bpp-phyl3  3.0.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
bpp::KroneckerWordSubstitutionModel Class Referenceabstract

Basal class for words of substitution models with multiple substitutions. More...

#include <Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h>

+ Inheritance diagram for bpp::KroneckerWordSubstitutionModel:
+ Collaboration diagram for bpp::KroneckerWordSubstitutionModel:

Public Member Functions

 KroneckerWordSubstitutionModel (ModelList &modelList, const std::string &prefix="")
 Build a new KroneckerWordSubstitutionModel object from a Vector of pointers to SubstitutionModels. More...
 
 KroneckerWordSubstitutionModel (ModelList &modelList, const std::vector< std::set< size_t >> &vPos, const std::string &prefix="")
 Build a new KroneckerWordSubstitutionModel object from a Vector of pointers to SubstitutionModels. More...
 
 KroneckerWordSubstitutionModel (std::unique_ptr< SubstitutionModelInterface > pmodel, unsigned int num, const std::string &prefix="")
 Build a new KroneckerWordSubstitutionModel object from a pointer to an SubstitutionModel and a number of desired models. More...
 
 KroneckerWordSubstitutionModel (std::unique_ptr< SubstitutionModelInterface > pmodel, unsigned int num, const std::vector< std::set< size_t >> &vPos, const std::string &prefix="")
 Build a new KroneckerWordSubstitutionModel object from a pointer to an SubstitutionModel and a number of desired models. More...
 
virtual ~KroneckerWordSubstitutionModel ()
 
KroneckerWordSubstitutionModel * clone () const override
 
virtual std::string getName () const override
 Get the name of the model. More...
 
void setNamespace (const std::string &prefix)
 
const SubstitutionModelInterface & nModel (size_t i) const
 returns the ith model, or throw an exception if i is not a valid number. More...
 
size_t getNumberOfModels () const
 
virtual void setFreq (std::map< int, double > &freqs)
 Estimation of the parameters of the models so that the equilibrium frequencies match the given ones. More...
 
bool computeFrequencies () const
 
void computeFrequencies (bool yn)
 
const Matrix< double > & generator () const
 
const Matrix< double > & exchangeabilityMatrix () const
 
const Matrix< double > & getPij_t (double t) const
 
const Matrix< double > & getdPij_dt (double t) const
 
const Matrix< double > & getd2Pij_dt2 (double t) const
 
double Sij (size_t i, size_t j) const
 
const Vdouble & getEigenValues () const
 
const Vdouble & getIEigenValues () const
 
bool isDiagonalizable () const
 
bool isNonSingular () const
 
const Matrix< double > & getRowLeftEigenVectors () const
 
const Matrix< double > & getColumnRightEigenVectors () const
 
virtual double Qij (size_t i, size_t j) const
 A method for computing all necessary matrices. More...
 
void enableEigenDecomposition (bool yn)
 Set if eigenValues and Vectors must be computed. More...
 
bool enableEigenDecomposition ()
 Tell if eigenValues and Vectors must be computed. 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...
 
virtual bool isScalable () const
 returns if model is scalable More...
 
double getScale () const
 return scale More...
 
void setScale (double scale)
 Multiplies the current generator by the given scale. More...
 
void normalize ()
 normalize the generator More...
 
void setDiagonal ()
 set the diagonal of the generator such that sum on each line equals 0. More...
 
const Alphabet & alphabet () const override
 
std::shared_ptr< const Alphabet > getAlphabet () const override
 
const StateMapInterface & stateMap () const override
 
std::shared_ptr< const StateMapInterface > getStateMap () const override
 
size_t getNumberOfStates () const override
 Get the number of states. More...
 
const std::vector< int > & getAlphabetStates () const override
 
std::string getAlphabetStateAsChar (size_t index) const override
 
int getAlphabetStateAsInt (size_t index) 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 Vdouble & getFrequencies () const override
 
virtual double freq (size_t i) const override
 
virtual double Pij_t (size_t i, size_t j, double t) const override
 
virtual double dPij_dt (size_t i, size_t j, double t) const override
 
virtual double d2Pij_dt2 (size_t i, size_t j, double t) const override
 
double getInitValue (size_t i, int state) const override
 
void setFreqFromData (const SequenceDataInterface &data, double pseudoCount=0) override
 Set equilibrium frequencies equal to the frequencies estimated from the data. More...
 
const FrequencySetInterface & frequencySet () const override
 
virtual void fireParameterChanged (const ParameterList &parameters) override
 Tells the model that a parameter value has changed. More...
 
void addRateParameter () override
 add a "rate" parameter to the model, that handles the overall rate of the process. More...
 
void setVerboseLevel (short level)
 
short verboseLevel () const
 
virtual double getRate () const override
 The rate of the substitution process. More...
 
virtual void setRate (double rate) override
 Set the rate of the model (must be positive). More...
 
const Eigen::VectorXd & Lik_t (const Eigen::VectorXd &values, double t) const override
 
const Eigen::VectorXd & dLik_dt (const Eigen::VectorXd &values, double t) const override
 
const Eigen::VectorXd & d2Lik_dt2 (const Eigen::VectorXd &values, double t) const override
 
virtual size_t getNumberOfIndependentParameters () const=0
 
size_t getNumberOfIndependentParameters () const
 
virtual void aliasParameters (const std::string &p1, const std::string &p2)=0
 
virtual void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0
 
void aliasParameters (const std::string &p1, const std::string &p2)
 
void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
 
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
 
void unaliasParameters (const std::string &p1, const std::string &p2)
 
virtual const ParameterList & getIndependentParameters () const=0
 
const ParameterList & getIndependentParameters () const
 
virtual std::vector< std::string > getAlias (const std::string &name) const=0
 
virtual std::vector< std::string > getAlias (const std::string &name) const
 
virtual std::map< std::string, std::string > getAliases () const=0
 
virtual std::map< std::string, std::string > getAliases () const
 
virtual bool hasParameter (const std::string &name) const=0
 
bool hasParameter (const std::string &name) const override
 
virtual const ParameterList & getParameters () const=0
 
const ParameterList & getParameters () const override
 
virtual const Parameter & parameter (const std::string &name) const=0
 
const Parameter & parameter (const std::string &name) const override
 
virtual double getParameterValue (const std::string &name) const=0
 
double getParameterValue (const std::string &name) const override
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 
void setAllParametersValues (const ParameterList &parameters) override
 
virtual void setParameterValue (const std::string &name, double value)=0
 
void setParameterValue (const std::string &name, double value) override
 
virtual void setParametersValues (const ParameterList &parameters)=0
 
void setParametersValues (const ParameterList &parameters) override
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 
bool matchParametersValues (const ParameterList &parameters) override
 
virtual void removeConstraint (const std::string &name)=0
 
void removeConstraint (const std::string &name) override
 
virtual void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
 
void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
 
virtual size_t getNumberOfParameters () const=0
 
size_t getNumberOfParameters () const override
 
virtual std::string getNamespace () const=0
 
std::string getNamespace () const override
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const=0
 
std::string getParameterNameWithoutNamespace (const std::string &name) const override
 
bool hasIndependentParameter (const std::string &name) const
 
ParameterList getAliasedParameters (const ParameterList &pl) const
 
ParameterList getFromParameters (const ParameterList &pl) const
 
std::string getFrom (const std::string &name) const
 
const std::shared_ptr< Parameter > & getParameter (const std::string &name) const
 

Protected Member Functions

 KroneckerWordSubstitutionModel (std::shared_ptr< const Alphabet > alph, std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix="")
 Constructor for the derived classes only. More...
 
void completeMatrices_ () override
 Called by updateMatrices to handle specific modifications for inheriting classes. More...
 
void initGenerators_ ()
 
bool checkChangingPositions_ ()
 checks that the vector of changing positions is valid More...
 
void setChangingPositions (const std::vector< std::set< size_t >> &vPos)
 
void updateMatrices_ ()
 Diagonalize the $Q$ matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...
 
Vdouble & getFrequencies_ () override
 
virtual ParameterList & getParameters_ ()=0
 
ParameterList & getParameters_ () override
 
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
 

Protected Attributes

std::vector< std::shared_ptr< SubstitutionModelInterface > > VSubMod_
 
std::vector< std::string > VnestedPrefix_
 
std::vector< double > Vrate_
 
bool isScalable_
 If the model is scalable (ie generator can be normalized automatically). More...
 
RowMatrix< double > generator_
 The generator matrix $Q$ of the model. More...
 
bool computeFreq_
 if the Frequencies must be computed from the generator More...
 
RowMatrix< double > exchangeability_
 The exchangeability matrix $S$ of the model, defined as $ S_{ij}=\frac{Q_{ij}}{\pi_j}$. When the model is reversible, this matrix is symmetric. More...
 
bool eigenDecompose_
 Tell if the eigen decomposition should be performed. More...
 
Vdouble eigenValues_
 The vector of eigen values. More...
 
Vdouble iEigenValues_
 The vector of the imaginary part of the eigen values. More...
 
bool isDiagonalizable_
 boolean value for diagonalizability in R of the generator_ More...
 
RowMatrix< double > rightEigenVectors_
 The $U^-1$ matrix made of right eigen vectors (by column). More...
 
bool isNonSingular_
 boolean value for non-singularity of rightEigenVectors_ More...
 
RowMatrix< double > leftEigenVectors_
 The $U$ matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular. More...
 
std::vector< RowMatrix< double > > vPowGen_
 vector of the powers of generator_ for Taylor development (if rightEigenVectors_ is singular). More...
 
RowMatrix< double > tmpMat_
 For computational issues. More...
 
std::shared_ptr< const Alphabet > alphabet_
 The alphabet relevant to this model. More...
 
std::shared_ptr< const StateMapInterface > stateMap_
 The map of model states with alphabet states. More...
 
size_t size_
 The number of states. More...
 
double rate_
 The rate of the model (default: 1). The generator (and all its vectorial components) is independent of the rate, since it should be normalized. More...
 
Vdouble freq_
 The vector $\pi_e$ of equilibrium frequencies. More...
 
RowMatrix< double > pijt_
 These ones are for bookkeeping: More...
 
RowMatrix< double > dpijt_
 
RowMatrix< double > d2pijt_
 
short verboseLevel_
 

Private Member Functions

void fillBasicGenerator_ ()
 First fill of the generator, from the position model. More...
 

Private Attributes

std::vector< std::set< size_t > > sChangingPos_
 vector of sets of simultaneously changing positions. More...
 
std::vector< RowMatrix< double > > vGenerators_
 vector of generators for computation purposes More...
 
bool newAlphabet_
 boolean flag to check if a specific WordAlphabet has been built More...
 
Eigen::VectorXd lik_
 
ParameterList independentParameters_
 
std::map< std::string, std::shared_ptr< AliasParameterListener > > aliasListenersRegister_
 
ParameterList parameters_
 
std::string prefix_
 

Detailed Description

Basal class for words of substitution models with multiple substitutions.

Author
Laurent Guéguen

The equilibrium frequency of each word is due to the combination of the multiple substitutions.

Definition at line 25 of file KroneckerWordSubstitutionModel.h.

Constructor & Destructor Documentation

◆ KroneckerWordSubstitutionModel() [1/5]

KroneckerWordSubstitutionModel::KroneckerWordSubstitutionModel ( ModelList &  modelList,
const std::string &  prefix = "" 
)

Build a new KroneckerWordSubstitutionModel object from a Vector of pointers to SubstitutionModels.

Parameters
modelListthe list of substitution models to use, in the order of the positions in the words from left to right. All the models must be different objects to avoid parameters redundancy, otherwise only the first model is used. The used models are owned by the instance.
prefixthe Namespace.

Definition at line 24 of file KroneckerWordSubstitutionModel.cpp.

References bpp::AbstractWordSubstitutionModel::updateMatrices_().

Referenced by clone().

◆ KroneckerWordSubstitutionModel() [2/5]

KroneckerWordSubstitutionModel::KroneckerWordSubstitutionModel ( ModelList &  modelList,
const std::vector< std::set< size_t >> &  vPos,
const std::string &  prefix = "" 
)

Build a new KroneckerWordSubstitutionModel object from a Vector of pointers to SubstitutionModels.

Parameters
modelListthe list of substitution models to use, in the order of the positions in the words from left to right. All the models must be different objects to avoid parameters redundancy, otherwise only the first model is used. The used models are owned by the instance.
vPosa vector of sets of simultaneously changing positions.
prefixthe Namespace.

Definition at line 58 of file KroneckerWordSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::enableEigenDecomposition(), and bpp::AbstractWordSubstitutionModel::updateMatrices_().

◆ KroneckerWordSubstitutionModel() [3/5]

KroneckerWordSubstitutionModel::KroneckerWordSubstitutionModel ( std::unique_ptr< SubstitutionModelInterface >  pmodel,
unsigned int  num,
const std::string &  prefix = "" 
)

Build a new KroneckerWordSubstitutionModel object from a pointer to an SubstitutionModel and a number of desired models.

Parameters
pmodelpointer to the substitution model to use in all the positions. It is owned by the instance.
numThe number of models involved.
prefixthe Namespace.

Definition at line 45 of file KroneckerWordSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::enableEigenDecomposition(), and bpp::AbstractWordSubstitutionModel::updateMatrices_().

◆ KroneckerWordSubstitutionModel() [4/5]

KroneckerWordSubstitutionModel::KroneckerWordSubstitutionModel ( std::unique_ptr< SubstitutionModelInterface >  pmodel,
unsigned int  num,
const std::vector< std::set< size_t >> &  vPos,
const std::string &  prefix = "" 
)

Build a new KroneckerWordSubstitutionModel object from a pointer to an SubstitutionModel and a number of desired models.

Parameters
pmodelpointer to the substitution model to use in all the positions. It is owned by the instance.
numThe number of models involved.
vPosa vector of sets of simultaneously changing positions.
prefixthe Namespace.

Definition at line 71 of file KroneckerWordSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::enableEigenDecomposition(), and bpp::AbstractWordSubstitutionModel::updateMatrices_().

◆ ~KroneckerWordSubstitutionModel()

virtual bpp::KroneckerWordSubstitutionModel::~KroneckerWordSubstitutionModel ( )
inlinevirtual

Definition at line 92 of file KroneckerWordSubstitutionModel.h.

◆ KroneckerWordSubstitutionModel() [5/5]

KroneckerWordSubstitutionModel::KroneckerWordSubstitutionModel ( std::shared_ptr< const Alphabet >  alph,
std::shared_ptr< const StateMapInterface >  stateMap,
const std::string &  prefix = "" 
)
protected

Constructor for the derived classes only.

Definition at line 35 of file KroneckerWordSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::enableEigenDecomposition().

Member Function Documentation

◆ addRateParameter()

void AbstractTransitionModel::addRateParameter ( )
overridevirtualinherited

add a "rate" parameter to the model, that handles the overall rate of the process.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 63 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::getNamespace(), bpp::Parameter::R_PLUS_STAR, and bpp::AbstractTransitionModel::rate_.

◆ alphabet()

const Alphabet& bpp::AbstractTransitionModel::alphabet ( ) const
inlineoverridevirtualinherited
Returns
A reference to the alphabet associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 167 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::alphabet_.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), and bpp::AbstractWordSubstitutionModel::operator=().

◆ checkChangingPositions_()

bool AbstractKroneckerWordSubstitutionModel::checkChangingPositions_ ( )
protectedinherited

checks that the vector of changing positions is valid

Definition at line 157 of file AbstractKroneckerWordSubstitutionModel.cpp.

References bpp::AbstractKroneckerWordSubstitutionModel::sChangingPos_, and bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::AbstractKroneckerWordSubstitutionModel::AbstractKroneckerWordSubstitutionModel(), and bpp::AbstractKroneckerWordSubstitutionModel::setChangingPositions().

◆ clone()

KroneckerWordSubstitutionModel* bpp::KroneckerWordSubstitutionModel::clone ( ) const
inlineoverridevirtual

Implements bpp::SubstitutionModelInterface.

Definition at line 94 of file KroneckerWordSubstitutionModel.h.

References KroneckerWordSubstitutionModel().

◆ completeMatrices_()

void bpp::KroneckerWordSubstitutionModel::completeMatrices_ ( )
inlineoverrideprotectedvirtual

Called by updateMatrices to handle specific modifications for inheriting classes.

Implements bpp::AbstractWordSubstitutionModel.

Definition at line 108 of file KroneckerWordSubstitutionModel.h.

◆ computeFrequencies() [1/2]

bool bpp::AbstractSubstitutionModel::computeFrequencies ( ) const
inlinevirtualinherited
Returns
Says if equilibrium frequencies should be computed

Reimplemented from bpp::AbstractTransitionModel.

Definition at line 404 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::computeFreq_.

Referenced by bpp::CodonAdHocSubstitutionModel::CodonAdHocSubstitutionModel(), bpp::CodonDistanceFrequenciesSubstitutionModel::CodonDistanceFrequenciesSubstitutionModel(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::CodonDistancePhaseFrequenciesSubstitutionModel(), bpp::CodonDistanceSubstitutionModel::CodonDistanceSubstitutionModel(), bpp::D1WalkSubstitutionModel::D1WalkSubstitutionModel(), bpp::F81::F81(), bpp::gBGC::gBGC(), bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel::KroneckerCodonDistanceFrequenciesSubstitutionModel(), bpp::KroneckerCodonDistanceSubstitutionModel::KroneckerCodonDistanceSubstitutionModel(), bpp::L95::L95(), bpp::POMO::POMO(), bpp::RN95::RN95(), bpp::RN95s::RN95s(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::WordSubstitutionModel::WordSubstitutionModel(), and bpp::YpR::YpR().

◆ computeFrequencies() [2/2]

void bpp::AbstractSubstitutionModel::computeFrequencies ( bool  yn)
inlinevirtualinherited
Returns
Set if equilibrium frequencies should be computed

Implements bpp::TransitionModelInterface.

Definition at line 406 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::computeFreq_.

◆ d2Lik_dt2()

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()

virtual double bpp::AbstractTransitionModel::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.

Reimplemented in bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 199 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::getd2Pij_dt2().

Referenced by bpp::JCprot::d2Pij_dt2().

◆ dLik_dt()

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()

virtual double bpp::AbstractTransitionModel::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.

Reimplemented in bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 198 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::getdPij_dt().

Referenced by bpp::JCprot::dPij_dt().

◆ enableEigenDecomposition() [1/2]

bool bpp::AbstractSubstitutionModel::enableEigenDecomposition ( )
inlinevirtualinherited

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModelInterface.

Definition at line 434 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractDFPSubstitutionModel::AbstractDFPSubstitutionModel(), bpp::AbstractKroneckerWordSubstitutionModel::AbstractKroneckerWordSubstitutionModel(), KroneckerWordSubstitutionModel(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), and bpp::WordSubstitutionModel::WordSubstitutionModel().

◆ enableEigenDecomposition() [2/2]

void bpp::AbstractSubstitutionModel::enableEigenDecomposition ( bool  yn)
inlinevirtualinherited

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModelInterface.

Definition at line 432 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

◆ exchangeabilityMatrix()

const Matrix<double>& bpp::AbstractSubstitutionModel::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 410 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

◆ fillBasicGenerator_()

void AbstractKroneckerWordSubstitutionModel::fillBasicGenerator_ ( )
privatevirtualinherited

First fill of the generator, from the position model.

Reimplemented from bpp::AbstractWordSubstitutionModel.

Definition at line 170 of file AbstractKroneckerWordSubstitutionModel.cpp.

References bpp::MatrixTools::add(), bpp::MatrixTools::fillDiag(), bpp::AbstractSubstitutionModel::generator(), bpp::AbstractSubstitutionModel::generator_, bpp::MatrixTools::getId(), bpp::AbstractTransitionModel::getNumberOfStates(), bpp::MatrixTools::kroneckerMult(), bpp::AbstractKroneckerWordSubstitutionModel::sChangingPos_, bpp::AbstractKroneckerWordSubstitutionModel::vGenerators_, and bpp::AbstractWordSubstitutionModel::VSubMod_.

◆ fireParameterChanged()

virtual void bpp::AbstractTransitionModel::fireParameterChanged ( const ParameterList &  parameters)
inlineoverridevirtualinherited

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::RegisterRatesSubstitutionModel, bpp::RE08, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::POMO, bpp::YpR, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::SENCA, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::CodonDistanceSubstitutionModel, and bpp::gBGC.

Definition at line 217 of file AbstractSubstitutionModel.h.

References bpp::AbstractParameterAliasable::fireParameterChanged(), bpp::AbstractParameterAliasable::getNamespace(), bpp::ParameterList::getParameterValue(), bpp::ParameterList::hasParameter(), bpp::AbstractTransitionModel::rate_, bpp::ParameterList::size(), and bpp::AbstractTransitionModel::updateMatrices_().

Referenced by bpp::gBGC::fireParameterChanged(), bpp::CodonDistanceSubstitutionModel::fireParameterChanged(), bpp::CodonAdHocSubstitutionModel::fireParameterChanged(), bpp::CodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::fireParameterChanged(), bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), bpp::KroneckerCodonDistanceSubstitutionModel::fireParameterChanged(), bpp::SENCA::fireParameterChanged(), bpp::D1WalkSubstitutionModel::fireParameterChanged(), bpp::EquiprobableSubstitutionModel::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::JCprot::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::LG08::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), and bpp::WAG01::fireParameterChanged().

◆ freq()

virtual double bpp::AbstractTransitionModel::freq ( size_t  i) const
inlineoverridevirtualinherited
Returns
Equilibrium frequency associated to character i.
See also
getFrequencies(), getStates()

Implements bpp::TransitionModelInterface.

Definition at line 195 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::freq_.

Referenced by bpp::CodonSameAARateSubstitutionModel::compute_().

◆ frequencySet()

const FrequencySetInterface& bpp::AbstractTransitionModel::frequencySet ( ) const
inlineoverridevirtualinherited
Returns
Get the FrequencySet of equilibrium of this model.
Exceptions
Exceptionif no FrequenceSet is associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, and bpp::CodonDistanceFrequenciesSubstitutionModel.

Definition at line 207 of file AbstractSubstitutionModel.h.

◆ generator()

const Matrix<double>& bpp::AbstractSubstitutionModel::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 $t$ 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 408 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

Referenced by bpp::AbstractKroneckerWordSubstitutionModel::fillBasicGenerator_().

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::AbstractTransitionModel::getAlphabet ( ) const
inlineoverridevirtualinherited
Returns
A pointer toward the alphabet associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 169 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::alphabet_.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::WordSubstitutionModel::completeMatrices_(), and bpp::RE08::getInitValue().

◆ getAlphabetStateAsChar()

std::string bpp::AbstractTransitionModel::getAlphabetStateAsChar ( size_t  index) const
inlineoverridevirtualinherited
Parameters
indexThe model state.
Returns
The corresponding alphabet state as character code.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 179 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

◆ getAlphabetStateAsInt()

int bpp::AbstractTransitionModel::getAlphabetStateAsInt ( size_t  index) const
inlineoverridevirtualinherited
Parameters
indexThe model state.
Returns
The corresponding alphabet state as character code.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 181 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices_(), and bpp::AbstractTransitionModel::getInitValue().

◆ getAlphabetStates()

const std::vector<int>& bpp::AbstractTransitionModel::getAlphabetStates ( ) const
inlineoverridevirtualinherited
Returns
The alphabet states of each state of the model, as a vector of int codes.
See also
Alphabet

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 177 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

Referenced by bpp::DFP07::DFP07(), bpp::YNGP_M3::YNGP_M3(), and bpp::YNGP_M8::YNGP_M8().

◆ getColumnRightEigenVectors()

const Matrix<double>& bpp::AbstractSubstitutionModel::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 428 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::rightEigenVectors_.

◆ getd2Pij_dt2()

const Matrix< double > & AbstractSubstitutionModel::getd2Pij_dt2 ( double  t) const
virtualinherited
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::AbstractTransitionModel.

Reimplemented in bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 557 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::add(), bpp::MatrixTools::copy(), bpp::AbstractTransitionModel::d2pijt_, bpp::AbstractSubstitutionModel::eigenValues_, bpp::VectorTools::exp(), bpp::numeric::exp(), bpp::MatrixTools::getId(), bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::isDiagonalizable_, bpp::AbstractSubstitutionModel::isNonSingular_, bpp::AbstractSubstitutionModel::leftEigenVectors_, bpp::MatrixTools::mult(), bpp::AbstractTransitionModel::rate_, bpp::AbstractSubstitutionModel::rightEigenVectors_, bpp::MatrixTools::scale(), bpp::AbstractTransitionModel::size_, bpp::VectorTools::sqr(), bpp::NumTools::sqr(), bpp::AbstractSubstitutionModel::tmpMat_, and bpp::AbstractSubstitutionModel::vPowGen_.

Referenced by bpp::JCprot::getd2Pij_dt2().

◆ getdPij_dt()

const Matrix< double > & AbstractSubstitutionModel::getdPij_dt ( double  t) const
virtualinherited
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::AbstractTransitionModel.

Reimplemented in bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 486 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::add(), bpp::MatrixTools::copy(), bpp::AbstractTransitionModel::dpijt_, bpp::AbstractSubstitutionModel::eigenValues_, bpp::VectorTools::exp(), bpp::numeric::exp(), bpp::MatrixTools::getId(), bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::isDiagonalizable_, bpp::AbstractSubstitutionModel::isNonSingular_, bpp::AbstractSubstitutionModel::leftEigenVectors_, bpp::MatrixTools::mult(), bpp::AbstractTransitionModel::rate_, bpp::AbstractSubstitutionModel::rightEigenVectors_, bpp::MatrixTools::scale(), bpp::AbstractTransitionModel::size_, bpp::AbstractSubstitutionModel::tmpMat_, and bpp::AbstractSubstitutionModel::vPowGen_.

Referenced by bpp::JCprot::getdPij_dt().

◆ getEigenValues()

const Vdouble& bpp::AbstractSubstitutionModel::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 418 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenValues_.

◆ getFrequencies()

const Vdouble& bpp::AbstractTransitionModel::getFrequencies ( ) const
inlineoverridevirtualinherited
Returns
A vector of all equilibrium frequencies.
See also
freq()

Implements bpp::TransitionModelInterface.

Definition at line 187 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::freq_.

Referenced by bpp::SENCA::setFreq().

◆ getFrequencies_()

Vdouble& bpp::AbstractTransitionModel::getFrequencies_ ( )
inlineoverrideprotectedvirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 268 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::freq_.

Referenced by bpp::CodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::fireParameterChanged(), bpp::CodonDistanceFrequenciesSubstitutionModel::setFreq(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::setFreq(), and bpp::DFPDistanceFrequenciesSubstitutionModel::setFreq().

◆ getIEigenValues()

const Vdouble& bpp::AbstractSubstitutionModel::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 420 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::iEigenValues_.

◆ getInitValue()

double AbstractTransitionModel::getInitValue ( size_t  i,
int  state 
) const
overridevirtualinherited

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
ithe index of the state in the model.
stateAn observed state in the sequence/site.
Returns
1 or 0 depending if the two states are compatible.
Exceptions
IndexOutOfBoundsExceptionif array position is out of range.
BadIntExceptionif states are not allowed in the associated alphabet.
See also
getStates();

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RE08.

Definition at line 70 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractTransitionModel::alphabet_, bpp::AbstractTransitionModel::getAlphabetStateAsInt(), and bpp::AbstractTransitionModel::size_.

◆ getModelStates() [1/2]

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

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

Parameters
codeThe alphabet state to check.
Returns
A vector of indices of model states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 185 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

◆ getModelStates() [2/2]

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

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

Parameters
codeThe alphabet state to check.
Returns
A vector of indices of model states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 183 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

◆ getName()

string KroneckerWordSubstitutionModel::getName ( ) const
overridevirtual

Get the name of the model.

Returns
The name of this model.

Implements bpp::BranchModelInterface.

Definition at line 86 of file KroneckerWordSubstitutionModel.cpp.

◆ getNumberOfModels()

size_t bpp::AbstractWordSubstitutionModel::getNumberOfModels ( ) const
inlineinherited

Definition at line 196 of file AbstractWordSubstitutionModel.h.

References bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::BppOSubstitutionModelFormat::write().

◆ getNumberOfStates()

size_t bpp::AbstractTransitionModel::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, bpp::RE08Codon, bpp::RE08Protein, bpp::RE08Nucleotide, bpp::YpR, bpp::gBGC, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, and bpp::BinarySubstitutionModel.

Definition at line 175 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices_(), bpp::AbstractKroneckerCodonSubstitutionModel::completeMatrices_(), bpp::AbstractKroneckerWordSubstitutionModel::fillBasicGenerator_(), bpp::AbstractWordSubstitutionModel::fillBasicGenerator_(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::AbstractMixedTransitionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::AbstractMixedTransitionModel::getdPij_dt(), bpp::RE08Nucleotide::getNumberOfStates(), bpp::RE08Protein::getNumberOfStates(), bpp::RE08Codon::getNumberOfStates(), bpp::WordSubstitutionModel::getPij_t(), bpp::AbstractMixedTransitionModel::getPij_t(), bpp::AbstractWordSubstitutionModel::setFreq(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::MixtureOfATransitionModel::updateMatrices_(), and bpp::MixtureOfTransitionModels::updateMatrices_().

◆ getPij_t()

const Matrix< double > & AbstractSubstitutionModel::getPij_t ( double  t) const
virtualinherited
Returns
All probabilities of change from state i to state j during time t.
See also
Pij_t()

Implements bpp::AbstractTransitionModel.

Reimplemented in bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 395 of file AbstractSubstitutionModel.cpp.

References bpp::abs(), bpp::MatrixTools::add(), bpp::MatrixTools::copy(), bpp::AbstractSubstitutionModel::eigenValues_, bpp::VectorTools::exp(), bpp::numeric::exp(), bpp::MatrixTools::getId(), bpp::BranchModelInterface::getName(), bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::isDiagonalizable_, bpp::AbstractSubstitutionModel::isNonSingular_, bpp::AbstractSubstitutionModel::leftEigenVectors_, bpp::MatrixTools::mult(), bpp::AbstractTransitionModel::pijt_, bpp::AbstractTransitionModel::rate_, bpp::AbstractSubstitutionModel::rightEigenVectors_, bpp::AbstractTransitionModel::size_, bpp::NumConstants::SMALL(), bpp::AbstractSubstitutionModel::tmpMat_, bpp::to_string(), and bpp::AbstractSubstitutionModel::vPowGen_.

Referenced by bpp::JCprot::getPij_t().

◆ getRate()

double AbstractTransitionModel::getRate ( ) const
overridevirtualinherited

The rate of the substitution process.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 45 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractTransitionModel::rate_.

◆ getRowLeftEigenVectors()

const Matrix<double>& bpp::AbstractSubstitutionModel::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 426 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::leftEigenVectors_.

◆ getScale()

double AbstractSubstitutionModel::getScale ( ) const
virtualinherited

return scale

Implements bpp::SubstitutionModelInterface.

Definition at line 632 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::diag(), bpp::AbstractTransitionModel::freq_, and bpp::AbstractSubstitutionModel::generator_.

Referenced by bpp::AbstractSubstitutionModel::normalize().

◆ getStateMap()

std::shared_ptr<const StateMapInterface> bpp::AbstractTransitionModel::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 173 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

Referenced by bpp::D1WalkSubstitutionModel::D1WalkSubstitutionModel(), and bpp::EquiprobableSubstitutionModel::EquiprobableSubstitutionModel().

◆ initGenerators_()

void AbstractKroneckerWordSubstitutionModel::initGenerators_ ( )
protectedinherited

Definition at line 142 of file AbstractKroneckerWordSubstitutionModel.cpp.

References bpp::AbstractKroneckerWordSubstitutionModel::vGenerators_, and bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel(), and bpp::AbstractKroneckerWordSubstitutionModel::AbstractKroneckerWordSubstitutionModel().

◆ isDiagonalizable()

bool bpp::AbstractSubstitutionModel::isDiagonalizable ( ) const
inlinevirtualinherited
Returns
True if the model is diagonalizable in R.

Implements bpp::SubstitutionModelInterface.

Definition at line 422 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isDiagonalizable_.

◆ isNonSingular()

bool bpp::AbstractSubstitutionModel::isNonSingular ( ) const
inlinevirtualinherited
Returns
True is the model is non-singular.

Implements bpp::SubstitutionModelInterface.

Definition at line 424 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isNonSingular_.

◆ isScalable()

virtual bool bpp::AbstractSubstitutionModel::isScalable ( ) const
inlinevirtualinherited

returns if model is scalable

Implements bpp::SubstitutionModelInterface.

Definition at line 469 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isScalable_.

Referenced by bpp::F84::updateMatrices_(), bpp::HKY85::updateMatrices_(), bpp::K80::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::T92::updateMatrices_(), bpp::TN93::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ Lik_t()

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
valuesAn vector of states on the site.
tthe branch length

Implements bpp::TransitionModelInterface.

Definition at line 30 of file AbstractSubstitutionModel.h.

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

◆ nModel()

const SubstitutionModelInterface& bpp::AbstractWordSubstitutionModel::nModel ( size_t  i) const
inlineinherited

returns the ith model, or throw an exception if i is not a valid number.

Definition at line 188 of file AbstractWordSubstitutionModel.h.

References bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::BppOSubstitutionModelFormat::write().

◆ normalize()

void AbstractSubstitutionModel::normalize ( )
virtualinherited

normalize the generator

Implements bpp::SubstitutionModelInterface.

Definition at line 673 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::getScale(), bpp::AbstractSubstitutionModel::isScalable_, and bpp::AbstractSubstitutionModel::setScale().

Referenced by bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::AbstractReversibleSubstitutionModel::updateMatrices_(), and bpp::gBGC::updateMatrices_().

◆ Pij_t()

virtual double bpp::AbstractTransitionModel::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.

Reimplemented in bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 197 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::getPij_t().

Referenced by bpp::JCprot::Pij_t().

◆ Qij()

virtual double bpp::AbstractSubstitutionModel::Qij ( size_t  i,
size_t  j 
) const
inlinevirtualinherited

A method for computing all necessary matrices.

Returns
The rate in the generator of change from state i to state j.
See also
getStates();

Implements bpp::SubstitutionModelInterface.

Definition at line 430 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

◆ setChangingPositions()

void AbstractKroneckerWordSubstitutionModel::setChangingPositions ( const std::vector< std::set< size_t >> &  vPos)
protectedinherited

Definition at line 133 of file AbstractKroneckerWordSubstitutionModel.cpp.

References bpp::AbstractKroneckerWordSubstitutionModel::checkChangingPositions_(), and bpp::AbstractKroneckerWordSubstitutionModel::sChangingPos_.

Referenced by bpp::AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel().

◆ setDiagonal()

void AbstractSubstitutionModel::setDiagonal ( )
virtualinherited

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

Implements bpp::SubstitutionModelInterface.

Definition at line 654 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::generator_, RowMatrix< double >::getRow(), and bpp::AbstractTransitionModel::size_.

Referenced by bpp::CodonSameAARateSubstitutionModel::compute_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::AbstractReversibleSubstitutionModel::updateMatrices_(), bpp::AbstractDFPSubstitutionModel::updateMatrices_(), bpp::POMO::updateMatrices_(), and bpp::RegisterRatesSubstitutionModel::updateMatrices_().

◆ setFreq()

void AbstractWordSubstitutionModel::setFreq ( std::map< int, double > &  freqs)
virtualinherited

Estimation of the parameters of the models so that the equilibrium frequencies match the given ones.

Parameters
freqsmap of the frequencies

When there is one submodel for all the positions, the submodel parameters are fit on the means of the frequencies on each position. Otherwise, each model is fit on the frequencies on its corresponding position in the word.

Reimplemented from bpp::AbstractTransitionModel.

Reimplemented in bpp::SENCA, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, and bpp::CodonAdHocSubstitutionModel.

Definition at line 349 of file AbstractWordSubstitutionModel.cpp.

References bpp::AbstractTransitionModel::getNumberOfStates(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractParameterAliasable::matchParametersValues(), and bpp::AbstractWordSubstitutionModel::VSubMod_.

◆ setFreqFromData()

void AbstractTransitionModel::setFreqFromData ( const SequenceDataInterface &  data,
double  pseudoCount = 0 
)
overridevirtualinherited

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

Parameters
dataThe sequences to use.
pseudoCountA 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.

Reimplemented in bpp::RE08, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::Coala, bpp::K80, and bpp::JCnuc.

Definition at line 88 of file AbstractSubstitutionModel.cpp.

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

◆ setNamespace()

void AbstractWordSubstitutionModel::setNamespace ( const std::string &  prefix)
virtualinherited

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::CodonAdHocSubstitutionModel, bpp::AbstractCodonSubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::SENCA, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, and bpp::CodonDistanceFrequenciesSubstitutionModel.

Definition at line 185 of file AbstractWordSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::setNamespace(), bpp::TextTools::toString(), bpp::AbstractWordSubstitutionModel::VnestedPrefix_, and bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel::setNamespace(), bpp::KroneckerCodonDistanceSubstitutionModel::setNamespace(), bpp::CodonDistanceSubstitutionModel::setNamespace(), and bpp::AbstractCodonSubstitutionModel::setNamespace().

◆ setRate()

void AbstractTransitionModel::setRate ( double  rate)
overridevirtualinherited

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

Parameters
ratemust be positive.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel, and bpp::AbstractMixedTransitionModel.

Definition at line 52 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::hasParameter(), bpp::AbstractTransitionModel::rate_, bpp::AbstractParameterAliasable::setParameterValue(), and bpp::TextTools::toString().

Referenced by bpp::AbstractMixedTransitionModel::setRate().

◆ setScalable()

void bpp::AbstractSubstitutionModel::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 461 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isScalable_.

◆ setScale()

void AbstractSubstitutionModel::setScale ( double  scale)
virtualinherited

Multiplies the current generator by the given scale.

Parameters
scalethe scale by which the generator is multiplied.

Implements bpp::SubstitutionModelInterface.

Definition at line 641 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::isScalable_, and bpp::MatrixTools::scale().

Referenced by bpp::AbstractSubstitutionModel::normalize(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::F84::updateMatrices_(), bpp::HKY85::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::K80::updateMatrices_(), bpp::L95::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::T92::updateMatrices_(), bpp::TN93::updateMatrices_(), bpp::POMO::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ setVerboseLevel()

void bpp::AbstractTransitionModel::setVerboseLevel ( short  level)
inlineinherited

Definition at line 239 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::verboseLevel_.

◆ Sij()

double bpp::AbstractSubstitutionModel::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 416 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

◆ stateMap()

const StateMapInterface& bpp::AbstractTransitionModel::stateMap ( ) const
inlineoverridevirtualinherited
Returns
The mapping of model states with alphabet states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 171 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

◆ updateMatrices_()

void AbstractWordSubstitutionModel::updateMatrices_ ( )
protectedvirtualinherited

Diagonalize the $Q$ matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices.

The generator_ matrix and freq_ vector must be initialized.

Eigen values and vectors are computed from the generator and assigned to the eigenValues_ for the real part, iEigenValues_ for the imaginary part, rightEigenVectors_ and leftEigenVectors_ variables. isDiagonalizable_ checks if the generator_ is diagonalizable in R.

The optional rate parameter is not taken into account in this method to prevent unnecessary computation.

!! Here there is no normalization of the generator.

Now check inversion and diagonalization

Reimplemented from bpp::AbstractSubstitutionModel.

Reimplemented in bpp::WordSubstitutionModel, and bpp::AbstractCodonSubstitutionModel.

Definition at line 209 of file AbstractWordSubstitutionModel.cpp.

References bpp::AbstractWordSubstitutionModel::completeMatrices_(), bpp::AbstractSubstitutionModel::computeFrequencies(), bpp::AbstractSubstitutionModel::enableEigenDecomposition(), bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractWordSubstitutionModel::fillBasicGenerator_(), bpp::AbstractTransitionModel::freq_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractTransitionModel::getNumberOfStates(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractSubstitutionModel::normalize(), bpp::AbstractSubstitutionModel::setDiagonal(), bpp::AbstractTransitionModel::size_, bpp::AbstractSubstitutionModel::updateMatrices_(), and bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel::KroneckerCodonDistanceFrequenciesSubstitutionModel(), bpp::KroneckerCodonDistanceSubstitutionModel::KroneckerCodonDistanceSubstitutionModel(), KroneckerWordSubstitutionModel(), bpp::AbstractCodonSubstitutionModel::updateMatrices_(), and bpp::WordSubstitutionModel::updateMatrices_().

◆ verboseLevel()

short bpp::AbstractTransitionModel::verboseLevel ( ) const
inlineinherited

Definition at line 241 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::verboseLevel_.

Member Data Documentation

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::AbstractTransitionModel::alphabet_
protectedinherited

The alphabet relevant to this model.

Definition at line 121 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractTransitionModel::alphabet(), bpp::POMO::getAllelicAlphabet(), bpp::AbstractTransitionModel::getAlphabet(), bpp::AbstractTransitionModel::getInitValue(), bpp::RE08::getInitValue(), bpp::AbstractNucleotideSubstitutionModel::getNucleicAlphabet(), bpp::AbstractReversibleNucleotideSubstitutionModel::getNucleicAlphabet(), bpp::RE08Nucleotide::getNucleicAlphabet(), bpp::AbstractProteinSubstitutionModel::getProteicAlphabet(), bpp::AbstractReversibleProteinSubstitutionModel::getProteicAlphabet(), bpp::RE08Protein::getProteicAlphabet(), and bpp::AbstractWordSubstitutionModel::operator=().

◆ computeFreq_

bool bpp::AbstractSubstitutionModel::computeFreq_
protectedinherited

if the Frequencies must be computed from the generator

Definition at line 303 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractSubstitutionModel::computeFrequencies(), and bpp::AbstractSubstitutionModel::operator=().

◆ d2pijt_

RowMatrix<double> bpp::AbstractTransitionModel::d2pijt_
mutableprotectedinherited

Definition at line 150 of file AbstractSubstitutionModel.h.

Referenced by bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), and bpp::AbstractMixedTransitionModel::getd2Pij_dt2().

◆ dpijt_

RowMatrix<double> bpp::AbstractTransitionModel::dpijt_
mutableprotectedinherited

Definition at line 149 of file AbstractSubstitutionModel.h.

Referenced by bpp::WordSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), and bpp::AbstractMixedTransitionModel::getdPij_dt().

◆ eigenDecompose_

bool bpp::AbstractSubstitutionModel::eigenDecompose_
protectedinherited

Tell if the eigen decomposition should be performed.

Definition at line 315 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::enableEigenDecomposition(), and bpp::AbstractSubstitutionModel::operator=().

◆ eigenValues_

Vdouble bpp::AbstractSubstitutionModel::eigenValues_
protectedinherited

The vector of eigen values.

Definition at line 320 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getEigenValues(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::setScale(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::BinarySubstitutionModel::updateMatrices_(), bpp::F84::updateMatrices_(), bpp::HKY85::updateMatrices_(), bpp::TwoParameterBinarySubstitutionModel::updateMatrices_(), bpp::EquiprobableSubstitutionModel::updateMatrices_(), bpp::F81::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::JCnuc::updateMatrices_(), bpp::K80::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::T92::updateMatrices_(), bpp::TN93::updateMatrices_(), bpp::JCprot::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ exchangeability_

RowMatrix<double> bpp::AbstractSubstitutionModel::exchangeability_
protectedinherited

The exchangeability matrix $S$ of the model, defined as $ S_{ij}=\frac{Q_{ij}}{\pi_j}$. When the model is reversible, this matrix is symmetric.

Definition at line 310 of file AbstractSubstitutionModel.h.

Referenced by bpp::Coala::Coala(), bpp::D1WalkSubstitutionModel::D1WalkSubstitutionModel(), bpp::LGL08_CAT::EmbeddedModel::EmbeddedModel(), bpp::AbstractSubstitutionModel::exchangeabilityMatrix(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::Coala::readFromFile(), bpp::AbstractSubstitutionModel::Sij(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::F84::updateMatrices_(), bpp::HKY85::updateMatrices_(), bpp::AbstractReversibleSubstitutionModel::updateMatrices_(), bpp::EquiprobableSubstitutionModel::updateMatrices_(), bpp::F81::updateMatrices_(), bpp::GTR::updateMatrices_(), bpp::JCnuc::updateMatrices_(), bpp::K80::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::SSR::updateMatrices_(), bpp::T92::updateMatrices_(), bpp::TN93::updateMatrices_(), bpp::JCprot::updateMatrices_(), bpp::RE08::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ freq_

Vdouble bpp::AbstractTransitionModel::freq_
protectedinherited

The vector $\pi_e$ of equilibrium frequencies.

Definition at line 143 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractTransitionModel::AbstractTransitionModel(), bpp::WordSubstitutionModel::completeMatrices_(), bpp::Coala::computeEquilibriumFrequencies(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::DSO78::DSO78(), bpp::EquiprobableSubstitutionModel::EquiprobableSubstitutionModel(), bpp::EquiprobableSubstitutionModel::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::JCprot::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::LG08::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::WAG01::fireParameterChanged(), bpp::AbstractTransitionModel::freq(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::AbstractTransitionModel::getFrequencies(), bpp::AbstractTransitionModel::getFrequencies_(), bpp::RE08::getPij_t(), bpp::AbstractSubstitutionModel::getScale(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::RE08::Pij_t(), bpp::RE08::RE08(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::D1WalkSubstitutionModel::setFreq(), bpp::EquiprobableSubstitutionModel::setFreq(), bpp::AbstractTransitionModel::setFreq(), bpp::DSO78::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::LG08::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::BinarySubstitutionModel::updateMatrices_(), bpp::F84::updateMatrices_(), bpp::HKY85::updateMatrices_(), bpp::TwoParameterBinarySubstitutionModel::updateMatrices_(), bpp::AbstractReversibleSubstitutionModel::updateMatrices_(), bpp::D1WalkSubstitutionModel::updateMatrices_(), bpp::EquiprobableSubstitutionModel::updateMatrices_(), bpp::MixtureOfATransitionModel::updateMatrices_(), bpp::MixtureOfTransitionModels::updateMatrices_(), bpp::F81::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::GTR::updateMatrices_(), bpp::JCnuc::updateMatrices_(), bpp::K80::updateMatrices_(), bpp::L95::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::SSR::updateMatrices_(), bpp::T92::updateMatrices_(), bpp::TN93::updateMatrices_(), bpp::POMO::updateMatrices_(), bpp::JCprot::updateMatrices_(), bpp::RE08::updateMatrices_(), bpp::YpR::updateMatrices_(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().

◆ generator_

RowMatrix<double> bpp::AbstractSubstitutionModel::generator_
protectedinherited

The generator matrix $Q$ of the model.

Definition at line 298 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices_(), bpp::AbstractKroneckerCodonSubstitutionModel::completeMatrices_(), bpp::CodonSameAARateSubstitutionModel::compute_(), bpp::AbstractKroneckerWordSubstitutionModel::fillBasicGenerator_(), bpp::AbstractWordSubstitutionModel::fillBasicGenerator_(), bpp::AbstractSubstitutionModel::generator(), bpp::AbstractSubstitutionModel::getScale(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::Qij(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::setDiagonal(), bpp::AnonymousSubstitutionModel::setGenerator(), bpp::AbstractSubstitutionModel::setScale(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::BinarySubstitutionModel::updateMatrices_(), bpp::F84::updateMatrices_(), bpp::HKY85::updateMatrices_(), bpp::TwoParameterBinarySubstitutionModel::updateMatrices_(), bpp::AbstractReversibleSubstitutionModel::updateMatrices_(), bpp::AbstractDFPSubstitutionModel::updateMatrices_(), bpp::EquiprobableSubstitutionModel::updateMatrices_(), bpp::F81::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::JCnuc::updateMatrices_(), bpp::K80::updateMatrices_(), bpp::L95::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::T92::updateMatrices_(), bpp::TN93::updateMatrices_(), bpp::POMO::updateMatrices_(), bpp::JCprot::updateMatrices_(), bpp::RE08::updateMatrices_(), bpp::RegisterRatesSubstitutionModel::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ iEigenValues_

Vdouble bpp::AbstractSubstitutionModel::iEigenValues_
protectedinherited

The vector of the imaginary part of the eigen values.

Definition at line 325 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getIEigenValues(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::setScale(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ isDiagonalizable_

bool bpp::AbstractSubstitutionModel::isDiagonalizable_
protectedinherited

boolean value for diagonalizability in R of the generator_

Definition at line 330 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::isDiagonalizable(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ isNonSingular_

bool bpp::AbstractSubstitutionModel::isNonSingular_
protectedinherited

boolean value for non-singularity of rightEigenVectors_

Definition at line 340 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::isNonSingular(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ isScalable_

bool bpp::AbstractSubstitutionModel::isScalable_
protectedinherited

If the model is scalable (ie generator can be normalized automatically).

Definition at line 293 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::isScalable(), bpp::AbstractSubstitutionModel::normalize(), bpp::AbstractSubstitutionModel::operator=(), bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel(), bpp::AbstractSubstitutionModel::setScalable(), and bpp::AbstractSubstitutionModel::setScale().

◆ leftEigenVectors_

RowMatrix<double> bpp::AbstractSubstitutionModel::leftEigenVectors_
protectedinherited

The $U$ matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular.

Definition at line 346 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getRowLeftEigenVectors(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::BinarySubstitutionModel::updateMatrices_(), bpp::F84::updateMatrices_(), bpp::HKY85::updateMatrices_(), bpp::TwoParameterBinarySubstitutionModel::updateMatrices_(), bpp::EquiprobableSubstitutionModel::updateMatrices_(), bpp::F81::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::JCnuc::updateMatrices_(), bpp::K80::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::T92::updateMatrices_(), bpp::TN93::updateMatrices_(), bpp::JCprot::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ 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().

◆ newAlphabet_

bool bpp::AbstractWordSubstitutionModel::newAlphabet_
privateinherited

boolean flag to check if a specific WordAlphabet has been built

Definition at line 109 of file AbstractWordSubstitutionModel.h.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), and bpp::AbstractWordSubstitutionModel::operator=().

◆ pijt_

RowMatrix<double> bpp::AbstractTransitionModel::pijt_
mutableprotectedinherited

These ones are for bookkeeping:

Definition at line 148 of file AbstractSubstitutionModel.h.

Referenced by bpp::WordSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), and bpp::AbstractMixedTransitionModel::getPij_t().

◆ rate_

double bpp::AbstractTransitionModel::rate_
protectedinherited

The rate of the model (default: 1). The generator (and all its vectorial components) is independent of the rate, since it should be normalized.

Definition at line 138 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractTransitionModel::addRateParameter(), bpp::BinarySubstitutionModel::d2Pij_dt2(), bpp::F84::d2Pij_dt2(), bpp::HKY85::d2Pij_dt2(), bpp::TwoParameterBinarySubstitutionModel::d2Pij_dt2(), bpp::EquiprobableSubstitutionModel::d2Pij_dt2(), bpp::F81::d2Pij_dt2(), bpp::JCnuc::d2Pij_dt2(), bpp::K80::d2Pij_dt2(), bpp::T92::d2Pij_dt2(), bpp::TN93::d2Pij_dt2(), bpp::JCprot::d2Pij_dt2(), bpp::BinarySubstitutionModel::dPij_dt(), bpp::F84::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::TwoParameterBinarySubstitutionModel::dPij_dt(), bpp::EquiprobableSubstitutionModel::dPij_dt(), bpp::F81::dPij_dt(), bpp::JCnuc::dPij_dt(), bpp::K80::dPij_dt(), bpp::T92::dPij_dt(), bpp::TN93::dPij_dt(), bpp::JCprot::dPij_dt(), bpp::AbstractTransitionModel::fireParameterChanged(), bpp::BinarySubstitutionModel::getd2Pij_dt2(), bpp::F84::getd2Pij_dt2(), bpp::HKY85::getd2Pij_dt2(), bpp::TwoParameterBinarySubstitutionModel::getd2Pij_dt2(), bpp::EquiprobableSubstitutionModel::getd2Pij_dt2(), bpp::F81::getd2Pij_dt2(), bpp::JCnuc::getd2Pij_dt2(), bpp::K80::getd2Pij_dt2(), bpp::T92::getd2Pij_dt2(), bpp::TN93::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::BinarySubstitutionModel::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::TwoParameterBinarySubstitutionModel::getdPij_dt(), bpp::EquiprobableSubstitutionModel::getdPij_dt(), bpp::F81::getdPij_dt(), bpp::JCnuc::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::BinarySubstitutionModel::getPij_t(), bpp::F84::getPij_t(), bpp::HKY85::getPij_t(), bpp::TwoParameterBinarySubstitutionModel::getPij_t(), bpp::EquiprobableSubstitutionModel::getPij_t(), bpp::F81::getPij_t(), bpp::JCnuc::getPij_t(), bpp::K80::getPij_t(), bpp::T92::getPij_t(), bpp::TN93::getPij_t(), bpp::JCprot::getPij_t(), bpp::WordSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractTransitionModel::getRate(), bpp::AbstractMixedTransitionModel::normalizeVRates(), bpp::BinarySubstitutionModel::Pij_t(), bpp::F84::Pij_t(), bpp::HKY85::Pij_t(), bpp::TwoParameterBinarySubstitutionModel::Pij_t(), bpp::EquiprobableSubstitutionModel::Pij_t(), bpp::F81::Pij_t(), bpp::JCnuc::Pij_t(), bpp::K80::Pij_t(), bpp::T92::Pij_t(), bpp::TN93::Pij_t(), bpp::JCprot::Pij_t(), bpp::AbstractMixedTransitionModel::setRate(), bpp::AbstractTransitionModel::setRate(), bpp::BinarySubstitutionModel::updateMatrices_(), bpp::TwoParameterBinarySubstitutionModel::updateMatrices_(), and bpp::MixtureOfTransitionModels::updateMatrices_().

◆ rightEigenVectors_

RowMatrix<double> bpp::AbstractSubstitutionModel::rightEigenVectors_
protectedinherited

The $U^-1$ matrix made of right eigen vectors (by column).

Definition at line 335 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getColumnRightEigenVectors(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::BinarySubstitutionModel::updateMatrices_(), bpp::F84::updateMatrices_(), bpp::HKY85::updateMatrices_(), bpp::TwoParameterBinarySubstitutionModel::updateMatrices_(), bpp::EquiprobableSubstitutionModel::updateMatrices_(), bpp::F81::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::JCnuc::updateMatrices_(), bpp::K80::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::T92::updateMatrices_(), bpp::TN93::updateMatrices_(), bpp::JCprot::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ sChangingPos_

std::vector<std::set< size_t> > bpp::AbstractKroneckerWordSubstitutionModel::sChangingPos_
privateinherited

vector of sets of simultaneously changing positions.

Shortcut : if empty, any number of any positions can change simultaneously

Definition at line 54 of file AbstractKroneckerWordSubstitutionModel.h.

Referenced by bpp::AbstractKroneckerWordSubstitutionModel::checkChangingPositions_(), bpp::AbstractKroneckerWordSubstitutionModel::fillBasicGenerator_(), bpp::AbstractKroneckerWordSubstitutionModel::operator=(), and bpp::AbstractKroneckerWordSubstitutionModel::setChangingPositions().

◆ size_

size_t bpp::AbstractTransitionModel::size_
protectedinherited

The number of states.

Definition at line 131 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractTransitionModel::AbstractTransitionModel(), bpp::D1WalkSubstitutionModel::D1WalkSubstitutionModel(), bpp::EquiprobableSubstitutionModel::d2Pij_dt2(), bpp::RE08::d2Pij_dt2(), bpp::EquiprobableSubstitutionModel::dPij_dt(), bpp::RE08::dPij_dt(), bpp::EquiprobableSubstitutionModel::getd2Pij_dt2(), bpp::JCnuc::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::RE08::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::EquiprobableSubstitutionModel::getdPij_dt(), bpp::JCnuc::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::RE08::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractTransitionModel::getInitValue(), bpp::RE08::getInitValue(), bpp::EquiprobableSubstitutionModel::getPij_t(), bpp::JCnuc::getPij_t(), bpp::JCprot::getPij_t(), bpp::RE08::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::EquiprobableSubstitutionModel::Pij_t(), bpp::RE08::Pij_t(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::setDiagonal(), bpp::T92::T92(), bpp::TN93::TN93(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::EquiprobableSubstitutionModel::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::RE08::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ stateMap_

std::shared_ptr<const StateMapInterface> bpp::AbstractTransitionModel::stateMap_
protectedinherited

The map of model states with alphabet states.

Definition at line 126 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::CodonSameAARateSubstitutionModel::compute_(), bpp::AbstractTransitionModel::getAlphabetStateAsChar(), bpp::AbstractTransitionModel::getAlphabetStateAsInt(), bpp::AbstractTransitionModel::getAlphabetStates(), bpp::AbstractTransitionModel::getModelStates(), bpp::AbstractTransitionModel::getNumberOfStates(), bpp::AbstractTransitionModel::getStateMap(), and bpp::AbstractTransitionModel::stateMap().

◆ tmpMat_

RowMatrix<double> bpp::AbstractSubstitutionModel::tmpMat_
mutableprotectedinherited

For computational issues.

Definition at line 357 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ verboseLevel_

short bpp::AbstractTransitionModel::verboseLevel_
protectedinherited

Definition at line 152 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractTransitionModel::setVerboseLevel(), bpp::AbstractSubstitutionModel::updateMatrices_(), and bpp::AbstractTransitionModel::verboseLevel().

◆ vGenerators_

std::vector< RowMatrix<double> > bpp::AbstractKroneckerWordSubstitutionModel::vGenerators_
privateinherited

vector of generators for computation purposes

Definition at line 59 of file AbstractKroneckerWordSubstitutionModel.h.

Referenced by bpp::AbstractKroneckerWordSubstitutionModel::fillBasicGenerator_(), bpp::AbstractKroneckerWordSubstitutionModel::initGenerators_(), and bpp::AbstractKroneckerWordSubstitutionModel::operator=().

◆ VnestedPrefix_

std::vector<std::string> bpp::AbstractWordSubstitutionModel::VnestedPrefix_
protectedinherited

Definition at line 117 of file AbstractWordSubstitutionModel.h.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel(), bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractWordSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::setNamespace(), and bpp::TripletSubstitutionModel::TripletSubstitutionModel().

◆ vPowGen_

std::vector< RowMatrix<double> > bpp::AbstractSubstitutionModel::vPowGen_
protectedinherited

vector of the powers of generator_ for Taylor development (if rightEigenVectors_ is singular).

Definition at line 352 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ Vrate_

std::vector<double> bpp::AbstractWordSubstitutionModel::Vrate_
protectedinherited

Definition at line 119 of file AbstractWordSubstitutionModel.h.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractWordSubstitutionModel::fillBasicGenerator_(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::WordSubstitutionModel::getPij_t(), bpp::AbstractWordSubstitutionModel::operator=(), bpp::TripletSubstitutionModel::TripletSubstitutionModel(), bpp::AbstractCodonSubstitutionModel::updateMatrices_(), and bpp::WordSubstitutionModel::updateMatrices_().

◆ VSubMod_

std::vector<std::shared_ptr<SubstitutionModelInterface> > bpp::AbstractWordSubstitutionModel::VSubMod_
protectedinherited

Vector of shared_ptr, to allow multiple positions to share the same model.

Definition at line 115 of file AbstractWordSubstitutionModel.h.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel(), bpp::AbstractKroneckerWordSubstitutionModel::AbstractKroneckerWordSubstitutionModel(), bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractKroneckerWordSubstitutionModel::checkChangingPositions_(), bpp::WordSubstitutionModel::completeMatrices_(), bpp::AbstractKroneckerWordSubstitutionModel::fillBasicGenerator_(), bpp::AbstractWordSubstitutionModel::fillBasicGenerator_(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::TripletSubstitutionModel::getName(), bpp::AbstractWordSubstitutionModel::getNumberOfModels(), bpp::WordSubstitutionModel::getPij_t(), bpp::AbstractKroneckerWordSubstitutionModel::initGenerators_(), bpp::AbstractWordSubstitutionModel::nModel(), bpp::AbstractWordSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::setFreq(), bpp::AbstractWordSubstitutionModel::setNamespace(), bpp::TripletSubstitutionModel::TripletSubstitutionModel(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::AbstractCodonSubstitutionModel::updateMatrices_(), bpp::WordSubstitutionModel::updateMatrices_(), and bpp::WordSubstitutionModel::WordSubstitutionModel().

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