bpp-phyl  2.2.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::K80 Class Referenceabstract

The Kimura 2-rates substitution model for nucleotides. More...

#include <Bpp/Phyl/Model/Nucleotide/K80.h>

+ Inheritance diagram for bpp::K80:
+ Collaboration diagram for bpp::K80:

Public Member Functions

 K80 (const NucleicAlphabet *alpha, double kappa=1.)
 
virtual ~K80 ()
 
K80 * clone () const
 
double Pij_t (size_t i, size_t j, double d) const
 
double dPij_dt (size_t i, size_t j, double d) const
 
double d2Pij_dt2 (size_t i, size_t j, double d) const
 
const Matrix< double > & getPij_t (double d) const
 
const Matrix< double > & getdPij_dt (double d) const
 
const Matrix< double > & getd2Pij_dt2 (double d) const
 
std::string getName () const
 Get the name of the model. More...
 
void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
 This method is disabled in this model since frequencies are not free parameters. More...
 
virtual size_t getNumberOfStates () const
 Get the number of states. More...
 
virtual const std::vector< int > & getAlphabetStates () const =0
 
virtual const StateMap & getStateMap () const =0
 
virtual std::vector< size_t > getModelStates (int code) const =0
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
virtual std::vector< size_t > getModelStates (const std::string &code) const =0
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
virtual int getAlphabetStateAsInt (size_t index) const =0
 
virtual std::string getAlphabetStateAsChar (size_t index) const =0
 
virtual double freq (size_t i) const =0
 
virtual double Qij (size_t i, size_t j) const =0
 
virtual const Vdouble & getFrequencies () const =0
 
virtual const Matrix< double > & getGenerator () const =0
 
virtual const Matrix< double > & getExchangeabilityMatrix () const =0
 
virtual double Sij (size_t i, size_t j) const =0
 
virtual void enableEigenDecomposition (bool yn)=0
 Set if eigenValues and Vectors must be computed. More...
 
virtual bool enableEigenDecomposition ()=0
 Tell if eigenValues and Vectors must be computed. More...
 
virtual const Vdouble & getEigenValues () const =0
 
virtual const Vdouble & getIEigenValues () const =0
 
virtual bool isDiagonalizable () const =0
 
virtual bool isNonSingular () const =0
 
virtual const Matrix< double > & getRowLeftEigenVectors () const =0
 
virtual const Matrix< double > & getColumnRightEigenVectors () const =0
 
virtual const Alphabet * getAlphabet () const =0
 
virtual double getInitValue (size_t i, int state) const =0 throw (IndexOutOfBoundsException, BadIntException)
 
virtual double getScale () const =0
 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...
 
virtual void setScale (double scale)=0
 Multiplies the current generator by the given scale. More...
 
virtual double getRate () const =0
 Get the rate. More...
 
virtual void setRate (double rate)=0
 Set the rate of the model (must be positive). More...
 
virtual void addRateParameter ()=0
 
virtual void setFreq (std::map< int, double > &frequencies)
 Set equilibrium frequencies. More...
 
virtual const FrequenciesSet * getFrequenciesSet () const
 If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0. More...
 
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
 
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
 
double getInitValue (size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException)
 
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...
 
virtual void fireParameterChanged (const ParameterList &parameters)
 Tells the model that a parameter value has changed. 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...
 

Protected Member Functions

void updateMatrices ()
 Compute and diagonalize the $Q$ matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...
 

Protected Attributes

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...
 

Private Attributes

double kappa_
 
double r_
 
double l_
 
double k_
 
double exp1_
 
double exp2_
 
RowMatrix< double > p_
 

Detailed Description

The Kimura 2-rates substitution model for nucleotides.

All two rates: one for transitions and one for transversions. This models include one parameter, the transition / transversion relative rate $\kappa$.

\[ S = \begin{pmatrix} \cdots & r & \kappa r & r \\ r & \cdots & r & \kappa r \\ \kappa r & r & \cdots & r \\ r & \kappa r & r & \cdots \\ \end{pmatrix} \]

\[ \pi = \left(\frac{1}{4}, \frac{1}{4}, \frac{1}{4}, \frac{1}{4}\right) \]

Normalization: $r$ is set so that $\sum_i Q_{i,i}\pi_i = -1$:

\[ S = \begin{pmatrix} -4 & \frac{4}{\kappa+2} & \frac{4\kappa}{\kappa+2} & \frac{4}{\kappa+2} \\ \frac{4}{\kappa+2} & -4 & \frac{4}{\kappa+2} & \frac{4\kappa}{\kappa+2} \\ \frac{4\kappa}{\kappa+2} & \frac{4}{\kappa+2} & -4 & \frac{4}{\kappa+2} \\ \frac{4}{\kappa+2} & \frac{4\kappa}{\kappa+2} & \frac{4}{\kappa+2} & -4 \\ \end{pmatrix} \]

The normalized generator is obtained by taking the dot product of $S$ and $\pi$:

\[ Q = S . \pi = \begin{pmatrix} -1 & \frac{1}{\kappa+2} & \frac{\kappa}{\kappa+2} & \frac{1}{\kappa+2} \\ \frac{1}{\kappa+2} & -1 & \frac{1}{\kappa+2} & \frac{\kappa}{\kappa+2} \\ \frac{\kappa}{\kappa+2} & \frac{1}{\kappa+2} & -1 & \frac{1}{\kappa+2} \\ \frac{1}{\kappa+2} & \frac{\kappa}{\kappa+2} & \frac{1}{\kappa+2} & -1 \\ \end{pmatrix} \]

The eigen values are $\left(0, -\frac{2\kappa+2}{\kappa+2}, -\frac{2\kappa+2}{\kappa+2}, -\frac{4}{\kappa+2}\right)$, the left eigen vectors are, by row:

\[ U = \begin{pmatrix} \frac{1}{4} & \frac{1}{4} & \frac{1}{4} & \frac{1}{4} \\ 0 & \frac{1}{2} & 0 & -\frac{1}{2} \\ \frac{1}{2} & 0 & -\frac{1}{2} & 0 \\ \frac{1}{4} & -\frac{1}{4} & \frac{1}{4} & -\frac{1}{4} \\ \end{pmatrix} \]

and the right eigen vectors are, by column:

\[ U^-1 = \begin{pmatrix} 1 & 0 & 1 & 1 \\ 1 & 1 & 0 & -1 \\ 1 & 0 & -1 & 1 \\ 1 & -1 & 0 & -1 \\ \end{pmatrix} \]

In addition, a rate_ factor defines the mean rate of the model.

The probabilities of changes are computed analytically using the formulas:

\[ P_{i,j}(t) = \begin{pmatrix} \frac{1}{2}A + \frac{1}{4}B + \frac{1}{4} & \frac{1}{4} - \frac{1}{4}B & -\frac{1}{2}A + \frac{1}{4}B + \frac{1}{4} & \frac{1}{4} - \frac{1}{4}B \\ \frac{1}{4} - \frac{1}{4}B & \frac{1}{2}A + \frac{1}{4}B + \frac{1}{4} & \frac{1}{4} - \frac{1}{4}B & -\frac{1}{2}A + \frac{1}{4}B + \frac{1}{4} \\ -\frac{1}{2}A + \frac{1}{4}B + \frac{1}{4} & \frac{1}{4} - \frac{1}{4}B & \frac{1}{2}A + \frac{1}{4}B + \frac{1}{4} & \frac{1}{4} - \frac{1}{4}B \\ \frac{1}{4} - \frac{1}{4}B & -\frac{1}{2}A + \frac{1}{4}B + \frac{1}{4} & \frac{1}{4} - \frac{1}{4}B & \frac{1}{2}A + \frac{1}{4}B + \frac{1}{4} \\ \end{pmatrix} \]

with $A=e^{-\frac{rate\_ * (2\kappa+2)t}{\kappa+2}}$ and $B = e^{-\frac{rate\_ * 4t}{\kappa+2}}$.

First and second order derivatives are also computed analytically using the formulas:

\[ \frac{\partial P_{i,j}(t)}{\partial t} = rate\_ * \begin{pmatrix} -\frac{2\kappa+2}{2(\kappa+2)}A - \frac{1}{\kappa+2}B & \frac{1}{\kappa+2}B & \frac{2\kappa+2}{2(\kappa+2)}A - \frac{1}{\kappa+2}B & \frac{1}{\kappa+2}B \\ \frac{1}{\kappa+2}B & -\frac{2\kappa+2}{2(\kappa+2)}A - \frac{1}{\kappa+2}B & \frac{1}{\kappa+2}B & \frac{2\kappa+2}{2(\kappa+2)}A - \frac{1}{\kappa+2}B \\ \frac{2\kappa+2}{2(\kappa+2)}A - \frac{1}{\kappa+2}B & \frac{1}{\kappa+2}B & -\frac{2\kappa+2}{2(\kappa+2)}A - \frac{1}{\kappa+2}B & \frac{1}{\kappa+2}B \\ \frac{1}{\kappa+2}B & \frac{2\kappa+2}{2(\kappa+2)}A - \frac{1}{\kappa+2}B & \frac{1}{\kappa+2}B & -\frac{2\kappa+2}{2(\kappa+2)}A - \frac{1}{\kappa+2}B \\ \end{pmatrix} \]

\begin{multline*} \frac{\partial^2 P_{i,j}(t)}{\partial t^2} = rate\_^2 * \\ \begin{pmatrix} \frac{{(2\kappa+2)}^2}{2{(\kappa+2)}^2}A - \frac{4}{{(\kappa+2)}^2}B & -\frac{4}{{(\kappa+2)}^2}B & -\frac{{(2\kappa+2)}^2}{2{(\kappa+2)}^2}A + \frac{4}{{(\kappa+2)}^2}B & -\frac{4}{{(\kappa+2)}^2}B \\ -\frac{4}{{(\kappa+2)}^2}B & \frac{{(2\kappa+2)}^2}{2{(\kappa+2)}^2}A + \frac{4}{{(\kappa+2)}^2}B & -\frac{4}{{(\kappa+2)}^2}B & -\frac{{(2\kappa+2)}^2}{2{(\kappa+2)}^2}A + \frac{4}{{(\kappa+2)}^2}B \\ -\frac{{(2\kappa+2)}^2}{2{(\kappa+2)}^2}A + \frac{4}{{(\kappa+2)}^2}B & -\frac{4}{{(\kappa+2)}^2}B & \frac{{(2\kappa+2)}^2}{2{(\kappa+2)}^2}A + \frac{4}{{(\kappa+2)}^2}B & -\frac{4}{{(\kappa+2)}^2}B \\ -\frac{4}{{(\kappa+2)}^2}B & -\frac{2{(\kappa+2)}^2}{2{(\kappa+2)}^2}A + \frac{4}{{(\kappa+2)}^2}B & -\frac{4}{{(\kappa+2)}^2}B & \frac{2{(\kappa+2)}^2}{{(2\kappa+2)}^2}A + \frac{4}{{(\kappa+2)}^2}B \\ \end{pmatrix} \end{multline*}

The parameter is named "kappa" and its value may be retrieve with the command

getParameterValue("kappa")

Reference:

  • Kimura M (1980), Journal_ Of Molecular Evolution_ 16(2) 111-20.

Definition at line 150 of file K80.h.

Constructor & Destructor Documentation

◆ K80()

K80::K80 ( const NucleicAlphabet *  alpha,
double  kappa = 1. 
)

Definition at line 53 of file K80.cpp.

References updateMatrices().

Referenced by clone().

◆ ~K80()

virtual bpp::K80::~K80 ( )
inlinevirtual

Definition at line 162 of file K80.h.

Member Function Documentation

◆ addRateParameter() [1/2]

void AbstractSubstitutionModel::addRateParameter ( )
virtualinherited

Implements bpp::SubstitutionModel.

Definition at line 433 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::rate_.

◆ addRateParameter() [2/2]

virtual void bpp::SubstitutionModel::addRateParameter ( )
pure virtualinherited

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::G2001, and bpp::TS98.

Referenced by bpp::AbstractBiblioSubstitutionModel::addRateParameter().

◆ clone()

K80* bpp::K80::clone ( ) const
inlinevirtual

Implements bpp::AbstractReversibleSubstitutionModel.

Definition at line 169 of file K80.h.

References K80().

◆ d2Pij_dt2()

double K80::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const
virtual
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()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 242 of file K80.cpp.

References exp1_, exp2_, k_, l_, r_, and bpp::AbstractSubstitutionModel::rate_.

◆ dPij_dt()

double K80::dPij_dt ( size_t  i,
size_t  j,
double  t 
) const
virtual
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()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 193 of file K80.cpp.

References exp1_, exp2_, k_, l_, r_, and bpp::AbstractSubstitutionModel::rate_.

◆ enableEigenDecomposition() [1/4]

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() [2/4]

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().

◆ enableEigenDecomposition() [3/4]

virtual void bpp::SubstitutionModel::enableEigenDecomposition ( bool  yn)
pure virtualinherited

Set if eigenValues and Vectors must be computed.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition(), and bpp::YpR::YpR().

◆ enableEigenDecomposition() [4/4]

virtual bool bpp::SubstitutionModel::enableEigenDecomposition ( )
pure virtualinherited

Tell if eigenValues and Vectors must be computed.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

◆ fireParameterChanged()

virtual void bpp::AbstractSubstitutionModel::fireParameterChanged ( const ParameterList &  parameters)
inlinevirtualinherited

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented in bpp::JCprot, bpp::YpR, bpp::RE08, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::DSO78, bpp::JTT92, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::LG08, bpp::CodonDistanceSubstitutionModel, bpp::gBGC, bpp::CodonRateFrequenciesSubstitutionModel, and bpp::CodonRateSubstitutionModel.

Definition at line 298 of file AbstractSubstitutionModel.h.

References bpp::SubstitutionModel::getName(), and bpp::AbstractSubstitutionModel::updateMatrices().

Referenced by bpp::CodonRateSubstitutionModel::fireParameterChanged(), bpp::CodonRateFrequenciesSubstitutionModel::fireParameterChanged(), bpp::gBGC::fireParameterChanged(), bpp::CodonDistanceSubstitutionModel::fireParameterChanged(), bpp::LG08::fireParameterChanged(), bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::fireParameterChanged(), bpp::WAG01::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::CodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), and bpp::JCprot::fireParameterChanged().

◆ freq() [1/2]

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

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::TwoTreeLikelihood::computeTreeD2Likelihood(), bpp::TwoTreeLikelihood::computeTreeDLikelihood(), and bpp::AbstractBiblioSubstitutionModel::freq().

◆ freq() [2/2]

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() [1/2]

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=().

◆ getAlphabet() [2/2]

virtual const Alphabet* bpp::SubstitutionModel::getAlphabet ( ) const
pure virtualinherited
Returns
Get the alphabet associated to this model.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AAExteriorSubstitutionRegister::AAExteriorSubstitutionRegister(), bpp::AAInteriorSubstitutionRegister::AAInteriorSubstitutionRegister(), bpp::SubstitutionModelSet::addModel(), bpp::DecompositionReward::alphabetIndexHasChanged(), bpp::ComprehensiveSubstitutionRegister::ComprehensiveSubstitutionRegister(), bpp::DecompositionReward::DecompositionReward(), bpp::DecompositionSubstitutionCount::DecompositionSubstitutionCount(), bpp::AbstractMutationProcess::detailedEvolve(), bpp::LaplaceSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::AbstractSubstitutionRegister::getAlphabet(), bpp::AbstractBiblioSubstitutionModel::getAlphabet(), bpp::MarkovModulatedSubstitutionModel::getAlphabet(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::DnDsSubstitutionRegister::getType(), bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister(), bpp::CategorySubstitutionRegister::setCategories(), bpp::LaplaceSubstitutionCount::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::DecompositionSubstitutionCount::setSubstitutionModel(), bpp::DecompositionReward::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::substitutionRegisterHasChanged(), bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), bpp::YpR::updateMatrices(), and bpp::BppOSubstitutionModelFormat::writeMixed_().

◆ getAlphabetStateAsChar() [1/2]

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_.

◆ getAlphabetStateAsChar() [2/2]

virtual std::string bpp::SubstitutionModel::getAlphabetStateAsChar ( size_t  index) const
pure virtualinherited
Parameters
indexThe model state.
Returns
The corresponding alphabet state as character code.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetStateAsChar(), bpp::TwoTreeLikelihood::getAlphabetStateAsChar(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsChar(), and bpp::SubstitutionModelSet::getAlphabetStateAsChar().

◆ getAlphabetStateAsInt() [1/2]

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_.

◆ getAlphabetStateAsInt() [2/2]

virtual int bpp::SubstitutionModel::getAlphabetStateAsInt ( size_t  index) const
pure virtualinherited
Parameters
indexThe model state.
Returns
The corresponding alphabet state as character code.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetStateAsInt(), bpp::TwoTreeLikelihood::getAlphabetStateAsInt(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsInt(), bpp::SubstitutionModelSet::getAlphabetStateAsInt(), bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(), bpp::CategorySubstitutionRegister::getCategory(), bpp::SiteSimulationResult::getSite(), bpp::CategorySubstitutionRegister::getType(), bpp::TsTvSubstitutionRegister::getType(), bpp::DnDsSubstitutionRegister::getType(), bpp::GCSynonymousSubstitutionRegister::getType(), and bpp::NonHomogeneousSequenceSimulator::multipleEvolve().

◆ getAlphabetStates() [1/2]

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

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionReward::computeBMatrice_(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::AbstractBiblioSubstitutionModel::getAlphabetStates(), bpp::TwoTreeLikelihood::getAlphabetStates(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStates(), bpp::SubstitutionModelSet::getAlphabetStates(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::CategorySubstitutionRegister::setCategories(), bpp::NaiveSubstitutionCount::setSubstitutionModel(), and bpp::LabelSubstitutionCount::setSubstitutionModel().

◆ getAlphabetStates() [2/2]

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() [1/2]

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_.

◆ getColumnRightEigenVectors() [2/2]

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

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::DecompositionReward::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getColumnRightEigenVectors(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

◆ getd2Pij_dt2()

const Matrix< double > & K80::getd2Pij_dt2 ( double  t) const
virtual
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()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 358 of file K80.cpp.

References exp1_, exp2_, k_, l_, p_, r_, and bpp::AbstractSubstitutionModel::rate_.

◆ getdPij_dt()

const Matrix< double > & K80::getdPij_dt ( double  t) const
virtual
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()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 326 of file K80.cpp.

References exp1_, exp2_, k_, l_, p_, r_, and bpp::AbstractSubstitutionModel::rate_.

◆ getEigenValues() [1/2]

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_.

◆ getEigenValues() [2/2]

virtual const Vdouble& bpp::SubstitutionModel::getEigenValues ( ) const
pure virtualinherited
Returns
A vector with all real parts of the eigen values of the generator of this model;

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::DecompositionReward::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getEigenValues(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

◆ getExchangeabilityMatrix() [1/2]

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_.

◆ getExchangeabilityMatrix() [2/2]

virtual const Matrix<double>& bpp::SubstitutionModel::getExchangeabilityMatrix ( ) const
pure virtualinherited
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 $S . \pi$.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::Coala::Coala(), bpp::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

◆ getFrequencies() [1/2]

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_.

◆ getFrequencies() [2/2]

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

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::TwoTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioSubstitutionModel::getFrequencies(), bpp::TwoTreeLikelihood::getRootFrequencies(), bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies(), bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

◆ 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() [1/2]

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_.

◆ getGenerator() [2/2]

virtual const Matrix<double>& bpp::SubstitutionModel::getGenerator ( ) const
pure virtualinherited
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()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::AbstractBiblioSubstitutionModel::getGenerator(), bpp::SimpleMutationProcess::SimpleMutationProcess(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

◆ getIEigenValues() [1/2]

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_.

◆ getIEigenValues() [2/2]

virtual const Vdouble& bpp::SubstitutionModel::getIEigenValues ( ) const
pure virtualinherited
Returns
A vector with all imaginary parts of the eigen values of the generator of this model;

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getIEigenValues().

◆ getInitValue() [1/2]

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.

◆ getInitValue() [2/2]

virtual double bpp::SubstitutionModel::getInitValue ( size_t  i,
int  state 
) const
throw (IndexOutOfBoundsException,
BadIntException
)
pure 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();

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getInitValue().

◆ getModelStates() [1/4]

virtual std::vector<size_t> bpp::SubstitutionModel::getModelStates ( int  code) const
pure virtualinherited

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.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getModelStates(), bpp::SubstitutionModelSet::getModelStates(), and bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates().

◆ getModelStates() [2/4]

virtual std::vector<size_t> bpp::SubstitutionModel::getModelStates ( const std::string &  code) const
pure virtualinherited

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.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

◆ getModelStates() [3/4]

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() [4/4]

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()

std::string bpp::K80::getName ( ) const
inlinevirtual

Get the name of the model.

Returns
The name of this model.

Implements bpp::SubstitutionModel.

Definition at line 179 of file K80.h.

◆ getNumberOfStates()

virtual size_t bpp::NucleotideSubstitutionModel::getNumberOfStates ( ) const
inlinevirtualinherited

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.

Reimplemented in bpp::gBGC.

Definition at line 68 of file NucleotideSubstitutionModel.h.

◆ getPij_t()

const Matrix< double > & K80::getPij_t ( double  t) const
virtual
Returns
All probabilities of change from state i to state j during time t.
See also
Pij_t()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 293 of file K80.cpp.

References exp1_, exp2_, k_, l_, p_, r_, and bpp::AbstractSubstitutionModel::rate_.

◆ getRate() [1/2]

double AbstractSubstitutionModel::getRate ( ) const
virtualinherited

Get the rate.

Implements bpp::SubstitutionModel.

Definition at line 415 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::rate_.

◆ getRate() [2/2]

virtual double bpp::SubstitutionModel::getRate ( ) const
pure virtualinherited

Get the rate.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::G2001, and bpp::TS98.

Referenced by bpp::AbstractBiblioSubstitutionModel::getRate(), and bpp::MarkovModulatedSubstitutionModel::getRate().

◆ getRowLeftEigenVectors() [1/2]

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_.

◆ getRowLeftEigenVectors() [2/2]

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

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::DecompositionReward::computeEigen_(), and bpp::AbstractBiblioSubstitutionModel::getRowLeftEigenVectors().

◆ getScale() [1/2]

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().

◆ getScale() [2/2]

virtual double bpp::SubstitutionModel::getScale ( ) const
pure 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.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getScale().

◆ getStateMap() [1/2]

virtual const StateMap& bpp::SubstitutionModel::getStateMap ( ) const
pure virtualinherited
Returns
The mapping of model states with alphabet states.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getStateMap(), bpp::SubstitutionModelSet::getStateMap(), and bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator().

◆ getStateMap() [2/2]

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() [1/2]

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_.

◆ isDiagonalizable() [2/2]

virtual bool bpp::SubstitutionModel::isDiagonalizable ( ) const
pure virtualinherited
Returns
True if the model is diagonalizable in R.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::isDiagonalizable().

◆ isNonSingular() [1/2]

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_.

◆ isNonSingular() [2/2]

virtual bool bpp::SubstitutionModel::isNonSingular ( ) const
pure virtualinherited
Returns
True is the model is non-singular.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::isNonSingular().

◆ Pij_t()

double K80::Pij_t ( size_t  i,
size_t  j,
double  t 
) const
virtual
Returns
The probability of change from state i to state j during time t.
See also
getPij_t(), getStates()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 144 of file K80.cpp.

References exp1_, exp2_, k_, l_, r_, and bpp::AbstractSubstitutionModel::rate_.

◆ Qij() [1/2]

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

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::UniformizationSubstitutionCount::fillBMatrices_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::AbstractMutationProcess::getTimeBeforeNextMutationEvent(), bpp::AbstractBiblioSubstitutionModel::Qij(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), and bpp::YpR::updateMatrices().

◆ Qij() [2/2]

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() [1/2]

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().

◆ setFreq() [2/2]

virtual void bpp::SubstitutionModel::setFreq ( std::map< int, double > &  frequencies)
inlinevirtualinherited

Set equilibrium frequencies.

Parameters
frequenciesThe map of the frequencies to use.

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

Definition at line 473 of file SubstitutionModel.h.

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

◆ setFreqFromData()

void bpp::K80::setFreqFromData ( const SequenceContainer &  data,
double  pseudoCount = 0 
)
inlinevirtual

This method is disabled in this model since frequencies are not free parameters.

Consider using the HKY85 model for instance if you want to set frequencies as parameters.

Parameters
dataUnused parameter.
pseudoCountUnused parameter.

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 189 of file K80.h.

◆ setRate() [1/2]

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().

◆ setRate() [2/2]

virtual void bpp::SubstitutionModel::setRate ( double  rate)
pure virtualinherited

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

Parameters
ratemust be positive.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::G2001, and bpp::TS98.

Referenced by bpp::AbstractBiblioSubstitutionModel::setRate(), and bpp::MarkovModulatedSubstitutionModel::setRate().

◆ setScale() [1/2]

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_.

◆ setScale() [2/2]

virtual void bpp::SubstitutionModel::setScale ( double  scale)
pure virtualinherited

Multiplies the current generator by the given scale.

Parameters
scalethe scale by which the generator is multiplied.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::setScale(), and bpp::MarkovModulatedSubstitutionModel::setScale().

◆ Sij() [1/2]

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_.

◆ Sij() [2/2]

virtual double bpp::SubstitutionModel::Sij ( size_t  i,
size_t  j 
) const
pure virtualinherited
Returns
The exchangeability between state i and state j.

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

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::Sij().

◆ updateMatrices()

void K80::updateMatrices ( )
protectedvirtual

Compute and diagonalize the $Q$ matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices.

The exchangeability_ matrix and freq_ vector must be initialized. This function computes the generator_ matrix with the formula

\[ Q = S \times \pi \]

where $Q$ is the generator matrix, $S$ is the exchangeability matrix and $Pi$ the diagonal matrix with frequencies.

The generator is then scaled so that

\[ \sum_i Q_{i,i} \times \pi_i = -1 \]

( $\pi_i$ are the equilibrium frequencies).

Eigen values and vectors are computed from the scaled generator and assigned to the eigenValues_, rightEigenVectors_ and leftEigenVectors_ variables.

Reimplemented from bpp::AbstractReversibleSubstitutionModel.

Definition at line 64 of file K80.cpp.

References bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractSubstitutionModel::freq_, bpp::AbstractSubstitutionModel::generator_, k_, kappa_, bpp::AbstractSubstitutionModel::leftEigenVectors_, r_, and bpp::AbstractSubstitutionModel::rightEigenVectors_.

Referenced by K80().

Member Data Documentation

◆ 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(), bpp::YpR::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), 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(), bpp::YpR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), updateMatrices(), bpp::T92::updateMatrices(), bpp::RE08::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

◆ exp1_

double bpp::K80::exp1_
mutableprivate

Definition at line 156 of file K80.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), and Pij_t().

◆ exp2_

double bpp::K80::exp2_
mutableprivate

Definition at line 156 of file K80.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), and Pij_t().

◆ 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(), bpp::YpR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), 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(), bpp::YpR::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), 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(), bpp::YpR::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(), bpp::YpR::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(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

◆ k_

double bpp::K80::k_
mutableprivate

Definition at line 156 of file K80.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), Pij_t(), and updateMatrices().

◆ kappa_

double bpp::K80::kappa_
private

Definition at line 155 of file K80.h.

Referenced by updateMatrices().

◆ l_

double bpp::K80::l_
mutableprivate

Definition at line 156 of file K80.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), and Pij_t().

◆ 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(), bpp::YpR::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

◆ p_

RowMatrix<double> bpp::K80::p_
mutableprivate

Definition at line 157 of file K80.h.

Referenced by getd2Pij_dt2(), getdPij_dt(), and getPij_t().

◆ 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=().

◆ r_

double bpp::K80::r_
private

Definition at line 155 of file K80.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), Pij_t(), and updateMatrices().

◆ 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(), 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(), 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(), 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(), 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(), 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(), 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(), bpp::YpR::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), 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(), bpp::YpR::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 bpp::YpR::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(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

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