bpp-phyl  2.1.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | Friends
bpp::T92 Class Reference

The Tamura (1992) substitution model for nucleotides. More...

#include <Bpp/Phyl/Model/Nucleotide/T92.h>

+ Inheritance diagram for bpp::T92:
+ Collaboration diagram for bpp::T92:

List of all members.

Public Member Functions

 T92 (const NucleicAlphabet *alpha, double kappa=1., double theta=0.5)
virtual ~T92 ()
T92 * clone () const
double Pij_t (int i, int j, double d) const
double dPij_dt (int i, int j, double d) const
double d2Pij_dt2 (int i, int 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.
void setFreq (std::map< int, double > &freqs)
 This method is over-defined to actualize the 'theta' parameter too.
virtual size_t getNumberOfStates () const
 Get the number of states.
virtual const std::vector< int > & getAlphabetChars () const =0
virtual int getAlphabetChar (size_t i) const =0
 Get the char in the alphabet corresponding to a given state in the model.
virtual std::vector< size_t > getModelStates (int i) const =0
 Get the state in the model corresponding to a particular char in the alphabet.
virtual double freq (size_t i) const =0
virtual double Qij (size_t i, size_t j) const =0
virtual double Pij_t (size_t i, size_t j, double t) const =0
virtual double dPij_dt (size_t i, size_t j, double t) const =0
virtual double d2Pij_dt2 (size_t i, size_t j, double t) 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.
virtual bool enableEigenDecomposition ()=0
 Tell if eigenValues and Vectors must be computed.
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.
virtual void setScale (double scale)=0
 Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.
virtual double getRate () const =0
 Get the rate.
virtual void setRate (double rate)=0
 Set the rate of the model (must be positive).
virtual void addRateParameter ()=0
virtual void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)=0
 Set equilibrium frequencies equal to the frequencies estimated from the data.
virtual const FrequenciesSet * getFrequenciesSet () const
 If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.
virtual size_t getNumberOfIndependentParameters () const =0
virtual void aliasParameters (const std::string &p1, const std::string &p2)=0
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
virtual const ParameterList & getIndependentParameters () const =0
virtual std::vector< std::string > getAlias (const std::string &name) const =0
virtual bool hasParameter (const std::string &name) const =0
virtual const ParameterList & getParameters () const =0
virtual const Parameter & getParameter (const std::string &name) const =0
virtual double getParameterValue (const std::string &name) const =0
virtual void setAllParametersValues (const ParameterList &parameters)=0
virtual void setParameterValue (const std::string &name, double value)=0
virtual void setParametersValues (const ParameterList &parameters)=0
virtual bool matchParametersValues (const ParameterList &parameters)=0
virtual size_t getNumberOfParameters () const =0
virtual void setNamespace (const std::string &prefix)=0
virtual std::string getNamespace () const =0
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const =0
const Alphabet * getAlphabet () const
const std::vector< int > & getAlphabetChars () const
int getAlphabetChar (size_t i) const
 Get the char in the alphabet corresponding to a given state in the model.
std::vector< size_t > getModelStates (int i) const
 Get the state in the model corresponding to a particular char in the alphabet.
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
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.
void enableEigenDecomposition (bool yn)
 Set if eigenValues and Vectors must be computed.
bool enableEigenDecomposition ()
 Tell if eigenValues and Vectors must be computed.
virtual void fireParameterChanged (const ParameterList &parameters)
 Tells the model that a parameter value has changed.
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.
void setScale (double scale)
 Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.
virtual double getRate () const
 Get the rate.
virtual void setRate (double rate)
 Set the rate of the model (must be positive).
size_t getNumberOfIndependentParameters () const
void aliasParameters (const std::string &p1, const std::string &p2)
void unaliasParameters (const std::string &p1, const std::string &p2)
const ParameterList & getIndependentParameters () const
std::vector< std::string > getAlias (const std::string &name) const
bool hasParameter (const std::string &name) const
const ParameterList & getParameters () const
const Parameter & getParameter (const std::string &name) const
double getParameterValue (const std::string &name) const
void setAllParametersValues (const ParameterList &parameters)
void setParameterValue (const std::string &name, double value)
void setParametersValues (const ParameterList &parameters)
bool matchParametersValues (const ParameterList &parameters)
size_t getNumberOfParameters () const
void setNamespace (const std::string &prefix)
std::string getNamespace () const
std::string getParameterNameWithoutNamespace (const std::string &name) const
std::string getFrom (const std::string &name) const

Protected Member Functions

void updateMatrices ()
 Compute and diagonalize the $Q$ matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices.
void addParameter_ (Parameter *parameter)
void addParameters_ (const ParameterList &parameters)
void deleteParameter_ (size_t index)
void resetParameters_ ()
Parameter & getParameter_ (const std::string &name)
Parameter & getParameter_ (size_t index)
const Parameter & getParameter_ (size_t index) const
Parameter & getParameterWithNamespace_ (const std::string &name)
const Parameter & getParameterWithNamespace_ (const std::string &name) const
ParameterList & getParameters_ ()

Protected Attributes

const Alphabet * alphabet_
 The alphabet relevant to this model.
size_t size_
 The size of the generator, i.e. the number of states.
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.
std::vector< int > chars_
 The list of supported chars.
RowMatrix< double > generator_
 The generator matrix $Q$ of the model.
Vdouble freq_
 The vector $\pi_e$ of equilibrium frequencies.
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.
RowMatrix< double > pijt_
 These ones are for bookkeeping:
RowMatrix< double > dpijt_
RowMatrix< double > d2pijt_
bool eigenDecompose_
 Tell if the eigen decomposition should be performed.
Vdouble eigenValues_
 The vector of eigen values.
Vdouble iEigenValues_
 The vector of the imaginary part of the eigen values.
bool isDiagonalizable_
 boolean value for diagonalizability in R of the generator_
RowMatrix< double > rightEigenVectors_
 The $U^-1$ matrix made of right eigen vectors (by column).
bool isNonSingular_
 boolean value for non-singularity of rightEigenVectors_
RowMatrix< double > leftEigenVectors_
 The $U$ matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular.
std::vector< RowMatrix< double > > vPowGen_
 vector of the powers of generator_ for Taylor development (if rightEigenVectors_ is singular).
RowMatrix< double > tmpMat_
 For computational issues.

Private Attributes

double kappa_
double theta_
double k_
double r_
double piA_
double piC_
double piG_
double piT_
double exp1_
double exp2_
double l_
RowMatrix< double > p_

Friends

class AbstractBiblioSubstitutionModel

Detailed Description

The Tamura (1992) substitution model for nucleotides.

This model is similar to the K80 model, but allows distinct equilibrium frequencies between GC and AT. This models hence includes two parameters, the transition / transversion relative rate $\kappa$ and the frequency of GC, $\theta$.

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

\[ \pi = \left(\frac{1-\theta}{2}, \frac{\theta}{2}, \frac{\theta}{2}, \frac{1 - \theta}{2}\right) \]

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

\[ S = \frac{1}{P}\begin{pmatrix} \frac{2\theta\kappa + 2}{\theta - 1} & 2 & 2\kappa & 2 \\ 2 & \frac{2(\theta-1)\kappa - 2}{\theta} & 2 & 2\kappa \\ 2\kappa & 2 & \frac{2(\theta-1)\kappa - 2}{\theta} & 2 \\ 2 & 2\kappa & 2 & \frac{2\theta\kappa + 2}{\theta - 1} \\ \end{pmatrix} \]

with $P=1+2\theta\kappa-2\theta^2\kappa$.

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

\[ Q = S . \pi = \frac{1}{P}\begin{pmatrix} -(\theta\kappa+1) & \theta & \theta\kappa & 1-\theta \\ 1-\theta & -((1-\theta)\kappa+1) & \theta & (1-\theta)\kappa \\ (1-\theta)\kappa & \theta & -((1-\theta)\kappa+1) & 1-\theta \\ 1-\theta & \theta\kappa & \theta & -(\theta\kappa+1) \\ \end{pmatrix} \]

The eigen values are $\left(0, -\frac{\kappa+1}{P}, -\frac{\kappa+1}{P}, -\frac{2}{P}\right)$, the left eigen vectors are, by row:

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

and the right eigen vectors are, by column:

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

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

The probabilities of changes are computed analytically using the formulas:

\begin{multline*} P_{i,j}(t) = \\ \begin{pmatrix} \theta A + \frac{1-\theta}{2}B + \frac{1-\theta}{2} & \frac{\theta}{2} - \frac{\theta}{2}B & -\theta A + \frac{\theta}{2}B + \frac{\theta}{2} & \frac{1-\theta}{2} - \frac{1-\theta}{2}B \\ \frac{1-\theta}{2} - \frac{1-\theta}{2}B & (1-\theta)A + \frac{\theta}{2}B + \frac{\theta}{2} & \frac{\theta}{2} - \frac{\theta}{2}B & -(1-\theta)A + \frac{1-\theta}{2}B + \frac{1-\theta}{2} \\ -(1-\theta)A + \frac{1-\theta}{2}B + \frac{1-\theta}{2} & \frac{\theta}{2} - \frac{\theta}{2}B & (1-\theta)A + \frac{\theta}{2}B + \frac{\theta}{2} & \frac{1-\theta}{2} - \frac{1-\theta}{2}B \\ \frac{1-\theta}{2} - \frac{1-\theta}{2}B & -\theta A + \frac{\theta}{2}B + \frac{\theta}{2} & \frac{\theta}{2} - \frac{\theta}{2}B & \theta A + \frac{1-\theta}{2}B + \frac{1-\theta}{2} \\ \end{pmatrix} \end{multline*}

with $A=e^{-\frac{rate\_ * (\kappa+1)t}{P}}$ and $B = e^{-\frac{rate\_ * 2t}{P}}$.

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

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

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

The parameters are named "kappa" and "theta" and their values may be retrieve with the commands 

 getParameterValue("kappa")
 getParameterValue("theta")

Reference:

  • Tamura K (1992), Molecular_ Biology And Evolution_ 9(5) 814-25.

Definition at line 159 of file T92.h.

Constructor & Destructor Documentation

T92::T92 ( const NucleicAlphabet *  alpha,
double  kappa = 1.,
double  theta = 0.5 
)

Definition at line 57 of file T92.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::FrequenciesSet::FREQUENCE_CONSTRAINT_SMALL, p_, bpp::Parameter::R_PLUS_STAR, bpp::RowMatrix< Scalar >::resize(), bpp::AbstractSubstitutionModel::size_, and updateMatrices().

Referenced by clone().

virtual bpp::T92::~T92 ( ) [inline, virtual]

Definition at line 171 of file T92.h.

Member Function Documentation

void AbstractSubstitutionModel::addRateParameter ( ) [virtual, inherited]

Implements bpp::SubstitutionModel.

Definition at line 434 of file AbstractSubstitutionModel.cpp.

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

virtual void bpp::SubstitutionModel::addRateParameter ( ) [pure virtual, inherited]

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

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

T92* bpp::T92::clone ( ) const [inline, virtual]

Implements bpp::AbstractReversibleSubstitutionModel.

Definition at line 178 of file T92.h.

References T92().

double T92::d2Pij_dt2 ( int  i,
int  j,
double  d 
) const

Definition at line 299 of file T92.cpp.

References exp1_, exp2_, k_, l_, piA_, piC_, piG_, piT_, r_, bpp::AbstractSubstitutionModel::rate_, and theta_.

virtual double bpp::SubstitutionModel::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const [pure virtual, inherited]
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()

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

Referenced by bpp::AbstractBiblioSubstitutionModel::d2Pij_dt2(), and bpp::RE08::d2Pij_dt2().

virtual double bpp::AbstractSubstitutionModel::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const [inline, virtual, inherited]
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::RE08, bpp::JCnuc, and bpp::BinarySubstitutionModel.

Definition at line 280 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getd2Pij_dt2().

double T92::dPij_dt ( int  i,
int  j,
double  d 
) const

Definition at line 245 of file T92.cpp.

References exp1_, exp2_, k_, l_, piA_, piC_, piG_, piT_, r_, bpp::AbstractSubstitutionModel::rate_, and theta_.

virtual double bpp::SubstitutionModel::dPij_dt ( size_t  i,
size_t  j,
double  t 
) const [pure virtual, inherited]
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()

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

Referenced by bpp::RE08::d2Pij_dt2(), bpp::AbstractBiblioSubstitutionModel::dPij_dt(), and bpp::RE08::dPij_dt().

virtual double bpp::AbstractSubstitutionModel::dPij_dt ( size_t  i,
size_t  j,
double  t 
) const [inline, virtual, inherited]
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::RE08, bpp::JCnuc, and bpp::BinarySubstitutionModel.

Definition at line 279 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getdPij_dt().

void bpp::AbstractSubstitutionModel::enableEigenDecomposition ( bool  yn) [inline, virtual, inherited]

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 288 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

bool bpp::AbstractSubstitutionModel::enableEigenDecomposition ( ) [inline, virtual, inherited]

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 290 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

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

virtual void bpp::SubstitutionModel::enableEigenDecomposition ( bool  yn) [pure virtual, inherited]

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(), bpp::gBGC::gBGC(), and bpp::YpR::YpR().

virtual bool bpp::SubstitutionModel::enableEigenDecomposition ( ) [pure virtual, inherited]

Tell if eigenValues and Vectors must be computed.

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

virtual void bpp::AbstractSubstitutionModel::fireParameterChanged ( const ParameterList &  parameters) [inline, virtual, inherited]

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

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

Definition at line 297 of file AbstractSubstitutionModel.h.

References bpp::SubstitutionModel::getName(), bpp::AbstractParameterAliasable::getNamespace(), bpp::ParameterList::size(), and bpp::AbstractSubstitutionModel::updateMatrices().

virtual double bpp::SubstitutionModel::freq ( size_t  i) const [pure virtual, inherited]
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(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::AbstractBiblioSubstitutionModel::freq(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::RE08::getPij_t(), bpp::RE08::Pij_t(), and bpp::RE08::updateMatrices().

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

Implements bpp::SubstitutionModel.

Definition at line 274 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

const Alphabet* bpp::AbstractSubstitutionModel::getAlphabet ( ) const [inline, virtual, inherited]
Returns:
Get the alphabet associated to this model.

Implements bpp::SubstitutionModel.

Definition at line 242 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=().

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

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

Referenced by bpp::SubstitutionModelSet::addModel(), bpp::DecompositionSubstitutionCount::DecompositionSubstitutionCount(), bpp::AbstractMutationProcess::detailedEvolve(), bpp::LaplaceSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::AbstractBiblioSubstitutionModel::getAlphabet(), bpp::MarkovModulatedSubstitutionModel::getAlphabet(), bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator(), bpp::LaplaceSubstitutionCount::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::DecompositionSubstitutionCount::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::substitutionRegisterHasChanged(), bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), bpp::YpR::updateMatrices(), and bpp::BppOSubstitutionModelFormat::writeMixed_().

virtual int bpp::SubstitutionModel::getAlphabetChar ( size_t  i) const [pure virtual, inherited]

Get the char in the alphabet corresponding to a given state in the model.

In most cases, this method will return i.

Parameters:
iThe index of the state.
Returns:
The corresponding state in the alphabet.
See also:
MarkovModulatedSubstitutionModel
getStates()

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

Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetChar(), bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(), and bpp::NonHomogeneousSequenceSimulator::multipleEvolve().

int bpp::AbstractSubstitutionModel::getAlphabetChar ( size_t  i) const [inline, virtual, inherited]

Get the char in the alphabet corresponding to a given state in the model.

In most cases, this method will return i.

Parameters:
iThe index of the state.
Returns:
The corresponding state in the alphabet.
See also:
MarkovModulatedSubstitutionModel
getStates()

Implements bpp::SubstitutionModel.

Definition at line 246 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::chars_.

virtual const std::vector<int>& bpp::SubstitutionModel::getAlphabetChars ( ) const [pure virtual, inherited]
Returns:
The supported states of the model, as a vector of int codes.
See also:
Alphabet

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

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

const std::vector<int>& bpp::AbstractSubstitutionModel::getAlphabetChars ( ) const [inline, virtual, inherited]
Returns:
The supported states of the model, as a vector of int codes.
See also:
Alphabet

Implements bpp::SubstitutionModel.

Definition at line 244 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::chars_.

const Matrix<double>& bpp::AbstractSubstitutionModel::getColumnRightEigenVectors ( ) const [inline, virtual, inherited]
Returns:
A matrix with right eigen vectors. Each column in the matrix stands for an eigen vector.

Implements bpp::SubstitutionModel.

Definition at line 272 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::rightEigenVectors_.

virtual const Matrix<double>& bpp::SubstitutionModel::getColumnRightEigenVectors ( ) const [pure virtual, inherited]
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::AbstractBiblioSubstitutionModel::getColumnRightEigenVectors(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

const Matrix< double > & T92::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 421 of file T92.cpp.

References exp1_, exp2_, k_, l_, p_, piA_, piC_, piG_, piT_, r_, bpp::AbstractSubstitutionModel::rate_, and theta_.

const Matrix< double > & T92::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 388 of file T92.cpp.

References exp1_, exp2_, k_, l_, p_, piA_, piC_, piG_, piT_, r_, bpp::AbstractSubstitutionModel::rate_, and theta_.

const Vdouble& bpp::AbstractSubstitutionModel::getEigenValues ( ) const [inline, virtual, inherited]
Returns:
A vector with all real parts of the eigen values of the generator of this model;

Implements bpp::SubstitutionModel.

Definition at line 262 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenValues_.

virtual const Vdouble& bpp::SubstitutionModel::getEigenValues ( ) const [pure virtual, inherited]
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::AbstractBiblioSubstitutionModel::getEigenValues(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

const Matrix<double>& bpp::AbstractSubstitutionModel::getExchangeabilityMatrix ( ) const [inline, virtual, inherited]
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 254 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

virtual const Matrix<double>& bpp::SubstitutionModel::getExchangeabilityMatrix ( ) const [pure virtual, inherited]
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::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix(), bpp::RE08::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const Vdouble& bpp::AbstractSubstitutionModel::getFrequencies ( ) const [inline, virtual, inherited]
Returns:
A vector of all equilibrium frequencies.
See also:
freq()

Implements bpp::SubstitutionModel.

Definition at line 250 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

Referenced by bpp::LG08::setFreqFromData(), bpp::DSO78::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), and bpp::JCprot::setFreqFromData().

virtual const Vdouble& bpp::SubstitutionModel::getFrequencies ( ) const [pure virtual, inherited]
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().

virtual const FrequenciesSet* bpp::SubstitutionModel::getFrequenciesSet ( ) const [inline, virtual, inherited]

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::AbstractCodonPhaseFrequenciesSubstitutionModel, and bpp::AbstractCodonFrequenciesSubstitutionModel.

Definition at line 463 of file SubstitutionModel.h.

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

const Matrix<double>& bpp::AbstractSubstitutionModel::getGenerator ( ) const [inline, virtual, inherited]
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 252 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

virtual const Matrix<double>& bpp::SubstitutionModel::getGenerator ( ) const [pure virtual, inherited]
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(), bpp::RE08::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

const Vdouble& bpp::AbstractSubstitutionModel::getIEigenValues ( ) const [inline, virtual, inherited]
Returns:
A vector with all imaginary parts of the eigen values of the generator of this model;

Implements bpp::SubstitutionModel.

Definition at line 264 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::iEigenValues_.

virtual const Vdouble& bpp::SubstitutionModel::getIEigenValues ( ) const [pure virtual, inherited]
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().

double AbstractSubstitutionModel::getInitValue ( size_t  i,
int  state 
) const throw (IndexOutOfBoundsException, BadIntException) [virtual, inherited]

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 350 of file AbstractSubstitutionModel.cpp.

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

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().

virtual std::vector<size_t> bpp::SubstitutionModel::getModelStates ( int  i) const [pure virtual, inherited]

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

Parameters:
iThe alphabet char 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::MarkovModulatedSubstitutionModel::getModelStates(), and bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates().

std::vector<size_t> bpp::AbstractSubstitutionModel::getModelStates ( int  i) const [inline, virtual, inherited]

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

Parameters:
iThe alphabet char to check.
Returns:
A vector of indices of model states.

Implements bpp::SubstitutionModel.

Definition at line 248 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::chars_, and bpp::VectorTools::whichAll().

std::string bpp::T92::getName ( ) const [inline, virtual]

Get the name of the model.

Returns:
The name of this model.

Implements bpp::SubstitutionModel.

Definition at line 188 of file T92.h.

virtual size_t bpp::NucleotideSubstitutionModel::getNumberOfStates ( ) const [inline, virtual, inherited]

Get the number of states.

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

Returns:
The number of different states in the model.

Implements bpp::SubstitutionModel.

Reimplemented in bpp::gBGC.

Definition at line 68 of file NucleotideSubstitutionModel.h.

const Matrix< double > & T92::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 355 of file T92.cpp.

References exp1_, exp2_, k_, l_, p_, piA_, piC_, piG_, piT_, r_, bpp::AbstractSubstitutionModel::rate_, and theta_.

double AbstractSubstitutionModel::getRate ( ) const [virtual, inherited]

Get the rate.

Implements bpp::SubstitutionModel.

Definition at line 416 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::rate_.

virtual double bpp::SubstitutionModel::getRate ( ) const [pure virtual, inherited]

Get the rate.

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

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

const Matrix<double>& bpp::AbstractSubstitutionModel::getRowLeftEigenVectors ( ) const [inline, virtual, inherited]
Returns:
A matrix with left eigen vectors. Each row in the matrix stands for an eigen vector.

Implements bpp::SubstitutionModel.

Definition at line 270 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::leftEigenVectors_.

virtual const Matrix<double>& bpp::SubstitutionModel::getRowLeftEigenVectors ( ) const [pure virtual, inherited]
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_(), and bpp::AbstractBiblioSubstitutionModel::getRowLeftEigenVectors().

double AbstractSubstitutionModel::getScale ( ) const [virtual, inherited]

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 401 of file AbstractSubstitutionModel.cpp.

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

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

virtual double bpp::SubstitutionModel::getScale ( ) const [pure virtual, inherited]

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().

bool bpp::AbstractSubstitutionModel::isDiagonalizable ( ) const [inline, virtual, inherited]
Returns:
True if the model is diagonalizable in R.

Implements bpp::SubstitutionModel.

Definition at line 266 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isDiagonalizable_.

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

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

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

bool bpp::AbstractSubstitutionModel::isNonSingular ( ) const [inline, virtual, inherited]
Returns:
True is the model is non-singular.

Implements bpp::SubstitutionModel.

Definition at line 268 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isNonSingular_.

virtual bool bpp::SubstitutionModel::isNonSingular ( ) const [pure virtual, inherited]
Returns:
True is the model is non-singular.

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

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

double T92::Pij_t ( int  i,
int  j,
double  d 
) const

Definition at line 191 of file T92.cpp.

References exp1_, exp2_, k_, l_, piA_, piC_, piG_, piT_, r_, bpp::AbstractSubstitutionModel::rate_, and theta_.

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

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

Referenced by bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::SimpleMutationProcess::evolve(), bpp::OneJumpSubstitutionCount::getNumberOfSubstitutions(), bpp::AbstractBiblioSubstitutionModel::Pij_t(), and bpp::RE08::Pij_t().

virtual double bpp::AbstractSubstitutionModel::Pij_t ( size_t  i,
size_t  j,
double  t 
) const [inline, virtual, inherited]
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::RE08, bpp::JCnuc, and bpp::BinarySubstitutionModel.

Definition at line 278 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getPij_t().

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

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

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

virtual double bpp::AbstractSubstitutionModel::Qij ( size_t  i,
size_t  j 
) const [inline, virtual, inherited]
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 276 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

void T92::setFreq ( std::map< int, double > &  freqs) [virtual]

This method is over-defined to actualize the 'theta' parameter too.

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 458 of file T92.cpp.

References bpp::AbstractParameterAliasable::setParameterValue(), and updateMatrices().

void AbstractSubstitutionModel::setFreqFromData ( const SequenceContainer &  data,
double  pseudoCount = 0 
) [virtual, inherited]

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

Parameters:
dataThe sequences to use.
pseudoCountA quantity $\psi$ to add to adjust the observed values in order to prevent issues due to missing states on small data set. The corrected frequencies shall be computed as

\[ \pi_i = \frac{n_i+\psi}{\sum_j (f_j+\psi)} \]

Implements bpp::SubstitutionModel.

Definition at line 367 of file AbstractSubstitutionModel.cpp.

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

virtual void bpp::SubstitutionModel::setFreqFromData ( const SequenceContainer &  data,
double  pseudoCount = 0 
) [pure virtual, inherited]

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

\[ \pi_i = \frac{n_i+\psi}{\sum_j (f_j+\psi)} \]

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

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

void AbstractSubstitutionModel::setRate ( double  rate) [virtual, inherited]

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

Parameters:
ratemust be positive.

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel.

Definition at line 423 of file AbstractSubstitutionModel.cpp.

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

virtual void bpp::SubstitutionModel::setRate ( double  rate) [pure virtual, inherited]

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

Parameters:
ratemust be positive.

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

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

void AbstractSubstitutionModel::setScale ( double  scale) [virtual, inherited]

Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.

When the generator is normalized, scale=1. Otherwise each element is multiplied such that the correct scale is set.

Implements bpp::SubstitutionModel.

Definition at line 410 of file AbstractSubstitutionModel.cpp.

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

virtual void bpp::SubstitutionModel::setScale ( double  scale) [pure virtual, inherited]

Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.

When the generator is normalized, scale=1. Otherwise each element is multiplied such that the correct scale is set.

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

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

double bpp::AbstractSubstitutionModel::Sij ( size_t  i,
size_t  j 
) const [inline, virtual, inherited]
Returns:
The exchangeability between state i and state j.

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

Implements bpp::SubstitutionModel.

Definition at line 256 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

virtual double bpp::SubstitutionModel::Sij ( size_t  i,
size_t  j 
) const [pure virtual, inherited]
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().

void T92::updateMatrices ( ) [protected, virtual]

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 82 of file T92.cpp.

References bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractSubstitutionModel::freq_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractParameterAliasable::getParameterValue(), k_, kappa_, bpp::AbstractSubstitutionModel::leftEigenVectors_, piA_, piC_, piG_, piT_, r_, bpp::AbstractSubstitutionModel::rightEigenVectors_, bpp::MatrixTools::scale(), and theta_.

Referenced by setFreq(), and T92().

Friends And Related Function Documentation

friend class AbstractBiblioSubstitutionModel [friend, inherited]

Definition at line 335 of file AbstractSubstitutionModel.h.

Member Data Documentation

const Alphabet* bpp::AbstractSubstitutionModel::alphabet_ [protected, inherited]

The alphabet relevant to this model.

Definition at line 84 of file AbstractSubstitutionModel.h.

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

std::vector<int> bpp::AbstractSubstitutionModel::chars_ [protected, inherited]

The list of supported chars.

Definition at line 102 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::AbstractSubstitutionModel(), bpp::AbstractSubstitutionModel::getAlphabetChar(), bpp::AbstractSubstitutionModel::getAlphabetChars(), bpp::AbstractSubstitutionModel::getModelStates(), bpp::AbstractSubstitutionModel::operator=(), and bpp::RE08::RE08().

RowMatrix<double> bpp::AbstractSubstitutionModel::d2pijt_ [mutable, protected, inherited]

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=().

RowMatrix<double> bpp::AbstractSubstitutionModel::dpijt_ [mutable, protected, inherited]

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=().

bool bpp::AbstractSubstitutionModel::eigenDecompose_ [protected, inherited]

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=().

Vdouble bpp::AbstractSubstitutionModel::eigenValues_ [protected, inherited]

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::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::TN93::updateMatrices(), bpp::K80::updateMatrices(), updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::AbstractSubstitutionModel::exchangeability_ [protected, inherited]

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::gBGC::updateMatrices(), bpp::SSR::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::K80::updateMatrices(), bpp::RE08::updateMatrices(), updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

double bpp::T92::exp1_ [mutable, private]

Definition at line 165 of file T92.h.

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

double bpp::T92::exp2_ [mutable, private]

Definition at line 165 of file T92.h.

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

Vdouble bpp::AbstractSubstitutionModel::freq_ [protected, inherited]

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::L95::updateMatrices(), bpp::gBGC::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(), bpp::K80::updateMatrices(), bpp::RE08::updateMatrices(), updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().

RowMatrix<double> bpp::AbstractSubstitutionModel::generator_ [protected, inherited]

The generator matrix $Q$ of the model.

Definition at line 107 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::Coala::Coala(), 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::L95::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::RE08::updateMatrices(), updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

Vdouble bpp::AbstractSubstitutionModel::iEigenValues_ [protected, inherited]

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().

bool bpp::AbstractSubstitutionModel::isDiagonalizable_ [protected, inherited]

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().

bool bpp::AbstractSubstitutionModel::isNonSingular_ [protected, inherited]

boolean value for non-singularity of rightEigenVectors_

Definition at line 161 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::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

double bpp::T92::k_ [private]

Definition at line 164 of file T92.h.

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

double bpp::T92::kappa_ [private]

Definition at line 164 of file T92.h.

Referenced by updateMatrices().

double bpp::T92::l_ [mutable, private]

Definition at line 165 of file T92.h.

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

RowMatrix<double> bpp::AbstractSubstitutionModel::leftEigenVectors_ [protected, inherited]

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

Definition at line 168 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::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::TN93::updateMatrices(), bpp::K80::updateMatrices(), updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::T92::p_ [mutable, private]

Definition at line 166 of file T92.h.

Referenced by getd2Pij_dt2(), getdPij_dt(), getPij_t(), and T92().

double bpp::T92::piA_ [private]

Definition at line 164 of file T92.h.

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

double bpp::T92::piC_ [private]

Definition at line 164 of file T92.h.

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

double bpp::T92::piG_ [private]

Definition at line 164 of file T92.h.

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

RowMatrix<double> bpp::AbstractSubstitutionModel::pijt_ [mutable, protected, inherited]

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=().

double bpp::T92::piT_ [private]

Definition at line 164 of file T92.h.

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

double bpp::T92::r_ [private]

Definition at line 164 of file T92.h.

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

double bpp::AbstractSubstitutionModel::rate_ [protected, inherited]

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 97 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(), 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(), 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(), 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(), 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(), 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(), Pij_t(), bpp::JCprot::Pij_t(), bpp::F84::Pij_t(), bpp::HKY85::Pij_t(), bpp::AbstractMixedSubstitutionModel::setRate(), bpp::AbstractSubstitutionModel::setRate(), and bpp::BinarySubstitutionModel::updateMatrices().

RowMatrix<double> bpp::AbstractSubstitutionModel::rightEigenVectors_ [protected, inherited]

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::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

size_t bpp::AbstractSubstitutionModel::size_ [protected, inherited]

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

Definition at line 89 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::JTT92::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::AbstractSubstitutionModel::setFreqFromData(), T92(), bpp::TN93::TN93(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RE08::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().

double bpp::T92::theta_ [private]

Definition at line 164 of file T92.h.

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

RowMatrix<double> bpp::AbstractSubstitutionModel::tmpMat_ [mutable, protected, inherited]

For computational issues.

Definition at line 182 of file AbstractSubstitutionModel.h.

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

std::vector< RowMatrix<double> > bpp::AbstractSubstitutionModel::vPowGen_ [protected, inherited]

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

Definition at line 175 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::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

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