the scale by which the generator is multiplied.

Implements bpp::SubstitutionModelInterface.

Definition at line 283 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::setScale(), and bpp::AbstractWrappedSubstitutionModel::substitutionModel_().

◆ Sij()

double bpp::AbstractTotallyWrappedSubstitutionModel::Sij	(	size_t	i,
		size_t	j
	)		const

inlinevirtualinherited

Returns: The exchangeability between state i and state j.

By definition Sij(i,j) = Sij(j,i).

Implements bpp::SubstitutionModelInterface.

Definition at line 236 of file AbstractWrappedModel.h.

References bpp::SubstitutionModelInterface::Sij(), and bpp::WrappedSubstitutionModelInterface::substitutionModel().

◆ stateMap()

const StateMapInterface& bpp::AbstractWrappedModel::stateMap ( ) const

inlineoverridevirtualinherited

Returns: The mapping of model states with alphabet states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 40 of file AbstractWrappedModel.h.

References bpp::WrappedModelInterface::model(), and bpp::BranchModelInterface::stateMap().

Referenced by bpp::RegisterRatesSubstitutionModel::stateMap().

◆ substitutionModel()

const SubstitutionModelInterface& bpp::KCM::substitutionModel ( ) const

inlineoverridevirtual

Implements bpp::WrappedSubstitutionModelInterface.

Definition at line 69 of file KCM.h.

References pmodel_.

◆ substitutionModel_()

SubstitutionModelInterface& bpp::KCM::substitutionModel_ ( )

inlineoverrideprotectedvirtual

Implements bpp::AbstractWrappedSubstitutionModel.

Definition at line 76 of file KCM.h.

References pmodel_.

◆ transitionModel() [1/2]

const TransitionModelInterface& bpp::AbstractWrappedSubstitutionModel::transitionModel ( ) const

inlinevirtualinherited

Implements bpp::WrappedTransitionModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 199 of file AbstractWrappedModel.h.

References bpp::WrappedSubstitutionModelInterface::substitutionModel().

Referenced by bpp::InMixedSubstitutionModel::d2Pij_dt2(), bpp::InMixedSubstitutionModel::dPij_dt(), bpp::InMixedSubstitutionModel::freq(), bpp::InMixedSubstitutionModel::getd2Pij_dt2(), bpp::InMixedSubstitutionModel::getdPij_dt(), bpp::InMixedSubstitutionModel::getFrequencies(), bpp::InMixedSubstitutionModel::getPij_t(), bpp::InMixedSubstitutionModel::getRate(), and bpp::InMixedSubstitutionModel::Pij_t().

◆ transitionModel() [2/2]

virtual const TransitionModelInterface& bpp::WrappedTransitionModelInterface::transitionModel ( ) const

pure virtualinherited

Implemented in bpp::RegisterRatesSubstitutionModel, bpp::AbstractFromSubstitutionModelTransitionModel, bpp::AbstractBiblioMixedTransitionModel, and bpp::AbstractWrappedSubstitutionModel.

◆ transitionModel_() [1/2]

TransitionModelInterface& bpp::AbstractWrappedSubstitutionModel::transitionModel_ ( )

inlineprotectedvirtualinherited

Implements bpp::AbstractWrappedTransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 205 of file AbstractWrappedModel.h.

References bpp::AbstractWrappedSubstitutionModel::substitutionModel_().

◆ transitionModel_() [2/2]

virtual TransitionModelInterface& bpp::AbstractWrappedTransitionModel::transitionModel_ ( )

protectedpure virtualinherited

Implemented in bpp::RegisterRatesSubstitutionModel, bpp::AbstractFromSubstitutionModelTransitionModel, bpp::AbstractBiblioMixedTransitionModel, and bpp::AbstractWrappedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::computeFrequencies(), bpp::AbstractTotallyWrappedTransitionModel::getFrequencies_(), bpp::AbstractWrappedTransitionModel::model_(), bpp::AbstractTotallyWrappedTransitionModel::setFreq(), bpp::AbstractTotallyWrappedTransitionModel::setFreqFromData(), and bpp::AbstractTotallyWrappedTransitionModel::setRate().

◆ updateMatrices_()

void bpp::AbstractBiblioSubstitutionModel::updateMatrices_ ( )

inlineoverrideprotectedvirtualinherited

Reimplemented from bpp::AbstractBiblioTransitionModel.

Definition at line 129 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioTransitionModel::updateMatrices_().

Referenced by bpp::GY94::GY94(), KCM(), bpp::MG94::MG94(), and bpp::YN98::YN98().

Member Data Documentation

◆ lik_

Eigen::VectorXd bpp::AbstractLkTransitionModel::lik_

mutableprivateinherited

Definition at line 23 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractLkTransitionModel::d2Lik_dt2(), bpp::AbstractLkTransitionModel::dLik_dt(), and bpp::AbstractLkTransitionModel::Lik_t().

◆ lParPmodel_

ParameterList bpp::AbstractBiblioTransitionModel::lParPmodel_

protectedinherited

Definition at line 30 of file AbstractBiblioSubstitutionModel.h.

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::DFP07::DFP07(), bpp::GY94::GY94(), KCM(), bpp::LG10_EX_EHO::LG10_EX_EHO(), bpp::LGL08_CAT::LGL08_CAT(), bpp::LLG08_EHO::LLG08_EHO(), bpp::LLG08_EX2::LLG08_EX2(), bpp::LLG08_EX3::LLG08_EX3(), bpp::LLG08_UL2::LLG08_UL2(), bpp::LLG08_UL3::LLG08_UL3(), bpp::MG94::MG94(), bpp::AbstractBiblioTransitionModel::operator=(), bpp::RELAX::RELAX(), bpp::AbstractBiblioTransitionModel::setNamespace(), bpp::AbstractBiblioTransitionModel::updateMatrices_(), bpp::RELAX::updateMatrices_(), bpp::YNGP_M3::updateMatrices_(), bpp::YN98::YN98(), bpp::YNGP_M1::YNGP_M1(), bpp::YNGP_M10::YNGP_M10(), bpp::YNGP_M2::YNGP_M2(), bpp::YNGP_M3::YNGP_M3(), bpp::YNGP_M7::YNGP_M7(), bpp::YNGP_M8::YNGP_M8(), and bpp::YNGP_M9::YNGP_M9().

◆ mapParNamesFromPmodel_

std::map<std::string, std::string> bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_

protectedinherited

Tools to make the link between the Parameters of the object and those of pmixmodel_.

Definition at line 28 of file AbstractBiblioSubstitutionModel.h.

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::DFP07::DFP07(), bpp::AbstractBiblioTransitionModel::getParNameFromPmodel(), bpp::AbstractBiblioTransitionModel::getPmodelParName(), bpp::GY94::GY94(), KCM(), bpp::LG10_EX_EHO::LG10_EX_EHO(), bpp::LGL08_CAT::LGL08_CAT(), bpp::LLG08_EHO::LLG08_EHO(), bpp::LLG08_EX2::LLG08_EX2(), bpp::LLG08_EX3::LLG08_EX3(), bpp::LLG08_UL2::LLG08_UL2(), bpp::LLG08_UL3::LLG08_UL3(), bpp::MG94::MG94(), bpp::AbstractBiblioTransitionModel::operator=(), bpp::RELAX::RELAX(), bpp::AbstractBiblioTransitionModel::setFreq(), bpp::AbstractBiblioTransitionModel::setNamespace(), bpp::AbstractBiblioTransitionModel::updateMatrices_(), bpp::RELAX::updateMatrices_(), bpp::YNGP_M3::updateMatrices_(), bpp::YN98::YN98(), bpp::YNGP_M1::YNGP_M1(), bpp::YNGP_M10::YNGP_M10(), bpp::YNGP_M2::YNGP_M2(), bpp::YNGP_M3::YNGP_M3(), bpp::YNGP_M7::YNGP_M7(), bpp::YNGP_M8::YNGP_M8(), and bpp::YNGP_M9::YNGP_M9().

◆ oneModel_

bool bpp::KCM::oneModel_

private

Definition at line 47 of file KCM.h.

Referenced by getName(), and operator=().

◆ pmodel_

std::unique_ptr<KroneckerCodonDistanceSubstitutionModel> bpp::KCM::pmodel_

private

Definition at line 46 of file KCM.h.

Referenced by getCodonsMulRate(), getGeneticCode(), KCM(), operator=(), substitutionModel(), and substitutionModel_().

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

Bpp/Phyl/Model/Codon/KCM.h
Bpp/Phyl/Model/Codon/KCM.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ KCM() [1/2]

◆ KCM() [2/2]

◆ ~KCM()

Member Function Documentation

◆ addRateParameter()

◆ alphabet()

◆ clone()

◆ codonFrequencySet()

◆ computeFrequencies() [1/2]

◆ computeFrequencies() [2/2]

◆ d2Lik_dt2() [1/2]

◆ d2Lik_dt2() [2/2]

◆ d2Pij_dt2()

◆ dLik_dt() [1/2]

◆ dLik_dt() [2/2]

◆ dPij_dt()

◆ enableEigenDecomposition() [1/2]

◆ enableEigenDecomposition() [2/2]

◆ exchangeabilityMatrix()

◆ fireParameterChanged()

◆ freq()

◆ frequencySet()

◆ generator()

◆ getAlphabet()

◆ getAlphabetStateAsChar()

◆ getAlphabetStateAsInt()

◆ getAlphabetStates()

◆ getCodonsMulRate()

◆ getColumnRightEigenVectors()

◆ getd2Pij_dt2()

◆ getdPij_dt()

◆ getEigenValues()

◆ getFrequencies()

◆ getFrequencies_()

◆ getGeneticCode()

◆ getIEigenValues()

◆ getInitValue()

◆ getModelStates() [1/2]

◆ getModelStates() [2/2]

◆ getName()

◆ getNumberOfStates()

◆ getParNameFromPmodel()

◆ getPij_t()

◆ getPmodelParName()

◆ getRate()

◆ getRowLeftEigenVectors()

◆ getScale()

◆ getStateMap()

◆ hasCodonFrequencySet()

◆ isDiagonalizable()

◆ isNonSingular()

◆ isScalable()

◆ Lik_t() [1/2]

◆ Lik_t() [2/2]

◆ model()

◆ model_()

◆ normalize()

◆ operator=()

◆ Pij_t()

◆ Qij()

◆ setDiagonal()

◆ setFreq()

◆ setFreqFromData()

◆ setNamespace()

◆ setRate()

◆ setScalable()

◆ setScale()

◆ Sij()

◆ stateMap()

◆ substitutionModel()

◆ substitutionModel_()

◆ transitionModel() [1/2]

◆ transitionModel() [2/2]

◆ transitionModel_() [1/2]