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

YpR model. More...

#include <Bpp/Phyl/Model/Nucleotide/YpR.h>

+ Inheritance diagram for bpp::YpR:
+ Collaboration diagram for bpp::YpR:

Public Member Functions

virtual ~YpR ()
 
const SubstitutionModel * getNestedModel () const
 
size_t getNumberOfStates () const
 Get the number of states. More...
 
virtual void updateMatrices ()
 Diagonalize the $Q$ matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...
 
virtual void setNamespace (const std::string &)
 
void fireParameterChanged (const ParameterList &parameters)
 Tells the model that a parameter value has changed. More...
 
virtual AbstractSubstitutionModel * clone () const =0
 
const Alphabet * getAlphabet () const
 
const StateMap & getStateMap () const
 
const std::vector< int > & getAlphabetStates () const
 
std::string getAlphabetStateAsChar (size_t index) const
 
int getAlphabetStateAsInt (size_t index) 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 const Vdouble & getFrequencies () const
 
const Matrix< double > & getGenerator () const
 
const Matrix< double > & getExchangeabilityMatrix () const
 
double Sij (size_t i, size_t j) const
 
virtual const Matrix< double > & getPij_t (double t) const
 
virtual const Matrix< double > & getdPij_dt (double t) const
 
virtual const Matrix< double > & getd2Pij_dt2 (double t) 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 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
 
double getInitValue (size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException)
 
void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
 Set equilibrium frequencies equal to the frequencies estimated from the data. More...
 
virtual void setFreq (std::map< int, double > &)
 Set equilibrium frequencies. 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 addRateParameter ()
 
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 double getRate () const
 Get the rate. More...
 
virtual void setRate (double rate)
 Set the rate of the model (must be positive). More...
 
virtual std::string getName () const =0
 Get the name of the model. More...
 
virtual const FrequenciesSet * getFrequenciesSet () const
 If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0. More...
 

Protected Member Functions

void check_model (SubstitutionModel *const) const throw (Exception)
 
 YpR (const RNY *, SubstitutionModel *const, const std::string &prefix)
 Build a new YpR substitution model, with no dependency parameters. More...
 
 YpR (const YpR &, const std::string &prefix)
 
 YpR (const YpR &ypr)
 
YpR & operator= (const YpR &ypr)
 
void updateMatrices (double, double, double, double, double, double, double, double)
 
string getNestedPrefix () const
 

Protected Attributes

SubstitutionModel * pmodel_
 
std::string _nestedPrefix
 
const Alphabet * alphabet_
 The alphabet relevant to this model. More...
 
std::auto_ptr< StateMap > stateMap_
 The map of model states with alphabet states. More...
 
size_t size_
 The size of the generator, i.e. 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...
 
RowMatrix< double > generator_
 The generator matrix $Q$ of the model. More...
 
Vdouble freq_
 The vector $\pi_e$ of equilibrium frequencies. 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 symetric. More...
 
RowMatrix< double > pijt_
 These ones are for bookkeeping: More...
 
RowMatrix< double > dpijt_
 
RowMatrix< double > d2pijt_
 
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...
 

Detailed Description

YpR model.

Author
Laurent Guéguen

Model YpR, on RNY triplets, with independent positions.

This model is made from neighbourhood parameters and a nucleotidic probabilistic model such that the R/Y condition is respected : with letters A, T, C, G

\[ M=\begin{pmatrix} . & \beta_T & \beta_C & \alpha_G \\ \beta_A & . & \alpha_C & \beta_G \\ \beta_A & \alpha_T & . & \beta_G \\ \alpha_A & \beta_T & \beta_C & . \end{pmatrix} \]

From this model, the rates are a multiplication of the rates for the letters of the triplet. For the first letter, on alphabet R, C, T:

\[ M_1=\begin{pmatrix} . & \beta_C & \beta_T \\ \beta_A + \beta_G & . & \alpha_T \\ \beta_A + \beta_G & \alpha_C & . \end{pmatrix} \]

For the second letter, on alphabet A, G, C, T:

\[ M_2=\begin{pmatrix} . & \alpha_G & \beta_C & \beta_T \\ \alpha_A & . & \beta_C & \beta_T \\ \beta_A & \beta_G & . & \alpha_T \\ \beta_A & \beta_G & \alpha_C & . \end{pmatrix} \]

For the third letter, on alphabet A, G, Y:

\[ M_3 = \begin{pmatrix} . & \alpha_G & \beta_C + \beta_T\\ \alpha_A & . & \beta_C + \beta_T\\ \beta_A & \beta_G & . \end{pmatrix}. \]

And the model is the "union" of the 3 matrices, since in the model only the mutations concerning only one position are not null. In addition to this, neighbour dependency parameters (in inherited models) give the extra mutation rates for transitions inside YpR dinucleotides. For example from CpG to CpA and TpG, in relative proportion to the single transition rate: CGx -> CAx += rcGA*G->A CGx -> TGx += rCgT*C->T xCG -> xCA += rcGA*G->A xCG -> xTG += rCgT*C->T

Other YpR neighbour dependency rates are: TG -> CG, TG -> TA, CA -> TA, CA -> CG, TA -> CA, TA -> TC

The generator in normalized such that there is on average a substitution per site per unit of time ON THE CENTRAL POSITION of the triplet.

See also
AbstractSubstitutionModel

Definition at line 123 of file YpR.h.

Constructor & Destructor Documentation

◆ YpR() [1/3]

YpR::YpR ( const RNY *  alph,
SubstitutionModel * const  pm,
const std::string &  prefix 
)
protected

Build a new YpR substitution model, with no dependency parameters.

Definition at line 54 of file YpR.cpp.

References _nestedPrefix, bpp::SubstitutionModel::enableEigenDecomposition(), and pmodel_.

◆ YpR() [2/3]

YpR::YpR ( const YpR &  ypr,
const std::string &  prefix 
)
protected

Definition at line 65 of file YpR.cpp.

References _nestedPrefix, and pmodel_.

◆ YpR() [3/3]

YpR::YpR ( const YpR &  ypr)
protected

Definition at line 75 of file YpR.cpp.

◆ ~YpR()

virtual bpp::YpR::~YpR ( )
inlinevirtual

Definition at line 157 of file YpR.h.

Member Function Documentation

◆ addRateParameter()

void AbstractSubstitutionModel::addRateParameter ( )
virtualinherited

Implements bpp::SubstitutionModel.

Definition at line 433 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::rate_.

◆ check_model()

void YpR::check_model ( SubstitutionModel * const  pm) const
throw (Exception
)
protected

Definition at line 355 of file YpR.cpp.

◆ clone()

virtual AbstractSubstitutionModel* bpp::AbstractSubstitutionModel::clone ( ) const
pure virtualinherited

Implements bpp::SubstitutionModel.

Implemented in bpp::AbstractReversibleSubstitutionModel, bpp::YpR_Gen, bpp::YpR_Sym, bpp::HKY85, bpp::F84, bpp::JCprot, bpp::T92, bpp::K80, bpp::GTR, bpp::RN95, bpp::MixtureOfSubstitutionModels, bpp::TN93, bpp::RE08, bpp::AbstractCodonSubstitutionModel, bpp::JCnuc, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::MixtureOfASubstitutionModel, bpp::WAG01, bpp::SSR, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::L95, bpp::DSO78, bpp::JTT92, bpp::LG08, bpp::CodonRateFrequenciesSubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::gBGC, bpp::WordSubstitutionModel, bpp::TripletSubstitutionModel, 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.

◆ d2Pij_dt2()

virtual double bpp::AbstractSubstitutionModel::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const
inlinevirtualinherited
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.

Reimplemented in bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, and bpp::BinarySubstitutionModel.

Definition at line 281 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getd2Pij_dt2().

◆ dPij_dt()

virtual double bpp::AbstractSubstitutionModel::dPij_dt ( size_t  i,
size_t  j,
double  t 
) const
inlinevirtualinherited
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.

Reimplemented in bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, and bpp::BinarySubstitutionModel.

Definition at line 280 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getdPij_dt().

◆ enableEigenDecomposition() [1/2]

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

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 289 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

◆ enableEigenDecomposition() [2/2]

bool bpp::AbstractSubstitutionModel::enableEigenDecomposition ( )
inlinevirtualinherited

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 291 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

◆ fireParameterChanged()

void bpp::YpR::fireParameterChanged ( const ParameterList &  parameters)
inlinevirtual

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 184 of file YpR.h.

◆ freq()

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

Implements bpp::SubstitutionModel.

Definition at line 275 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

◆ getAlphabet()

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

Implements bpp::SubstitutionModel.

Definition at line 237 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::alphabet_.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::WordSubstitutionModel::completeMatrices(), bpp::AbstractWordSubstitutionModel::extractAlph(), bpp::AbstractWordSubstitutionModel::getNumberOfStates(), and bpp::AbstractWordSubstitutionModel::operator=().

◆ getAlphabetStateAsChar()

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

Implements bpp::SubstitutionModel.

Definition at line 243 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::stateMap_.

◆ getAlphabetStateAsInt()

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

Implements bpp::SubstitutionModel.

Definition at line 245 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::stateMap_.

◆ getAlphabetStates()

const std::vector<int>& bpp::AbstractSubstitutionModel::getAlphabetStates ( ) const
inlinevirtualinherited
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 241 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::stateMap_.

◆ 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::SubstitutionModel.

Definition at line 273 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::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::WordSubstitutionModel.

Definition at line 274 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::d2pijt_, bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::isDiagonalizable_, bpp::AbstractSubstitutionModel::isNonSingular_, bpp::AbstractSubstitutionModel::leftEigenVectors_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rightEigenVectors_, bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::tmpMat_, and bpp::AbstractSubstitutionModel::vPowGen_.

Referenced by bpp::AbstractSubstitutionModel::d2Pij_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::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::WordSubstitutionModel.

Definition at line 205 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::dpijt_, bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::isDiagonalizable_, bpp::AbstractSubstitutionModel::isNonSingular_, bpp::AbstractSubstitutionModel::leftEigenVectors_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rightEigenVectors_, bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::tmpMat_, and bpp::AbstractSubstitutionModel::vPowGen_.

Referenced by bpp::AbstractSubstitutionModel::dPij_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::SubstitutionModel.

Definition at line 263 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenValues_.

◆ getExchangeabilityMatrix()

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

Definition at line 255 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

◆ getFrequencies()

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

Implements bpp::SubstitutionModel.

Definition at line 251 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

◆ getFrequenciesSet()

virtual const FrequenciesSet* bpp::SubstitutionModel::getFrequenciesSet ( ) const
inlinevirtualinherited

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

Reimplemented in bpp::JCprot, bpp::AbstractBiblioSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::DSO78, bpp::JTT92, bpp::LG08, bpp::YNGKP_M1, bpp::YNGKP_M8, bpp::YNGKP_M7, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::YNGKP_M3, bpp::YNGKP_M2, and bpp::AbstractCodonFrequenciesSubstitutionModel.

Definition at line 479 of file SubstitutionModel.h.

Referenced by bpp::AbstractBiblioSubstitutionModel::getFrequenciesSet(), and bpp::BppOSubstitutionModelFormat::write().

◆ getGenerator()

const Matrix<double>& bpp::AbstractSubstitutionModel::getGenerator ( ) 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. 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 253 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

◆ 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::SubstitutionModel.

Definition at line 265 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::iEigenValues_.

◆ getInitValue()

double AbstractSubstitutionModel::getInitValue ( size_t  i,
int  state 
) const
throw (IndexOutOfBoundsException,
BadIntException
)
virtualinherited

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.

Reimplemented in bpp::RE08.

Definition at line 349 of file AbstractSubstitutionModel.cpp.

◆ getModelStates() [1/2]

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

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 247 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::stateMap_.

◆ getModelStates() [2/2]

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

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 249 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::stateMap_.

◆ 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_(), bpp::AbstractBiblioSubstitutionModel::updateMatrices(), and bpp::BppOSubstitutionModelFormat::write().

◆ getNestedModel()

const SubstitutionModel* bpp::YpR::getNestedModel ( ) const
inline

Definition at line 176 of file YpR.h.

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

◆ getNestedPrefix()

string bpp::YpR::getNestedPrefix ( ) const
inlineprotected

Definition at line 168 of file YpR.h.

◆ getNumberOfStates()

size_t bpp::YpR::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 178 of file YpR.h.

◆ 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::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::WordSubstitutionModel.

Definition at line 134 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::isDiagonalizable_, bpp::AbstractSubstitutionModel::isNonSingular_, bpp::AbstractSubstitutionModel::leftEigenVectors_, bpp::AbstractSubstitutionModel::pijt_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::rightEigenVectors_, bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::tmpMat_, and bpp::AbstractSubstitutionModel::vPowGen_.

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

◆ getRate()

double AbstractSubstitutionModel::getRate ( ) const
virtualinherited

Get the rate.

Implements bpp::SubstitutionModel.

Definition at line 415 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::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::SubstitutionModel.

Definition at line 271 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::leftEigenVectors_.

◆ getScale()

double AbstractSubstitutionModel::getScale ( ) const
virtualinherited

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 400 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::freq_, and bpp::AbstractSubstitutionModel::generator_.

Referenced by bpp::AbstractReversibleSubstitutionModel::updateMatrices().

◆ getStateMap()

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

Implements bpp::SubstitutionModel.

Definition at line 239 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::stateMap_.

◆ isDiagonalizable()

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

Implements bpp::SubstitutionModel.

Definition at line 267 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::SubstitutionModel.

Definition at line 269 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isNonSingular_.

◆ operator=()

YpR& bpp::YpR::operator= ( const YpR &  ypr)
inlineprotected

Definition at line 147 of file YpR.h.

References _nestedPrefix, bpp::SubstitutionModel::clone(), and pmodel_.

◆ Pij_t()

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

Implements bpp::SubstitutionModel.

Reimplemented in bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, and bpp::BinarySubstitutionModel.

Definition at line 279 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getPij_t().

◆ Qij()

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

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel.

Definition at line 277 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

◆ setFreq()

void AbstractSubstitutionModel::setFreq ( std::map< int, double > &  frequencies)
virtualinherited

Set equilibrium frequencies.

Parameters
frequenciesThe map of the frequencies to use.

Reimplemented from bpp::SubstitutionModel.

Reimplemented in bpp::F84, bpp::HKY85, bpp::T92, bpp::MixtureOfSubstitutionModels, bpp::AbstractWordSubstitutionModel, bpp::GTR, bpp::RN95, bpp::TN93, bpp::RN95s, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::MixtureOfASubstitutionModel, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::BinarySubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::SSR, bpp::L95, and bpp::CodonRateFrequenciesSubstitutionModel.

Definition at line 388 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::freq_, bpp::AbstractSubstitutionModel::size_, and bpp::AbstractSubstitutionModel::updateMatrices().

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

◆ setFreqFromData()

void AbstractSubstitutionModel::setFreqFromData ( const SequenceContainer &  data,
double  pseudoCount = 0 
)
virtualinherited

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.

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

Definition at line 366 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::setFreq(), and bpp::AbstractSubstitutionModel::size_.

◆ setNamespace()

void YpR::setNamespace ( const std::string &  prefix)
virtual

Definition at line 386 of file YpR.cpp.

References _nestedPrefix, and pmodel_.

◆ setRate()

void AbstractSubstitutionModel::setRate ( double  rate)
virtualinherited

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

Parameters
ratemust be positive.

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel.

Definition at line 422 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::rate_.

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

◆ 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::SubstitutionModel.

Definition at line 409 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::generator_.

◆ 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::SubstitutionModel.

Definition at line 257 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

◆ updateMatrices() [1/2]

void YpR::updateMatrices ( double  CgT,
double  cGA,
double  TgC,
double  tGA,
double  CaT,
double  cAG,
double  TaC,
double  tAC 
)
protected

Definition at line 88 of file YpR.cpp.

References bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractSubstitutionModel::freq_, bpp::AbstractSubstitutionModel::generator_, bpp::SubstitutionModel::getAlphabet(), bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::isDiagonalizable_, bpp::AbstractSubstitutionModel::isNonSingular_, bpp::AbstractSubstitutionModel::leftEigenVectors_, pmodel_, bpp::SubstitutionModel::Qij(), bpp::AbstractSubstitutionModel::rightEigenVectors_, bpp::AbstractSubstitutionModel::size_, bpp::AbstractSubstitutionModel::tmpMat_, and bpp::AbstractSubstitutionModel::vPowGen_.

◆ updateMatrices() [2/2]

void YpR::updateMatrices ( )
virtual

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.

Reimplemented from bpp::AbstractSubstitutionModel.

Reimplemented in bpp::YpR_Gen, and bpp::YpR_Sym.

Definition at line 82 of file YpR.cpp.

Referenced by bpp::YpR_Sym::updateMatrices(), and bpp::YpR_Gen::updateMatrices().

Member Data Documentation

◆ _nestedPrefix

std::string bpp::YpR::_nestedPrefix
protected

Definition at line 133 of file YpR.h.

Referenced by operator=(), setNamespace(), and YpR().

◆ alphabet_

const Alphabet* bpp::AbstractSubstitutionModel::alphabet_
protectedinherited

The alphabet relevant to this model.

Definition at line 86 of file AbstractSubstitutionModel.h.

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

◆ d2pijt_

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

Definition at line 129 of file AbstractSubstitutionModel.h.

Referenced by bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::AbstractMixedSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), and bpp::AbstractSubstitutionModel::operator=().

◆ dpijt_

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

Definition at line 128 of file AbstractSubstitutionModel.h.

Referenced by bpp::WordSubstitutionModel::getdPij_dt(), bpp::AbstractMixedSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), and bpp::AbstractSubstitutionModel::operator=().

◆ eigenDecompose_

bool bpp::AbstractSubstitutionModel::eigenDecompose_
protectedinherited

Tell if the eigen decomposition should be performed.

Definition at line 134 of file AbstractSubstitutionModel.h.

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

◆ eigenValues_

Vdouble bpp::AbstractSubstitutionModel::eigenValues_
protectedinherited

The vector of eigen values.

Definition at line 139 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getEigenValues(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::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 symetric.

Definition at line 122 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::Coala::Coala(), bpp::LGL08_CAT::EmbeddedModel::EmbeddedModel(), bpp::AbstractSubstitutionModel::getExchangeabilityMatrix(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::Coala::readFromFile(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::AbstractSubstitutionModel::Sij(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::SSR::updateMatrices(), bpp::RN95s::updateMatrices(), updateMatrices(), bpp::GTR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::RE08::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

◆ freq_

Vdouble bpp::AbstractSubstitutionModel::freq_
protectedinherited

The vector $\pi_e$ of equilibrium frequencies.

Definition at line 113 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::AbstractSubstitutionModel(), bpp::WordSubstitutionModel::completeMatrices(), bpp::Coala::computeEquilibriumFrequencies(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::DSO78::DSO78(), bpp::LG08::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::WAG01::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::JCprot::fireParameterChanged(), bpp::AbstractSubstitutionModel::freq(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::AbstractSubstitutionModel::getFrequencies(), bpp::RN95s::getPij_t(), bpp::RE08::getPij_t(), bpp::RN95::getPij_t(), bpp::AbstractSubstitutionModel::getScale(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::AbstractSubstitutionModel::operator=(), bpp::RN95s::Pij_t(), bpp::RE08::Pij_t(), bpp::RN95::Pij_t(), bpp::RE08::RE08(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::AbstractSubstitutionModel::setFreq(), bpp::LG08::setFreqFromData(), bpp::DSO78::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::L95::updateMatrices(), bpp::SSR::updateMatrices(), bpp::MixtureOfASubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::MixtureOfSubstitutionModels::updateMatrices(), updateMatrices(), bpp::GTR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::RE08::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::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 108 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractCodonSubstitutionModel::completeMatrices(), bpp::AbstractSubstitutionModel::getGenerator(), bpp::AbstractSubstitutionModel::getScale(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::Qij(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::setScale(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::L95::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::RE08::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

◆ iEigenValues_

Vdouble bpp::AbstractSubstitutionModel::iEigenValues_
protectedinherited

The vector of the imaginary part of the eigen values.

Definition at line 144 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::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

◆ isDiagonalizable_

bool bpp::AbstractSubstitutionModel::isDiagonalizable_
protectedinherited

boolean value for diagonalizability in R of the generator_

Definition at line 150 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::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

◆ isNonSingular_

bool bpp::AbstractSubstitutionModel::isNonSingular_
protectedinherited

boolean value for non-singularity of rightEigenVectors_

Definition at line 160 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::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

◆ 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 166 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getRowLeftEigenVectors(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

◆ pijt_

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

These ones are for bookkeeping:

Definition at line 127 of file AbstractSubstitutionModel.h.

Referenced by bpp::WordSubstitutionModel::getPij_t(), bpp::AbstractMixedSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), and bpp::AbstractSubstitutionModel::operator=().

◆ pmodel_

SubstitutionModel* bpp::YpR::pmodel_
protected

Definition at line 127 of file YpR.h.

Referenced by operator=(), setNamespace(), updateMatrices(), and YpR().

◆ rate_

double bpp::AbstractSubstitutionModel::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 103 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::addRateParameter(), bpp::RN95s::d2Pij_dt2(), bpp::JCnuc::d2Pij_dt2(), bpp::TN93::d2Pij_dt2(), bpp::RN95::d2Pij_dt2(), bpp::K80::d2Pij_dt2(), bpp::T92::d2Pij_dt2(), bpp::JCprot::d2Pij_dt2(), bpp::HKY85::d2Pij_dt2(), bpp::F84::d2Pij_dt2(), bpp::RN95s::dPij_dt(), bpp::JCnuc::dPij_dt(), bpp::TN93::dPij_dt(), bpp::RN95::dPij_dt(), bpp::K80::dPij_dt(), bpp::T92::dPij_dt(), bpp::JCprot::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::F84::dPij_dt(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::RN95s::getd2Pij_dt2(), bpp::JCnuc::getd2Pij_dt2(), bpp::TN93::getd2Pij_dt2(), bpp::RN95::getd2Pij_dt2(), bpp::K80::getd2Pij_dt2(), bpp::T92::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::F84::getd2Pij_dt2(), bpp::HKY85::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::RN95s::getdPij_dt(), bpp::JCnuc::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::RN95::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::WordSubstitutionModel::getPij_t(), bpp::RN95s::getPij_t(), bpp::JCnuc::getPij_t(), bpp::TN93::getPij_t(), bpp::RN95::getPij_t(), bpp::K80::getPij_t(), bpp::T92::getPij_t(), bpp::JCprot::getPij_t(), bpp::F84::getPij_t(), bpp::HKY85::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getRate(), bpp::AbstractMixedSubstitutionModel::normalizeVRates(), bpp::AbstractSubstitutionModel::operator=(), bpp::RN95s::Pij_t(), bpp::JCnuc::Pij_t(), bpp::TN93::Pij_t(), bpp::RN95::Pij_t(), bpp::K80::Pij_t(), bpp::T92::Pij_t(), bpp::JCprot::Pij_t(), bpp::F84::Pij_t(), bpp::HKY85::Pij_t(), bpp::AbstractMixedSubstitutionModel::setRate(), bpp::AbstractSubstitutionModel::setRate(), and bpp::BinarySubstitutionModel::updateMatrices().

◆ rightEigenVectors_

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

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

Definition at line 155 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::getColumnRightEigenVectors(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

◆ size_

size_t bpp::AbstractSubstitutionModel::size_
protectedinherited

The size of the generator, i.e. the number of states.

Definition at line 96 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::AbstractSubstitutionModel(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::JCnuc::getd2Pij_dt2(), bpp::RE08::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::JCnuc::getdPij_dt(), bpp::RE08::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::RE08::getNumberOfStates(), bpp::JCnuc::getPij_t(), bpp::RE08::getPij_t(), bpp::JCprot::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::Pij_t(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::setFreq(), bpp::LG08::setFreqFromData(), bpp::DSO78::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::AbstractSubstitutionModel::setFreqFromData(), bpp::T92::T92(), bpp::TN93::TN93(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), updateMatrices(), bpp::RN95::updateMatrices(), bpp::RE08::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

◆ stateMap_

std::auto_ptr<StateMap> bpp::AbstractSubstitutionModel::stateMap_
protectedinherited

The map of model states with alphabet states.

Definition at line 91 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getAlphabetStateAsChar(), bpp::AbstractSubstitutionModel::getAlphabetStateAsInt(), bpp::AbstractSubstitutionModel::getAlphabetStates(), bpp::AbstractSubstitutionModel::getModelStates(), bpp::AbstractSubstitutionModel::getStateMap(), and bpp::AbstractSubstitutionModel::operator=().

◆ tmpMat_

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

For computational issues.

Definition at line 177 of file AbstractSubstitutionModel.h.

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

◆ 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 172 of file AbstractSubstitutionModel.h.

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

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