bpp-phyl3  3.0.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::RE08 Class Referenceabstract

The Rivas-Eddy substitution model with gap characters. More...

#include <Bpp/Phyl/Model/RE08.h>

+ Inheritance diagram for bpp::RE08:
+ Collaboration diagram for bpp::RE08:

Public Member Functions

 RE08 (std::unique_ptr< ReversibleSubstitutionModelInterface > simpleModel, double lambda=0.1, double mu=0.1)
 Build a new Rivas & Eddy model from a standard substitution model. More...
 
 RE08 (const RE08 &model)
 
RE08 & operator= (const RE08 &model)
 
virtual ~RE08 ()
 
RE08 * clone () const override
 
double Pij_t (size_t i, size_t j, double d) const override
 
double dPij_dt (size_t i, size_t j, double d) const override
 
double d2Pij_dt2 (size_t i, size_t j, double d) const override
 
const Matrix< double > & getPij_t (double d) const override
 
const Matrix< double > & getdPij_dt (double d) const override
 
const Matrix< double > & getd2Pij_dt2 (double d) const override
 
std::string getName () const override
 Get the name of the model. More...
 
void setFreqFromData (const SequenceDataInterface &data, double pseudoCount=0) override
 This method is forwarded to the simple model. More...
 
void setFreq (std::map< int, double > &frequencies) override
 Set equilibrium frequencies. More...
 
void fireParameterChanged (const ParameterList &parameters) override
 Tells the model that a parameter value has changed. More...
 
double getInitValue (size_t i, int state) const override
 
void setNamespace (const std::string &prefix) override
 
const ReversibleSubstitutionModelInterface & nestedModel () const
 
bool computeFrequencies () const
 
void computeFrequencies (bool yn)
 
const Matrix< double > & generator () const
 
const Matrix< double > & exchangeabilityMatrix () const
 
double Sij (size_t i, size_t j) const
 
const Vdouble & getEigenValues () const
 
const Vdouble & getIEigenValues () const
 
bool isDiagonalizable () const
 
bool isNonSingular () const
 
const Matrix< double > & getRowLeftEigenVectors () const
 
const Matrix< double > & getColumnRightEigenVectors () const
 
virtual double Qij (size_t i, size_t j) const
 A method for computing all necessary matrices. More...
 
void enableEigenDecomposition (bool yn)
 Set if eigenValues and Vectors must be computed. More...
 
bool enableEigenDecomposition ()
 Tell if eigenValues and Vectors must be computed. More...
 
void setScalable (bool scalable)
 sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example. More...
 
virtual bool isScalable () const
 returns if model is scalable More...
 
double getScale () const
 return scale More...
 
void setScale (double scale)
 Multiplies the current generator by the given scale. More...
 
void normalize ()
 normalize the generator More...
 
void setDiagonal ()
 set the diagonal of the generator such that sum on each line equals 0. More...
 
const Alphabet & alphabet () const override
 
std::shared_ptr< const Alphabet > getAlphabet () const override
 
const StateMapInterface & stateMap () const override
 
std::shared_ptr< const StateMapInterface > getStateMap () const override
 
size_t getNumberOfStates () const override
 Get the number of states. More...
 
const std::vector< int > & getAlphabetStates () const override
 
std::string getAlphabetStateAsChar (size_t index) const override
 
int getAlphabetStateAsInt (size_t index) const override
 
std::vector< size_t > getModelStates (int code) const override
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
std::vector< size_t > getModelStates (const std::string &code) const override
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
const Vdouble & getFrequencies () const override
 
virtual double freq (size_t i) const override
 
const FrequencySetInterface & frequencySet () const override
 
void addRateParameter () override
 add a "rate" parameter to the model, that handles the overall rate of the process. More...
 
void setVerboseLevel (short level)
 
short verboseLevel () const
 
virtual double getRate () const override
 The rate of the substitution process. More...
 
virtual void setRate (double rate) override
 Set the rate of the model (must be positive). More...
 
const Eigen::VectorXd & Lik_t (const Eigen::VectorXd &values, double t) const override
 
const Eigen::VectorXd & dLik_dt (const Eigen::VectorXd &values, double t) const override
 
const Eigen::VectorXd & d2Lik_dt2 (const Eigen::VectorXd &values, double t) const override
 
virtual size_t getNumberOfIndependentParameters () const=0
 
size_t getNumberOfIndependentParameters () const
 
virtual void aliasParameters (const std::string &p1, const std::string &p2)=0
 
virtual void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0
 
void aliasParameters (const std::string &p1, const std::string &p2)
 
void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
 
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
 
void unaliasParameters (const std::string &p1, const std::string &p2)
 
virtual const ParameterList & getIndependentParameters () const=0
 
const ParameterList & getIndependentParameters () const
 
virtual std::vector< std::string > getAlias (const std::string &name) const=0
 
virtual std::vector< std::string > getAlias (const std::string &name) const
 
virtual std::map< std::string, std::string > getAliases () const=0
 
virtual std::map< std::string, std::string > getAliases () const
 
virtual bool hasParameter (const std::string &name) const=0
 
bool hasParameter (const std::string &name) const override
 
virtual const ParameterList & getParameters () const=0
 
const ParameterList & getParameters () const override
 
virtual const Parameter & parameter (const std::string &name) const=0
 
const Parameter & parameter (const std::string &name) const override
 
virtual double getParameterValue (const std::string &name) const=0
 
double getParameterValue (const std::string &name) const override
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 
void setAllParametersValues (const ParameterList &parameters) override
 
virtual void setParameterValue (const std::string &name, double value)=0
 
void setParameterValue (const std::string &name, double value) override
 
virtual void setParametersValues (const ParameterList &parameters)=0
 
void setParametersValues (const ParameterList &parameters) override
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 
bool matchParametersValues (const ParameterList &parameters) override
 
virtual void removeConstraint (const std::string &name)=0
 
void removeConstraint (const std::string &name) override
 
virtual void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
 
void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
 
virtual size_t getNumberOfParameters () const=0
 
size_t getNumberOfParameters () const override
 
virtual std::string getNamespace () const=0
 
std::string getNamespace () const override
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const=0
 
std::string getParameterNameWithoutNamespace (const std::string &name) const override
 
bool hasIndependentParameter (const std::string &name) const
 
ParameterList getAliasedParameters (const ParameterList &pl) const
 
ParameterList getFromParameters (const ParameterList &pl) const
 
std::string getFrom (const std::string &name) const
 
const std::shared_ptr< Parameter > & getParameter (const std::string &name) const
 

Protected Member Functions

void updateMatrices_ () override
 Compute and diagonalize the $Q$ matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...
 
ReversibleSubstitutionModelInterface & nestedModel_ ()
 
Vdouble & getFrequencies_ () override
 
virtual ParameterList & getParameters_ ()=0
 
ParameterList & getParameters_ () override
 
const std::shared_ptr< Parameter > & getParameter (size_t i) const
 
std::shared_ptr< Parameter > & getParameter (size_t i)
 
void addParameter_ (Parameter *parameter)
 
void addParameters_ (const ParameterList &parameters)
 
void shareParameter_ (const std::shared_ptr< Parameter > &parameter)
 
void shareParameters_ (const ParameterList &parameters)
 
void includeParameters_ (const ParameterList &parameters)
 
void deleteParameter_ (size_t index)
 
void deleteParameter_ (std::string &name)
 
void deleteParameters_ (const std::vector< std::string > &names)
 
void resetParameters_ ()
 
Parameter & getParameter_ (const std::string &name)
 
Parameter & getParameter_ (size_t index)
 
const Parameter & getParameter_ (size_t index) const
 
Parameter & getParameterWithNamespace_ (const std::string &name)
 
const Parameter & getParameterWithNamespace_ (const std::string &name) const
 

Protected Attributes

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

Private Attributes

std::unique_ptr< ReversibleSubstitutionModelInterface > simpleModel_
 
RowMatrix< double > simpleGenerator_
 
RowMatrix< double > simpleExchangeabilities_
 
double exp_
 
RowMatrix< double > p_
 
double lambda_
 
double mu_
 
std::string nestedPrefix_
 
Eigen::VectorXd lik_
 
ParameterList independentParameters_
 
std::map< std::string, std::shared_ptr< AliasParameterListener > > aliasListenersRegister_
 
ParameterList parameters_
 
std::string prefix_
 

Detailed Description

The Rivas-Eddy substitution model with gap characters.

This model expends any reversible substitution model with gaps as an additional state. Although the conditional substitution process is reversible, the insertion/deletion process needs not be. The model hence adds two parameters for insertion and deletions, $\lambda$ and $\mu$. If we note $Q$ the (simple) transition matrix (= Markov generator) and $Q^\epsilon$ the extended one, we have:

\[ Q^\epsilon = \left( \begin{array}{ccc|c} & & & \mu \\ & \rule{0cm}{1cm}\rule{1cm}{0cm}Q-\mu\delta_{ij} & & \vdots \\ & & & \mu \\ \hline \lambda\pi_1 & \ldots & \lambda\pi_n & -\lambda \\ \end{array} \right) \]

where $n$ is the number of states of the simple model (in most case equal to the size of the alphabet) and $(\pi_1,\ldots,\pi_n)$ is the vector of equilibrium frequencies of the conditional model. $\delta_{ij}$ is 1 if i=j, 0 otherwise. Note that in the original paper $Q$ is noted as $R$, and $Q_t$ is used for the probability matrix, which is referred here as $P^\epsilon(t)$ for consistency with the documentation of other models.

The extended Markov model is reversible, and the equilibrium frequencies are

\[ \pi^\epsilon = \left( \pi \cdot \frac{\lambda}{\lambda + \mu}, \frac{\mu}{\lambda + \mu}\right). \]

The corresponding exchangeability matrix is:

\[ S^\epsilon = \left( \begin{array}{ccc|c} & & & \lambda + \mu \\ & \rule{0cm}{1cm}\rule{1cm}{0cm}(S - \frac{\mu\delta_{ij}}{\pi_i})\frac{\lambda+\mu}{\lambda} & & \vdots \\ & & & \lambda + \mu \\ \hline \lambda + \mu & \ldots & \lambda + \mu & - (\lambda + \mu) \\ \end{array} \right) \]

The eigen values and vectors are computed numerically, but the transition probabilities are computed analytically from the simple substitution model, together with the first and second order derivatives according to time.

Please note that the original Rivas and Eddy method uses this substitution model with a modification of the Felsenstein algorithm.

Reference:

  • Rivas E and Eddy SR (2008), Probabilistic Phylogenetic Inference with Insertions and Deletions, 4(9):e1000172, in PLoS Computational Biology.

Definition at line 64 of file RE08.h.

Constructor & Destructor Documentation

◆ RE08() [1/2]

RE08::RE08 ( std::unique_ptr< ReversibleSubstitutionModelInterface >  simpleModel,
double  lambda = 0.1,
double  mu = 0.1 
)

Build a new Rivas & Eddy model from a standard substitution model.

The alphabet and number of states for the extended model will be derived from the simple one.

Parameters
simpleModelThe simple model to use to build the extended one. THE RE08 class will own the simple one, meaning that it will be destroyed together with the RE08 instance, and cloned when cloning the RE08 instance. To prevent the original simple model to be destroyed, you should make a copy of it before creating the RE08 instance.
lambdaInsertion rate.
muDeletion rate.

Definition at line 15 of file RE08.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractTransitionModel::freq_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::leftEigenVectors_, nestedPrefix_, p_, bpp::Parameter::R_PLUS, RowMatrix< double >::resize(), bpp::AbstractSubstitutionModel::rightEigenVectors_, simpleModel_, bpp::AbstractTransitionModel::size_, and updateMatrices_().

Referenced by clone().

◆ RE08() [2/2]

bpp::RE08::RE08 ( const RE08 &  model)
inline

Definition at line 94 of file RE08.h.

◆ ~RE08()

virtual bpp::RE08::~RE08 ( )
inlinevirtual

Definition at line 122 of file RE08.h.

Member Function Documentation

◆ addRateParameter()

void AbstractTransitionModel::addRateParameter ( )
overridevirtualinherited

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 63 of file AbstractSubstitutionModel.cpp.

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

◆ alphabet()

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 167 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::alphabet_.

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

◆ clone()

RE08* bpp::RE08::clone ( ) const
inlineoverridevirtual

Implements bpp::AbstractReversibleSubstitutionModel.

Reimplemented in bpp::RE08Codon, bpp::RE08Protein, and bpp::RE08Nucleotide.

Definition at line 124 of file RE08.h.

References RE08().

◆ computeFrequencies() [1/2]

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

Reimplemented from bpp::AbstractTransitionModel.

Definition at line 404 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::computeFreq_.

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

◆ computeFrequencies() [2/2]

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

Implements bpp::TransitionModelInterface.

Definition at line 406 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::computeFreq_.

◆ d2Lik_dt2()

const Eigen::VectorXd& bpp::AbstractLkTransitionModel::d2Lik_dt2 ( const Eigen::VectorXd &  values,
double  t 
) const
inlineoverridevirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 64 of file AbstractSubstitutionModel.h.

References bpp::TransitionModelInterface::getd2Pij_dt2(), and bpp::AbstractLkTransitionModel::lik_.

◆ d2Pij_dt2()

double RE08::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const
overridevirtual
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::AbstractTransitionModel.

Definition at line 151 of file RE08.cpp.

References bpp::exp(), bpp::AbstractTransitionModel::freq_, lambda_, mu_, simpleModel_, and bpp::AbstractTransitionModel::size_.

◆ dLik_dt()

const Eigen::VectorXd& bpp::AbstractLkTransitionModel::dLik_dt ( const Eigen::VectorXd &  values,
double  t 
) const
inlineoverridevirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 47 of file AbstractSubstitutionModel.h.

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

◆ dPij_dt()

double RE08::dPij_dt ( size_t  i,
size_t  j,
double  t 
) const
overridevirtual
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::AbstractTransitionModel.

Definition at line 120 of file RE08.cpp.

References bpp::exp(), bpp::AbstractTransitionModel::freq_, lambda_, mu_, simpleModel_, and bpp::AbstractTransitionModel::size_.

◆ enableEigenDecomposition() [1/2]

bool bpp::AbstractSubstitutionModel::enableEigenDecomposition ( )
inlinevirtualinherited

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModelInterface.

Definition at line 434 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

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

◆ enableEigenDecomposition() [2/2]

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

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModelInterface.

Definition at line 432 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

◆ exchangeabilityMatrix()

const Matrix<double>& bpp::AbstractSubstitutionModel::exchangeabilityMatrix ( ) const
inlinevirtualinherited
Returns
The matrix of exchangeability terms. It is recommended that exchangeability matrix be normalized so that the normalized generator be obtained directly by the dot product $S . \pi$.

Implements bpp::SubstitutionModelInterface.

Definition at line 410 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

◆ fireParameterChanged()

void bpp::RE08::fireParameterChanged ( const ParameterList &  parameters)
inlineoverridevirtual

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractTransitionModel.

Definition at line 152 of file RE08.h.

References bpp::AbstractParameterAliasable::getParameter_(), bpp::Parameter::getValue(), lambda_, mu_, simpleModel_, and updateMatrices_().

◆ freq()

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

Implements bpp::TransitionModelInterface.

Definition at line 195 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::freq_.

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

◆ frequencySet()

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

Implements bpp::BranchModelInterface.

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

Definition at line 207 of file AbstractSubstitutionModel.h.

◆ generator()

const Matrix<double>& bpp::AbstractSubstitutionModel::generator ( ) const
inlinevirtualinherited
Returns
The normalized Markov generator matrix, i.e. all normalized rates of changes from state i to state j. The generator is normalized so that (i) $ \forall i; \sum_j Q_{i,j} = 0 $, meaning that $ $ \forall i; Q_{i,i} = -\sum_{j \neq i}Q_{i,j}$, and (ii) $ \sum_i Q_{i,i} \times \pi_i = -1$. This means that, under normalization, the mean rate of replacement at equilibrium is 1 and that time $t$ are measured in units of expected number of changes per site. Additionally, the rate_ attribute provides the possibility to increase or decrease this mean rate.

See Kosiol and Goldman (2005), Molecular Biology And Evolution 22(2) 193-9.

See also
Qij()

Implements bpp::SubstitutionModelInterface.

Definition at line 408 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

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

◆ getAlphabet()

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 169 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::alphabet_.

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

◆ getAlphabetStateAsChar()

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 179 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

◆ getAlphabetStateAsInt()

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 181 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

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

◆ getAlphabetStates()

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 177 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

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

◆ getColumnRightEigenVectors()

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

Implements bpp::SubstitutionModelInterface.

Definition at line 428 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::rightEigenVectors_.

◆ getd2Pij_dt2()

const Matrix< double > & RE08::getd2Pij_dt2 ( double  t) const
overridevirtual
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 237 of file RE08.cpp.

References bpp::exp(), bpp::AbstractTransitionModel::freq_, lambda_, mu_, p_, simpleModel_, and bpp::AbstractTransitionModel::size_.

◆ getdPij_dt()

const Matrix< double > & RE08::getdPij_dt ( double  t) const
overridevirtual
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 209 of file RE08.cpp.

References bpp::exp(), bpp::AbstractTransitionModel::freq_, lambda_, mu_, p_, simpleModel_, and bpp::AbstractTransitionModel::size_.

◆ getEigenValues()

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

Implements bpp::SubstitutionModelInterface.

Definition at line 418 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenValues_.

◆ getFrequencies()

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

Implements bpp::TransitionModelInterface.

Definition at line 187 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::freq_.

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

◆ getFrequencies_()

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

Implements bpp::TransitionModelInterface.

Definition at line 268 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::freq_.

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

◆ getIEigenValues()

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

Implements bpp::SubstitutionModelInterface.

Definition at line 420 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::iEigenValues_.

◆ getInitValue()

double RE08::getInitValue ( size_t  i,
int  state 
) const
overridevirtual

This method is used to initialize likelihoods in recursions. It typically sends 1 if i = state, 0 otherwise, where i is one of the possible states of the alphabet allowed in the model and state is the observed state in the considered sequence/site.

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

Reimplemented from bpp::AbstractTransitionModel.

Definition at line 267 of file RE08.cpp.

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

◆ getModelStates() [1/2]

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

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

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 185 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

◆ getModelStates() [2/2]

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

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

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 183 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

◆ getName()

std::string bpp::RE08::getName ( ) const
inlineoverridevirtual

Get the name of the model.

Returns
The name of this model.

Implements bpp::BranchModelInterface.

Definition at line 134 of file RE08.h.

◆ getNumberOfStates()

size_t bpp::AbstractTransitionModel::getNumberOfStates ( ) const
inlineoverridevirtualinherited

Get the number of states.

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

See also
getAlphabetChars for the list of supported states.
Returns
The number of different states in the model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel, bpp::RE08Codon, bpp::RE08Protein, bpp::RE08Nucleotide, bpp::YpR, bpp::gBGC, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, and bpp::BinarySubstitutionModel.

Definition at line 175 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

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

◆ getPij_t()

const Matrix< double > & RE08::getPij_t ( double  t) const
overridevirtual
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 183 of file RE08.cpp.

References bpp::exp(), bpp::AbstractTransitionModel::freq_, lambda_, mu_, p_, simpleModel_, and bpp::AbstractTransitionModel::size_.

◆ getRate()

double AbstractTransitionModel::getRate ( ) const
overridevirtualinherited

The rate of the substitution process.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 45 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractTransitionModel::rate_.

◆ getRowLeftEigenVectors()

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

Implements bpp::SubstitutionModelInterface.

Definition at line 426 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::leftEigenVectors_.

◆ getScale()

double AbstractSubstitutionModel::getScale ( ) const
virtualinherited

return scale

Implements bpp::SubstitutionModelInterface.

Definition at line 632 of file AbstractSubstitutionModel.cpp.

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

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

◆ getStateMap()

std::shared_ptr<const StateMapInterface> bpp::AbstractTransitionModel::getStateMap ( ) const
inlineoverridevirtualinherited
Returns
A shared_ptr to the mapping of model states with alphabet states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 173 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

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

◆ isDiagonalizable()

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

Implements bpp::SubstitutionModelInterface.

Definition at line 422 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isDiagonalizable_.

◆ isNonSingular()

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

Implements bpp::SubstitutionModelInterface.

Definition at line 424 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isNonSingular_.

◆ isScalable()

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

returns if model is scalable

Implements bpp::SubstitutionModelInterface.

Definition at line 469 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isScalable_.

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

◆ Lik_t()

const Eigen::VectorXd& bpp::AbstractLkTransitionModel::Lik_t ( const Eigen::VectorXd &  values,
double  t 
) const
inlineoverridevirtualinherited

This method is used to compute likelihoods in recursions. It computes the probability of a vector given a start state.

Parameters
valuesAn vector of states on the site.
tthe branch length

Implements bpp::TransitionModelInterface.

Definition at line 30 of file AbstractSubstitutionModel.h.

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

◆ nestedModel()

const ReversibleSubstitutionModelInterface& bpp::RE08::nestedModel ( ) const
inline

Definition at line 164 of file RE08.h.

References simpleModel_.

Referenced by bpp::RE08Codon::codonFrequencySet(), bpp::RE08Nucleotide::nestedModel(), bpp::RE08Protein::nestedModel(), bpp::RE08Codon::nestedModel(), and bpp::BppOSubstitutionModelFormat::write().

◆ nestedModel_()

ReversibleSubstitutionModelInterface& bpp::RE08::nestedModel_ ( )
inlineprotected

Definition at line 172 of file RE08.h.

References simpleModel_.

Referenced by bpp::RE08Codon::setFreq().

◆ normalize()

void AbstractSubstitutionModel::normalize ( )
virtualinherited

normalize the generator

Implements bpp::SubstitutionModelInterface.

Definition at line 673 of file AbstractSubstitutionModel.cpp.

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

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

◆ operator=()

RE08& bpp::RE08::operator= ( const RE08 &  model)
inline

Definition at line 107 of file RE08.h.

References exp_, lambda_, mu_, nestedPrefix_, bpp::AbstractParameterAliasable::operator=(), bpp::AbstractSubstitutionModel::operator=(), p_, simpleExchangeabilities_, simpleGenerator_, and simpleModel_.

◆ Pij_t()

double RE08::Pij_t ( size_t  i,
size_t  j,
double  t 
) const
overridevirtual
Returns
The probability of change from state i to state j during time t.
See also
getPij_t(), getStates()

Reimplemented from bpp::AbstractTransitionModel.

Definition at line 90 of file RE08.cpp.

References bpp::exp(), bpp::AbstractTransitionModel::freq_, lambda_, mu_, simpleModel_, and bpp::AbstractTransitionModel::size_.

◆ Qij()

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

A method for computing all necessary matrices.

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

Implements bpp::SubstitutionModelInterface.

Definition at line 430 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

◆ setDiagonal()

void AbstractSubstitutionModel::setDiagonal ( )
virtualinherited

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

Implements bpp::SubstitutionModelInterface.

Definition at line 654 of file AbstractSubstitutionModel.cpp.

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

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

◆ setFreq()

void bpp::RE08::setFreq ( std::map< int, double > &  frequencies)
inlineoverridevirtual

Set equilibrium frequencies.

Parameters
frequenciesThe map of the frequencies to use.

Reimplemented from bpp::AbstractTransitionModel.

Reimplemented in bpp::RE08Codon.

Definition at line 147 of file RE08.h.

References simpleModel_.

◆ setFreqFromData()

void bpp::RE08::setFreqFromData ( const SequenceDataInterface &  data,
double  pseudoCount = 0 
)
inlineoverridevirtual

This method is forwarded to the simple model.

Parameters
dataThe data to be passed to the simple model (gaps will be ignored).
pseudoCountA (typically small) value to add to each count to avoid 0 estimates.

Reimplemented from bpp::AbstractTransitionModel.

Definition at line 142 of file RE08.h.

References simpleModel_.

◆ setNamespace()

void RE08::setNamespace ( const std::string &  prefix)
overridevirtual

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 286 of file RE08.cpp.

References nestedPrefix_, bpp::AbstractParameterAliasable::setNamespace(), and simpleModel_.

◆ setRate()

void AbstractTransitionModel::setRate ( double  rate)
overridevirtualinherited

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

Parameters
ratemust be positive.

Implements bpp::BranchModelInterface.

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

Definition at line 52 of file AbstractSubstitutionModel.cpp.

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

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

◆ setScalable()

void bpp::AbstractSubstitutionModel::setScalable ( bool  scalable)
inlinevirtualinherited

sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example.

Implements bpp::SubstitutionModelInterface.

Definition at line 461 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isScalable_.

◆ setScale()

void AbstractSubstitutionModel::setScale ( double  scale)
virtualinherited

Multiplies the current generator by the given scale.

Parameters
scalethe scale by which the generator is multiplied.

Implements bpp::SubstitutionModelInterface.

Definition at line 641 of file AbstractSubstitutionModel.cpp.

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

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

◆ setVerboseLevel()

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

Definition at line 239 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::verboseLevel_.

◆ Sij()

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

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

Implements bpp::SubstitutionModelInterface.

Definition at line 416 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

◆ stateMap()

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 171 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

◆ updateMatrices_()

void RE08::updateMatrices_ ( )
overrideprotectedvirtual

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 46 of file RE08.cpp.

References bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractTransitionModel::freq_, bpp::AbstractSubstitutionModel::generator_, lambda_, mu_, simpleExchangeabilities_, simpleGenerator_, simpleModel_, bpp::AbstractTransitionModel::size_, and bpp::AbstractSubstitutionModel::updateMatrices_().

Referenced by fireParameterChanged(), and RE08().

◆ verboseLevel()

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

Definition at line 241 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::verboseLevel_.

Member Data Documentation

◆ alphabet_

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

The alphabet relevant to this model.

Definition at line 121 of file AbstractSubstitutionModel.h.

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

◆ computeFreq_

bool bpp::AbstractSubstitutionModel::computeFreq_
protectedinherited

if the Frequencies must be computed from the generator

Definition at line 303 of file AbstractSubstitutionModel.h.

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

◆ d2pijt_

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

Definition at line 150 of file AbstractSubstitutionModel.h.

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

◆ dpijt_

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

Definition at line 149 of file AbstractSubstitutionModel.h.

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

◆ eigenDecompose_

bool bpp::AbstractSubstitutionModel::eigenDecompose_
protectedinherited

Tell if the eigen decomposition should be performed.

Definition at line 315 of file AbstractSubstitutionModel.h.

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

◆ eigenValues_

Vdouble bpp::AbstractSubstitutionModel::eigenValues_
protectedinherited

The vector of eigen values.

Definition at line 320 of file AbstractSubstitutionModel.h.

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

◆ exchangeability_

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

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

Definition at line 310 of file AbstractSubstitutionModel.h.

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

◆ exp_

double bpp::RE08::exp_
mutableprivate

Definition at line 71 of file RE08.h.

Referenced by operator=().

◆ freq_

Vdouble bpp::AbstractTransitionModel::freq_
protectedinherited

The vector $\pi_e$ of equilibrium frequencies.

Definition at line 143 of file AbstractSubstitutionModel.h.

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

◆ generator_

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

The generator matrix $Q$ of the model.

Definition at line 298 of file AbstractSubstitutionModel.h.

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

◆ iEigenValues_

Vdouble bpp::AbstractSubstitutionModel::iEigenValues_
protectedinherited

The vector of the imaginary part of the eigen values.

Definition at line 325 of file AbstractSubstitutionModel.h.

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

◆ isDiagonalizable_

bool bpp::AbstractSubstitutionModel::isDiagonalizable_
protectedinherited

boolean value for diagonalizability in R of the generator_

Definition at line 330 of file AbstractSubstitutionModel.h.

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

◆ isNonSingular_

bool bpp::AbstractSubstitutionModel::isNonSingular_
protectedinherited

boolean value for non-singularity of rightEigenVectors_

Definition at line 340 of file AbstractSubstitutionModel.h.

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

◆ isScalable_

bool bpp::AbstractSubstitutionModel::isScalable_
protectedinherited

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

Definition at line 293 of file AbstractSubstitutionModel.h.

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

◆ lambda_

double bpp::RE08::lambda_
private

Definition at line 73 of file RE08.h.

Referenced by d2Pij_dt2(), dPij_dt(), fireParameterChanged(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), operator=(), Pij_t(), and updateMatrices_().

◆ leftEigenVectors_

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

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

Definition at line 346 of file AbstractSubstitutionModel.h.

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

◆ lik_

Eigen::VectorXd bpp::AbstractLkTransitionModel::lik_
mutableprivateinherited

Definition at line 23 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractLkTransitionModel::d2Lik_dt2(), bpp::AbstractLkTransitionModel::dLik_dt(), and bpp::AbstractLkTransitionModel::Lik_t().

◆ mu_

double bpp::RE08::mu_
private

Definition at line 74 of file RE08.h.

Referenced by d2Pij_dt2(), dPij_dt(), fireParameterChanged(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), operator=(), Pij_t(), and updateMatrices_().

◆ nestedPrefix_

std::string bpp::RE08::nestedPrefix_
private

Definition at line 75 of file RE08.h.

Referenced by operator=(), RE08(), and setNamespace().

◆ p_

RowMatrix<double> bpp::RE08::p_
mutableprivate

Definition at line 72 of file RE08.h.

Referenced by getd2Pij_dt2(), getdPij_dt(), getPij_t(), operator=(), and RE08().

◆ pijt_

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

These ones are for bookkeeping:

Definition at line 148 of file AbstractSubstitutionModel.h.

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

◆ rate_

double bpp::AbstractTransitionModel::rate_
protectedinherited

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

Definition at line 138 of file AbstractSubstitutionModel.h.

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

◆ rightEigenVectors_

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

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

Definition at line 335 of file AbstractSubstitutionModel.h.

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

◆ simpleExchangeabilities_

RowMatrix<double> bpp::RE08::simpleExchangeabilities_
private

Definition at line 70 of file RE08.h.

Referenced by operator=(), and updateMatrices_().

◆ simpleGenerator_

RowMatrix<double> bpp::RE08::simpleGenerator_
private

Definition at line 69 of file RE08.h.

Referenced by operator=(), and updateMatrices_().

◆ simpleModel_

std::unique_ptr<ReversibleSubstitutionModelInterface> bpp::RE08::simpleModel_
private

Definition at line 68 of file RE08.h.

Referenced by d2Pij_dt2(), dPij_dt(), fireParameterChanged(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), nestedModel(), nestedModel_(), operator=(), Pij_t(), RE08(), setFreq(), setFreqFromData(), setNamespace(), and updateMatrices_().

◆ size_

size_t bpp::AbstractTransitionModel::size_
protectedinherited

The number of states.

Definition at line 131 of file AbstractSubstitutionModel.h.

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

◆ stateMap_

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

The map of model states with alphabet states.

Definition at line 126 of file AbstractSubstitutionModel.h.

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

◆ tmpMat_

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

For computational issues.

Definition at line 357 of file AbstractSubstitutionModel.h.

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

◆ verboseLevel_

short bpp::AbstractTransitionModel::verboseLevel_
protectedinherited

Definition at line 152 of file AbstractSubstitutionModel.h.

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

◆ vPowGen_

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

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

Definition at line 352 of file AbstractSubstitutionModel.h.

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

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