bpp-phyl  2.2.0
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
bpp::AbstractBiblioSubstitutionModel Class Referenceabstract

Partial implementation of the SubstitutionModel interface for models that are set for matching the bibliography, and are only defined through a link to a "real" model. More...

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

+ Inheritance diagram for bpp::AbstractBiblioSubstitutionModel:
+ Collaboration diagram for bpp::AbstractBiblioSubstitutionModel:

Public Member Functions

 AbstractBiblioSubstitutionModel (const std::string &prefix)
 
 AbstractBiblioSubstitutionModel (const AbstractBiblioSubstitutionModel &model)
 
AbstractBiblioSubstitutionModel & operator= (const AbstractBiblioSubstitutionModel &model)
 
virtual ~AbstractBiblioSubstitutionModel ()
 
virtual AbstractBiblioSubstitutionModel * clone () const =0
 
virtual const SubstitutionModel & getModel () const =0
 
const std::vector< int > & getAlphabetStates () const
 
const StateMap & getStateMap () const
 
int getAlphabetStateAsInt (size_t i) const
 
std::string getAlphabetStateAsChar (size_t i) const
 
std::vector< size_t > getModelStates (int code) const
 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
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
virtual double freq (size_t i) const
 
virtual double Qij (size_t i, size_t j) const
 
virtual double Pij_t (size_t i, size_t j, double t) const
 
virtual double dPij_dt (size_t i, size_t j, double t) const
 
virtual double d2Pij_dt2 (size_t i, size_t j, double t) const
 
virtual const Vdouble & getFrequencies () const
 
const Matrix< double > & getGenerator () const
 
const Matrix< double > & getExchangeabilityMatrix () const
 
double Sij (size_t i, size_t j) 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
 
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
 
double getRate () const
 Get the rate. More...
 
void setRate (double rate)
 Set the rate of the model (must be positive). More...
 
void addRateParameter ()
 
void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
 Set equilibrium frequencies equal to the frequencies estimated from the data. More...
 
void setFreq (std::map< int, double > &frequ)
 Set equilibrium frequencies. More...
 
const Alphabet * getAlphabet () const
 
size_t getNumberOfStates () const
 Get the number of states. More...
 
double getInitValue (size_t i, int state) const throw (BadIntException)
 
const FrequenciesSet * getFrequenciesSet () const
 If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0. More...
 
virtual void fireParameterChanged (const ParameterList &parameters)
 Tells the model that a parameter value has changed. 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...
 
virtual std::string getName () const =0
 Get the name of the model. More...
 

Protected Member Functions

virtual void updateMatrices ()
 
virtual SubstitutionModel & getModel ()=0
 

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_
 

Detailed Description

Partial implementation of the SubstitutionModel interface for models that are set for matching the bibliography, and are only defined through a link to a "real" model.

Definition at line 57 of file AbstractBiblioSubstitutionModel.h.

Constructor & Destructor Documentation

◆ AbstractBiblioSubstitutionModel() [1/2]

AbstractBiblioSubstitutionModel::AbstractBiblioSubstitutionModel ( const std::string &  prefix)

Definition at line 45 of file AbstractBiblioSubstitutionModel.cpp.

◆ AbstractBiblioSubstitutionModel() [2/2]

AbstractBiblioSubstitutionModel::AbstractBiblioSubstitutionModel ( const AbstractBiblioSubstitutionModel &  model)

Definition at line 52 of file AbstractBiblioSubstitutionModel.cpp.

◆ ~AbstractBiblioSubstitutionModel()

virtual bpp::AbstractBiblioSubstitutionModel::~AbstractBiblioSubstitutionModel ( )
inlinevirtual

Definition at line 79 of file AbstractBiblioSubstitutionModel.h.

Member Function Documentation

◆ addRateParameter()

void AbstractBiblioSubstitutionModel::addRateParameter ( )
virtual

Implements bpp::SubstitutionModel.

Definition at line 84 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::SubstitutionModel::addRateParameter(), getModel(), getRate(), lParPmodel_, and mapParNamesFromPmodel_.

◆ clone()

virtual AbstractBiblioSubstitutionModel* bpp::AbstractBiblioSubstitutionModel::clone ( ) const
pure virtual

Implements bpp::SubstitutionModel.

Implemented in bpp::LLG08_EX3, bpp::LLG08_EHO, bpp::LLG08_UL3, bpp::LG10_EX_EHO, bpp::LGL08_CAT, bpp::LLG08_EX2, bpp::LLG08_UL2, bpp::GY94, bpp::YN98, bpp::MG94, bpp::YNGKP_M1, bpp::YNGKP_M8, bpp::YNGKP_M7, bpp::YNGKP_M3, bpp::YNGKP_M2, and bpp::AbstractBiblioMixedSubstitutionModel.

◆ d2Pij_dt2()

virtual double bpp::AbstractBiblioSubstitutionModel::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const
inlinevirtual
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::SubstitutionModel.

Definition at line 112 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::d2Pij_dt2(), and getModel().

◆ dPij_dt()

virtual double bpp::AbstractBiblioSubstitutionModel::dPij_dt ( size_t  i,
size_t  j,
double  t 
) const
inlinevirtual
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::SubstitutionModel.

Definition at line 111 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::dPij_dt(), and getModel().

◆ enableEigenDecomposition() [1/2]

void bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition ( bool  yn)
inlinevirtual

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 128 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::enableEigenDecomposition(), and getModel().

◆ enableEigenDecomposition() [2/2]

bool bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition ( )
inlinevirtual

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 130 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::enableEigenDecomposition(), and getModel().

◆ fireParameterChanged()

virtual void bpp::AbstractBiblioSubstitutionModel::fireParameterChanged ( const ParameterList &  parameters)
inlinevirtual

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Definition at line 177 of file AbstractBiblioSubstitutionModel.h.

References updateMatrices().

◆ freq()

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

Implements bpp::SubstitutionModel.

Definition at line 106 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::freq(), and getModel().

◆ getAlphabet()

const Alphabet* bpp::AbstractBiblioSubstitutionModel::getAlphabet ( ) const
inlinevirtual
Returns
Get the alphabet associated to this model.

Implements bpp::SubstitutionModel.

Definition at line 153 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getAlphabet(), and getModel().

◆ getAlphabetStateAsChar()

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

Implements bpp::SubstitutionModel.

Definition at line 100 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getAlphabetStateAsChar(), and getModel().

◆ getAlphabetStateAsInt()

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

Implements bpp::SubstitutionModel.

Definition at line 98 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getAlphabetStateAsInt(), and getModel().

◆ getAlphabetStates()

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

Implements bpp::SubstitutionModel.

Definition at line 94 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getAlphabetStates(), and getModel().

Referenced by bpp::YNGKP_M1::YNGKP_M1(), bpp::YNGKP_M2::YNGKP_M2(), bpp::YNGKP_M3::YNGKP_M3(), bpp::YNGKP_M7::YNGKP_M7(), and bpp::YNGKP_M8::YNGKP_M8().

◆ getColumnRightEigenVectors()

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::getColumnRightEigenVectors ( ) const
inlinevirtual
Returns
A matrix with right eigen vectors. Each column in the matrix stands for an eigen vector.

Implements bpp::SubstitutionModel.

Definition at line 141 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getColumnRightEigenVectors(), and getModel().

◆ getd2Pij_dt2()

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::getd2Pij_dt2 ( double  t) const
inlinevirtual
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::SubstitutionModel.

Definition at line 126 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getd2Pij_dt2(), and getModel().

◆ getdPij_dt()

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::getdPij_dt ( double  t) const
inlinevirtual
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::SubstitutionModel.

Definition at line 124 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getdPij_dt(), and getModel().

◆ getEigenValues()

const Vdouble& bpp::AbstractBiblioSubstitutionModel::getEigenValues ( ) const
inlinevirtual
Returns
A vector with all real parts of the eigen values of the generator of this model;

Implements bpp::SubstitutionModel.

Definition at line 136 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getEigenValues(), and getModel().

◆ getExchangeabilityMatrix()

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix ( ) const
inlinevirtual
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::SubstitutionModel.

Definition at line 118 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getExchangeabilityMatrix(), and getModel().

◆ getFrequencies()

virtual const Vdouble& bpp::AbstractBiblioSubstitutionModel::getFrequencies ( ) const
inlinevirtual
Returns
A vector of all equilibrium frequencies.
See also
freq()

Implements bpp::SubstitutionModel.

Definition at line 114 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getFrequencies(), and getModel().

◆ getFrequenciesSet()

const FrequenciesSet* bpp::AbstractBiblioSubstitutionModel::getFrequenciesSet ( ) const
inlinevirtual

If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.

Reimplemented from bpp::SubstitutionModel.

Reimplemented in bpp::YNGKP_M1, bpp::YNGKP_M8, bpp::YNGKP_M7, bpp::YNGKP_M3, and bpp::YNGKP_M2.

Definition at line 159 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getFrequenciesSet(), and getModel().

◆ getGenerator()

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::getGenerator ( ) const
inlinevirtual
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. Additionnaly, the rate_ attibute 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::SubstitutionModel.

Definition at line 116 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getGenerator(), and getModel().

◆ getIEigenValues()

const Vdouble& bpp::AbstractBiblioSubstitutionModel::getIEigenValues ( ) const
inlinevirtual
Returns
A vector with all imaginary parts of the eigen values of the generator of this model;

Implements bpp::SubstitutionModel.

Definition at line 138 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getIEigenValues(), and getModel().

◆ getInitValue()

double bpp::AbstractBiblioSubstitutionModel::getInitValue ( size_t  i,
int  state 
) const
throw (BadIntException
)
inlinevirtual

This method is used to initialize likelihoods in reccursions. 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::SubstitutionModel.

Definition at line 157 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getInitValue(), and getModel().

◆ getModel() [1/2]

virtual const SubstitutionModel& bpp::AbstractBiblioSubstitutionModel::getModel ( ) const
pure virtual

Implemented in bpp::LLG08_EX3, bpp::LLG08_EHO, bpp::LLG08_UL3, bpp::LG10_EX_EHO, bpp::LGL08_CAT, bpp::LLG08_EX2, bpp::LLG08_UL2, bpp::GY94, bpp::YN98, bpp::YNGKP_M1, bpp::YNGKP_M8, bpp::MG94, bpp::YNGKP_M7, bpp::YNGKP_M3, and bpp::YNGKP_M2.

Referenced by addRateParameter(), d2Pij_dt2(), dPij_dt(), enableEigenDecomposition(), freq(), getAlphabet(), getAlphabetStateAsChar(), getAlphabetStateAsInt(), getAlphabetStates(), getColumnRightEigenVectors(), getd2Pij_dt2(), getdPij_dt(), getEigenValues(), getExchangeabilityMatrix(), getFrequencies(), getFrequenciesSet(), getGenerator(), getIEigenValues(), getInitValue(), getModelStates(), getNumberOfStates(), getPij_t(), getRate(), getRowLeftEigenVectors(), getScale(), getStateMap(), isDiagonalizable(), isNonSingular(), Pij_t(), Qij(), setFreq(), setFreqFromData(), setRate(), setScale(), Sij(), and updateMatrices().

◆ getModel() [2/2]

virtual SubstitutionModel& bpp::AbstractBiblioSubstitutionModel::getModel ( )
protectedpure virtual

Implemented in bpp::LLG08_EX3, bpp::LLG08_EHO, bpp::LLG08_UL3, bpp::LG10_EX_EHO, bpp::LGL08_CAT, bpp::LLG08_EX2, bpp::LLG08_UL2, bpp::YN98, bpp::YNGKP_M1, bpp::GY94, bpp::YNGKP_M8, bpp::YNGKP_M7, bpp::YNGKP_M3, bpp::YNGKP_M2, and bpp::MG94.

◆ getModelStates() [1/2]

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

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::SubstitutionModel.

Definition at line 102 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::getModelStates().

◆ getModelStates() [2/2]

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

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::SubstitutionModel.

Definition at line 104 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::getModelStates().

◆ getName()

virtual std::string bpp::SubstitutionModel::getName ( ) const
pure virtualinherited

Get the name of the model.

Returns
The name of this model.

Implemented in bpp::YpR_Gen, bpp::YpR_Sym, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::GTR, bpp::TN93, bpp::RE08, bpp::MixtureOfSubstitutionModels, bpp::JCnuc, bpp::RN95s, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::BinarySubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::MixtureOfASubstitutionModel, bpp::LLG08_EX3, bpp::WordSubstitutionModel, bpp::LLG08_EHO, bpp::LLG08_UL3, bpp::WAG01, bpp::SSR, bpp::LG10_EX_EHO, bpp::CodonDistanceSubstitutionModel, bpp::L95, bpp::LGL08_CAT, bpp::LLG08_EX2, bpp::LLG08_UL2, bpp::DSO78, bpp::JTT92, bpp::CodonRateFrequenciesSubstitutionModel, bpp::LG08, bpp::YNGKP_M1, bpp::G2001, bpp::gBGC, bpp::YNGKP_M8, bpp::GY94, bpp::YNGKP_M7, bpp::YN98, bpp::YNGKP_M3, bpp::TS98, bpp::TripletSubstitutionModel, bpp::YNGKP_M2, bpp::MG94, bpp::CodonRateSubstitutionModel, bpp::Coala, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_EHO::EmbeddedModel, bpp::LLG08_UL3::EmbeddedModel, bpp::LG10_EX_EHO::EmbeddedModel, bpp::LGL08_CAT::EmbeddedModel, bpp::LLG08_EX2::EmbeddedModel, and bpp::LLG08_UL2::EmbeddedModel.

Referenced by bpp::AbstractCodonFitnessSubstitutionModel::AbstractCodonFitnessSubstitutionModel(), bpp::AbstractSubstitutionModel::fireParameterChanged(), bpp::MixtureOfSubstitutionModels::getSubmodelNumbers(), bpp::BppOSubstitutionModelFormat::readMixed_(), updateMatrices(), and bpp::BppOSubstitutionModelFormat::write().

◆ getNumberOfStates()

size_t bpp::AbstractBiblioSubstitutionModel::getNumberOfStates ( ) const
inlinevirtual

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::SubstitutionModel.

Definition at line 155 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::getNumberOfStates().

◆ getPij_t()

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

Implements bpp::SubstitutionModel.

Definition at line 122 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::getPij_t().

◆ getRate()

double bpp::AbstractBiblioSubstitutionModel::getRate ( ) const
inlinevirtual

Get the rate.

Implements bpp::SubstitutionModel.

Definition at line 143 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::getRate().

Referenced by addRateParameter(), 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(), and bpp::LLG08_UL3::LLG08_UL3().

◆ getRowLeftEigenVectors()

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::getRowLeftEigenVectors ( ) const
inlinevirtual
Returns
A matrix with left eigen vectors. Each row in the matrix stands for an eigen vector.

Implements bpp::SubstitutionModel.

Definition at line 140 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::getRowLeftEigenVectors().

◆ getScale()

double bpp::AbstractBiblioSubstitutionModel::getScale ( ) const
inlinevirtual

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::SubstitutionModel.

Definition at line 190 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::getScale().

◆ getStateMap()

const StateMap& bpp::AbstractBiblioSubstitutionModel::getStateMap ( ) const
inlinevirtual
Returns
The mapping of model states with alphabet states.

Implements bpp::SubstitutionModel.

Definition at line 96 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::getStateMap().

◆ isDiagonalizable()

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

Implements bpp::SubstitutionModel.

Definition at line 132 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::isDiagonalizable().

◆ isNonSingular()

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

Implements bpp::SubstitutionModel.

Definition at line 134 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::isNonSingular().

◆ operator=()

AbstractBiblioSubstitutionModel & AbstractBiblioSubstitutionModel::operator= ( const AbstractBiblioSubstitutionModel &  model)

Definition at line 60 of file AbstractBiblioSubstitutionModel.cpp.

References lParPmodel_, and mapParNamesFromPmodel_.

Referenced by bpp::AbstractBiblioMixedSubstitutionModel::operator=(), bpp::MG94::operator=(), bpp::GY94::operator=(), bpp::YN98::operator=(), and bpp::YNGKP_M1::operator=().

◆ Pij_t()

virtual double bpp::AbstractBiblioSubstitutionModel::Pij_t ( size_t  i,
size_t  j,
double  t 
) const
inlinevirtual
Returns
The probability of change from state i to state j during time t.
See also
getPij_t(), getStates()

Implements bpp::SubstitutionModel.

Definition at line 110 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::Pij_t().

◆ Qij()

virtual double bpp::AbstractBiblioSubstitutionModel::Qij ( size_t  i,
size_t  j 
) const
inlinevirtual
Returns
The rate in the generator of change from state i to state j.
See also
getStates();

Implements bpp::SubstitutionModel.

Definition at line 108 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::Qij().

◆ setFreq()

void AbstractBiblioSubstitutionModel::setFreq ( std::map< int, double > &  frequencies)
virtual

Set equilibrium frequencies.

Parameters
frequenciesThe map of the frequencies to use.

Reimplemented from bpp::SubstitutionModel.

Definition at line 95 of file AbstractBiblioSubstitutionModel.cpp.

References getModel(), mapParNamesFromPmodel_, and bpp::SubstitutionModel::setFreq().

◆ setFreqFromData()

void AbstractBiblioSubstitutionModel::setFreqFromData ( const SequenceContainer &  data,
double  pseudoCount = 0 
)
virtual

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::SubstitutionModel.

Definition at line 110 of file AbstractBiblioSubstitutionModel.cpp.

References getModel(), mapParNamesFromPmodel_, and bpp::SubstitutionModel::setFreqFromData().

◆ setRate()

void bpp::AbstractBiblioSubstitutionModel::setRate ( double  rate)
inlinevirtual

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

Parameters
ratemust be positive.

Implements bpp::SubstitutionModel.

Definition at line 145 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::setRate().

◆ setScale()

void bpp::AbstractBiblioSubstitutionModel::setScale ( double  scale)
inlinevirtual

Multiplies the current generator by the given scale.

Parameters
scalethe scale by which the generator is multiplied.

Implements bpp::SubstitutionModel.

Definition at line 192 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::setScale().

◆ Sij()

double bpp::AbstractBiblioSubstitutionModel::Sij ( size_t  i,
size_t  j 
) const
inlinevirtual
Returns
The exchangeability between state i and state j.

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

Implements bpp::SubstitutionModel.

Definition at line 120 of file AbstractBiblioSubstitutionModel.h.

References getModel(), and bpp::SubstitutionModel::Sij().

◆ updateMatrices()

void AbstractBiblioSubstitutionModel::updateMatrices ( )
protectedvirtual

Reimplemented in bpp::YNGKP_M1, bpp::YNGKP_M8, bpp::YNGKP_M7, bpp::YNGKP_M3, and bpp::YNGKP_M2.

Definition at line 70 of file AbstractBiblioSubstitutionModel.cpp.

References getModel(), bpp::SubstitutionModel::getName(), lParPmodel_, and mapParNamesFromPmodel_.

Referenced by fireParameterChanged(), bpp::GY94::GY94(), 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::YNGKP_M2::updateMatrices(), bpp::YNGKP_M7::updateMatrices(), bpp::YNGKP_M8::updateMatrices(), bpp::YNGKP_M1::updateMatrices(), and bpp::YN98::YN98().

Member Data Documentation

◆ lParPmodel_

ParameterList bpp::AbstractBiblioSubstitutionModel::lParPmodel_
protected

Definition at line 70 of file AbstractBiblioSubstitutionModel.h.

Referenced by addRateParameter(), bpp::GY94::GY94(), 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(), operator=(), bpp::YNGKP_M3::updateMatrices(), updateMatrices(), bpp::YN98::YN98(), bpp::YNGKP_M1::YNGKP_M1(), bpp::YNGKP_M2::YNGKP_M2(), bpp::YNGKP_M3::YNGKP_M3(), bpp::YNGKP_M7::YNGKP_M7(), and bpp::YNGKP_M8::YNGKP_M8().

◆ mapParNamesFromPmodel_

std::map<std::string, std::string> bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_
protected

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

Definition at line 68 of file AbstractBiblioSubstitutionModel.h.

Referenced by addRateParameter(), bpp::GY94::GY94(), 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(), operator=(), setFreq(), setFreqFromData(), bpp::YNGKP_M3::updateMatrices(), updateMatrices(), bpp::YN98::YN98(), bpp::YNGKP_M1::YNGKP_M1(), bpp::YNGKP_M2::YNGKP_M2(), bpp::YNGKP_M3::YNGKP_M3(), bpp::YNGKP_M7::YNGKP_M7(), and bpp::YNGKP_M8::YNGKP_M8().

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