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

Interface for all substitution models. More...

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

+ Inheritance diagram for bpp::SubstitutionModelInterface:
+ Collaboration diagram for bpp::SubstitutionModelInterface:

Public Member Functions

 SubstitutionModelInterface ()
 
virtual ~SubstitutionModelInterface ()
 
SubstitutionModelInterface * clone () const override=0
 
virtual double Qij (size_t i, size_t j) const =0
 A method for computing all necessary matrices. More...
 
virtual const Matrix< double > & generator () const =0
 
virtual const Matrix< double > & exchangeabilityMatrix () const =0
 
virtual double Sij (size_t i, size_t j) const =0
 
virtual void enableEigenDecomposition (bool yn)=0
 Set if eigenValues and Vectors must be computed. More...
 
virtual bool enableEigenDecomposition ()=0
 Tell if eigenValues and Vectors must be computed. More...
 
virtual const Vdouble & getEigenValues () const =0
 
virtual const Vdouble & getIEigenValues () const =0
 
virtual bool isDiagonalizable () const =0
 
virtual bool isNonSingular () const =0
 
virtual const Matrix< double > & getRowLeftEigenVectors () const =0
 
virtual const Matrix< double > & getColumnRightEigenVectors () const =0
 
virtual void setScalable (bool scalable)=0
 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 =0
 returns if model is scalable More...
 
virtual double getScale () const =0
 Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale. More...
 
virtual void setScale (double scale)=0
 Multiplies the current generator by the given scale. More...
 
virtual void normalize ()=0
 Normalize the generator. More...
 
virtual void setDiagonal ()=0
 set the diagonal of the generator such that sum on each line equals 0. More...
 
virtual double freq (size_t i) 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 bool computeFrequencies () const =0
 
virtual void computeFrequencies (bool yn)=0
 
virtual const Matrix< double > & getPij_t (double t) const =0
 
virtual const Matrix< double > & getdPij_dt (double t) const =0
 
virtual const Matrix< double > & getd2Pij_dt2 (double t) const =0
 
virtual const Eigen::VectorXd & Lik_t (const Eigen::VectorXd &values, double t) const =0
 
virtual const Eigen::VectorXd & dLik_dt (const Eigen::VectorXd &values, double t) const =0
 
virtual const Eigen::VectorXd & d2Lik_dt2 (const Eigen::VectorXd &values, double t) const =0
 
virtual void setFreqFromData (const SequenceDataInterface &data, double pseudoCount=0)=0
 Set equilibrium frequencies equal to the frequencies estimated from the data. More...
 
virtual void setFreq (std::map< int, double > &frequencies)=0
 Set equilibrium frequencies. More...
 
virtual std::string getName () const =0
 Get the name of the model. More...
 
virtual const std::vector< int > & getAlphabetStates () const =0
 
virtual const StateMapInterface & stateMap () const =0
 
virtual std::shared_ptr< const StateMapInterface > getStateMap () const =0
 
virtual std::vector< size_t > getModelStates (int code) const =0
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
virtual std::vector< size_t > getModelStates (const std::string &code) const =0
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
virtual int getAlphabetStateAsInt (size_t index) const =0
 
virtual std::string getAlphabetStateAsChar (size_t index) const =0
 
virtual const Alphabet & alphabet () const =0
 
virtual std::shared_ptr< const Alphabet > getAlphabet () const =0
 
virtual const FrequencySetInterface & frequencySet () const =0
 
virtual size_t getNumberOfStates () const =0
 Get the number of states. More...
 
virtual double getInitValue (size_t i, int state) const =0
 
virtual double getRate () const =0
 Get the rate. More...
 
virtual void setRate (double rate)=0
 Set the rate of the model (must be positive). More...
 
virtual void addRateParameter ()=0
 
virtual size_t getNumberOfIndependentParameters () const=0
 
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
 
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 std::map< std::string, std::string > getAliases () const=0
 
virtual bool hasParameter (const std::string &name) const=0
 
virtual const ParameterList & getParameters () const=0
 
virtual const Parameter & parameter (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 void removeConstraint (const std::string &name)=0
 
virtual void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=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
 

Protected Member Functions

virtual Vdouble & getFrequencies_ ()=0
 
virtual ParameterList & getParameters_ ()=0
 

Detailed Description

Interface for all substitution models.

A substitution model is based on a Markov generator $Q$, the size of which depends on the alphabet used (4 for nucleotides, 20 for proteins, etc.). Each SubstitutionModel object hence includes a pointer toward an alphabet, and provides a method to retrieve the alphabet used (getAlphabet() method).

What we want from a substitution model is to compute the probabilities of state j at time t geven state j at time 0 ( $P_{i,j}(t)$). Typically, this is computed using the formula

\[ P(t) = e^{r \times t \times Q}, \]

where $P(t)$ is the matrix with all probabilities $P_{i,j}(t)$, and $ r $ the rate. For some models, the $P_{i,j}(t)$'s can be computed analytically.

For more complex models, we need to use a eigen-decomposition of $Q$:

\[ Q = U^{-1} . D . U, \]

where $D = diag(\lambda_i)$ is a diagonal matrix. Hence

\[ P(t) = e^{r \times t \times Q} = U^{-1} . e^{r \times D \times t} . U, \]

where $e^{r \times D \times t} = diag\left(e^{r \times \lambda_i \times t}\right)$ is a diagonal matrix with all terms equal to exp the terms in $D$ multiplied per $ r \times t $. $U$ is the matrix of left eigen vectors (by row), and $U^{-1}$ is the matrix of right eigen vectors (by column). The values in $D$ are the eigen values of $Q$. All $Q,U,U^{-1}$ and $D$ (its diagonal) may be retrieved from the class (getEigenValues(), getRowRightEigenVectors() and getColumnLeftEigenVectors() functions).

First and second order derivatives of $P(t)$ with respect to $t$ can also be retrieved. These methods may be useful for optimization processes. Derivatives may be computed analytically, or using the general formulas:

\[ \frac{\partial P(t)}{\partial t} = U^{-1} . diag\left(r \times \lambda_i \times e^{r \times \lambda_i \times t}\right) . U \]

and

\[ \frac{\partial^2 P(t)}{\partial t^2} = U^{-1} . diag\left(r^2 \times \lambda_i^2 \times e^{r \times \lambda_i \times t}\right) . U \]

If Q is not symmetric, then the eigenvalue matrix D is block diagonal with the real eigenvalues in 1-by-1 blocks and any complex eigenvalues, a + i*b, in 2-by-2 blocks, [a, b; -b, a]. That is, if the complex eigenvalues look like 


          a + ib   .        .    .
          .        a - ib   .    .
          .        .        x    .
          .        .        .    y

then D looks like 


          a          b      .    .
         -b          a      .    .
          .          .      x    .
          .          .      .    y

and exp(tD) equals 


          exp(ta)cos(tb)   exp(ta)sin(tb)  .        .
         -exp(ta)sin(tb)   exp(ta)cos(tb)  .        .
          .                .               exp(tx)  .
          .                .               .        exp(ty)

If U is singular, it cannot be inverted. In this case exp(tQ) is approximated using Taylor decomposition:

\[ P(t) = Id + tQ + \frac{(tQ)^2}{2!} + ... + \frac{(tQ)^n}{n!} + ... \]

To prevent approximation issues, if \f$ max(tQ) \f$ is too high (currently above 0.5), \f$ t \f$ is divided in an ad hoc way (e.g. by \f$ N \f$), and we compute \f$ P(t) = (P(t/N))^N \f$ with a Taylor decomposition for \f$ P(t/N) \f$.

In this case, derivatives according to \f$ t \f$ are computed analytically too.

Definition at line 401 of file SubstitutionModel.h.

Constructor & Destructor Documentation

◆ SubstitutionModelInterface()

bpp::SubstitutionModelInterface::SubstitutionModelInterface ( )
inline

Definition at line 405 of file SubstitutionModel.h.

◆ ~SubstitutionModelInterface()

virtual bpp::SubstitutionModelInterface::~SubstitutionModelInterface ( )
inlinevirtual

Definition at line 406 of file SubstitutionModel.h.

Member Function Documentation

◆ addRateParameter()

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

Implemented in bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::FromMixtureSubstitutionModel, bpp::AbstractTransitionModel, bpp::AbstractFromSubstitutionModelTransitionModel, and bpp::AbstractBiblioTransitionModel.

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::AbstractFromSubstitutionModelTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), bpp::InMixedSubstitutionModel::addRateParameter(), bpp::MultinomialFromTransitionModel::addRateParameter(), bpp::TransitionFromTransitionModel::addRateParameter(), and bpp::BppOSubstitutionModelFormat::updateParameters_().

◆ alphabet()

virtual const Alphabet& bpp::BranchModelInterface::alphabet ( ) const
pure virtualinherited
Returns
A reference to the alphabet associated to this model.

Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractWrappedModel, and bpp::AbstractTransitionModel.

Referenced by bpp::SubstitutionModelSet::addModel(), bpp::AbstractWrappedModel::alphabet(), bpp::NonHomogeneousSubstitutionProcess::createHomogeneousSubstitutionProcess(), bpp::NonHomogeneousSubstitutionProcess::createNonHomogeneousSubstitutionProcess(), and bpp::SENCA::setFreq().

◆ clone()

SubstitutionModelInterface* bpp::SubstitutionModelInterface::clone ( ) const
overridepure virtual

Implements bpp::TransitionModelInterface.

Implemented in bpp::ReversibleSubstitutionModelInterface, bpp::AbstractReversibleProteinSubstitutionModel, bpp::AbstractProteinSubstitutionModel, bpp::ProteinReversibleSubstitutionModelInterface, bpp::ProteinSubstitutionModelInterface, bpp::AbstractReversibleNucleotideSubstitutionModel, bpp::AbstractNucleotideSubstitutionModel, bpp::NucleotideReversibleSubstitutionModelInterface, bpp::NucleotideSubstitutionModelInterface, bpp::MarkovModulatedSubstitutionModel, bpp::CodonReversibleSubstitutionModelInterface, bpp::CodonSubstitutionModelInterface, bpp::AbstractKroneckerCodonSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::AbstractCodonSubstitutionModel, bpp::AbstractReversibleSubstitutionModel, bpp::WordSubstitutionModel, bpp::TS98, bpp::RegisterRatesSubstitutionModel, bpp::RE08Codon, bpp::RE08Protein, bpp::RE08Nucleotide, bpp::RE08, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LLG08_UL3::EmbeddedModel, bpp::LLG08_UL2::EmbeddedModel, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_EX2::EmbeddedModel, bpp::LLG08_EHO::EmbeddedModel, bpp::LGL08_CAT::EmbeddedModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::Coala, bpp::POMO, bpp::YpR_Gen, bpp::YpR_Sym, bpp::TN93, bpp::T92, bpp::SSR, bpp::RN95s, bpp::RN95, bpp::L95, bpp::K80, bpp::JCnuc, bpp::GTR, bpp::gBGC, bpp::F81, bpp::KroneckerWordSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::FromMixtureSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, bpp::YN98, bpp::TripletSubstitutionModel, bpp::SENCA, bpp::MG94, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::GY94, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AnonymousSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::LG10_EX_EHO::EmbeddedModel, bpp::HKY85, bpp::F84, bpp::CodonDistanceSubstitutionModel, and bpp::BinarySubstitutionModel.

◆ computeFrequencies() [1/2]

virtual bool bpp::TransitionModelInterface::computeFrequencies ( ) const
pure virtualinherited
Returns
Says if equilibrium frequencies should be computed

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractFromSubstitutionModelTransitionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::computeFrequencies(), bpp::InMixedSubstitutionModel::computeFrequencies(), bpp::RELAX::RELAX(), bpp::SENCA::SENCA(), bpp::YNGP_M1::YNGP_M1(), bpp::YNGP_M10::YNGP_M10(), bpp::YNGP_M2::YNGP_M2(), bpp::YNGP_M3::YNGP_M3(), bpp::YNGP_M7::YNGP_M7(), bpp::YNGP_M8::YNGP_M8(), and bpp::YNGP_M9::YNGP_M9().

◆ computeFrequencies() [2/2]

virtual void bpp::TransitionModelInterface::computeFrequencies ( bool  yn)
pure virtualinherited
Returns
Set if equilibrium frequencies should be computed

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractFromSubstitutionModelTransitionModel, and bpp::AbstractSubstitutionModel.

◆ d2Lik_dt2()

virtual const Eigen::VectorXd& bpp::TransitionModelInterface::d2Lik_dt2 ( const Eigen::VectorXd &  values,
double  t 
) const
pure virtualinherited

Implements bpp::BranchModelInterface.

Implemented in bpp::AbstractLkTransitionModel.

◆ d2Pij_dt2()

virtual double bpp::TransitionModelInterface::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const
pure virtualinherited
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::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::d2Pij_dt2(), bpp::InMixedSubstitutionModel::d2Pij_dt2(), and bpp::OneChangeRegisterTransitionModel::d2Pij_dt2().

◆ dLik_dt()

virtual const Eigen::VectorXd& bpp::TransitionModelInterface::dLik_dt ( const Eigen::VectorXd &  values,
double  t 
) const
pure virtualinherited

Implements bpp::BranchModelInterface.

Implemented in bpp::AbstractLkTransitionModel.

◆ dPij_dt()

virtual double bpp::TransitionModelInterface::dPij_dt ( size_t  i,
size_t  j,
double  t 
) const
pure virtualinherited
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::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::AbstractTotallyWrappedTransitionModel::dPij_dt(), and bpp::InMixedSubstitutionModel::dPij_dt().

◆ enableEigenDecomposition() [1/2]

virtual bool bpp::SubstitutionModelInterface::enableEigenDecomposition ( )
pure virtual

Tell if eigenValues and Vectors must be computed.

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel().

◆ enableEigenDecomposition() [2/2]

virtual void bpp::SubstitutionModelInterface::enableEigenDecomposition ( bool  yn)
pure virtual

Set if eigenValues and Vectors must be computed.

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::enableEigenDecomposition(), and bpp::InMixedSubstitutionModel::enableEigenDecomposition().

◆ exchangeabilityMatrix()

virtual const Matrix<double>& bpp::SubstitutionModelInterface::exchangeabilityMatrix ( ) const
pure virtual
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::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::Coala::Coala(), bpp::AbstractTotallyWrappedSubstitutionModel::exchangeabilityMatrix(), and bpp::InMixedSubstitutionModel::exchangeabilityMatrix().

◆ freq()

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

Implemented in bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, and bpp::AbstractTransitionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::freq(), bpp::InMixedSubstitutionModel::freq(), bpp::OneChangeRegisterTransitionModel::freq(), and bpp::OneChangeTransitionModel::freq().

◆ frequencySet()

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

Implemented in bpp::RegisterRatesSubstitutionModel, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, bpp::YN98, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::AbstractWrappedTransitionModel, bpp::AbstractWrappedModel, bpp::AbstractTransitionModel, and bpp::AbstractBiblioMixedTransitionModel.

Referenced by bpp::RE08Codon::codonFrequencySet(), bpp::AbstractWrappedModel::frequencySet(), bpp::AbstractWrappedTransitionModel::frequencySet(), bpp::OneChangeRegisterTransitionModel::frequencySet(), bpp::OneChangeTransitionModel::frequencySet(), and bpp::BppOSubstitutionModelFormat::write().

◆ generator()

virtual const Matrix<double>& bpp::SubstitutionModelInterface::generator ( ) const
pure virtual
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()

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::dPij_dt(), bpp::AbstractTotallyWrappedSubstitutionModel::generator(), bpp::InMixedSubstitutionModel::generator(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), bpp::OneChangeRegisterTransitionModel::getPij_t(), bpp::OneChangeRegisterTransitionModel::Pij_t(), bpp::OneChangeRegisterTransitionModel::updateMatrices_(), and bpp::RegisterRatesSubstitutionModel::updateMatrices_().

◆ getAlphabet()

virtual std::shared_ptr<const Alphabet> bpp::BranchModelInterface::getAlphabet ( ) const
pure virtualinherited
Returns
A pointer toward the alphabet associated to this model.

Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractWrappedModel, and bpp::AbstractTransitionModel.

Referenced by bpp::NonHomogeneousSubstitutionProcess::addModel(), bpp::YpR::checkModel(), bpp::NonHomogeneousSubstitutionProcess::createHomogeneousSubstitutionProcess(), bpp::NonHomogeneousSubstitutionProcess::createNonHomogeneousSubstitutionProcess(), bpp::AbstractWrappedModel::getAlphabet(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::SENCA::setFreq(), bpp::NonHomogeneousSubstitutionProcess::setModel(), and bpp::BppOSubstitutionModelFormat::writeMixed_().

◆ getAlphabetStateAsChar()

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

Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractTransitionModel, and bpp::AbstractWrappedModel.

Referenced by bpp::AbstractWrappedModel::getAlphabetStateAsChar(), and bpp::SubstitutionModelSet::getAlphabetStateAsChar().

◆ getAlphabetStateAsInt()

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

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::AbstractTransitionModel, bpp::RegisterRatesSubstitutionModel, and bpp::AbstractWrappedModel.

Referenced by bpp::AbstractWrappedModel::getAlphabetStateAsInt(), bpp::SubstitutionModelSet::getAlphabetStateAsInt(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns().

◆ getAlphabetStates()

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

Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractWrappedModel, and bpp::AbstractTransitionModel.

Referenced by bpp::SubstitutionModelSet::getAlphabetStates(), and bpp::AbstractWrappedModel::getAlphabetStates().

◆ getColumnRightEigenVectors()

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

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getColumnRightEigenVectors(), and bpp::InMixedSubstitutionModel::getColumnRightEigenVectors().

◆ getd2Pij_dt2()

virtual const Matrix<double>& bpp::TransitionModelInterface::getd2Pij_dt2 ( double  t) const
pure virtualinherited
Returns
All second order derivatives of the probability of change from state i to state j with respect to time t, at time t.
See also
d2Pij_dt2()

Implemented in bpp::AbstractTransitionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by bpp::AbstractLkTransitionModel::d2Lik_dt2(), bpp::AbstractTotallyWrappedTransitionModel::getd2Pij_dt2(), bpp::InMixedSubstitutionModel::getd2Pij_dt2(), and bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2().

◆ getdPij_dt()

virtual const Matrix<double>& bpp::TransitionModelInterface::getdPij_dt ( double  t) const
pure virtualinherited
Returns
Get all first order derivatives of the probability of change from state i to state j with respect to time t, at time t.
See also
dPij_dt()

Implemented in bpp::AbstractTransitionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by bpp::AbstractLkTransitionModel::dLik_dt(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::AbstractTotallyWrappedTransitionModel::getdPij_dt(), bpp::InMixedSubstitutionModel::getdPij_dt(), and bpp::OneChangeRegisterTransitionModel::getdPij_dt().

◆ getEigenValues()

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

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getEigenValues(), and bpp::InMixedSubstitutionModel::getEigenValues().

◆ getFrequencies()

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

Implemented in bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, and bpp::AbstractTransitionModel.

Referenced by bpp::EquilibriumFrequenciesFromModel::compute(), bpp::AbstractTotallyWrappedTransitionModel::getFrequencies(), bpp::InMixedSubstitutionModel::getFrequencies(), bpp::OneChangeRegisterTransitionModel::getFrequencies(), and bpp::OneChangeTransitionModel::getFrequencies().

◆ getFrequencies_()

virtual Vdouble& bpp::TransitionModelInterface::getFrequencies_ ( )
protectedpure virtualinherited

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, and bpp::AbstractFromSubstitutionModelTransitionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::getFrequencies_(), and bpp::InMixedSubstitutionModel::getFrequencies_().

◆ getIEigenValues()

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

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getIEigenValues(), and bpp::InMixedSubstitutionModel::getIEigenValues().

◆ getInitValue()

virtual double bpp::BranchModelInterface::getInitValue ( size_t  i,
int  state 
) const
pure virtualinherited

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();

Implemented in bpp::TransitionFromTransitionModel, bpp::RE08, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MultinomialFromTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, and bpp::AbstractTransitionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::getInitValue(), bpp::InMixedSubstitutionModel::getInitValue(), bpp::MultinomialFromTransitionModel::getInitValue(), bpp::OneChangeRegisterTransitionModel::getInitValue(), bpp::OneChangeTransitionModel::getInitValue(), and bpp::TransitionFromTransitionModel::getInitValue().

◆ getModelStates() [1/2]

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

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

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

Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractWrappedModel, and bpp::AbstractTransitionModel.

◆ getModelStates() [2/2]

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

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

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

Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractWrappedModel, and bpp::AbstractTransitionModel.

Referenced by bpp::SubstitutionModelSet::getModelStates(), and bpp::AbstractWrappedModel::getModelStates().

◆ getName()

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

Get the name of the model.

Returns
The name of this model.

Implemented in bpp::WordSubstitutionModel, bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::RE08, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LLG08_UL3, bpp::LLG08_UL3::EmbeddedModel, bpp::LLG08_UL2, bpp::LLG08_UL2::EmbeddedModel, bpp::LLG08_EX3, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_EX2, bpp::LLG08_EX2::EmbeddedModel, bpp::LLG08_EHO, bpp::LLG08_EHO::EmbeddedModel, bpp::LGL08_CAT, bpp::LGL08_CAT::EmbeddedModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::Coala, bpp::POMO, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::YpR_Gen, bpp::YpR_Sym, bpp::TN93, bpp::T92, bpp::SSR, bpp::RN95s, bpp::RN95, bpp::L95, bpp::K80, bpp::JCnuc, bpp::GTR, bpp::gBGC, bpp::F81, bpp::MultinomialFromTransitionModel, bpp::MixtureOfTransitionModels, bpp::MixtureOfATransitionModel, bpp::KroneckerWordSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::FromMixtureSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, bpp::YNGP_M9, bpp::YNGP_M8, bpp::YNGP_M7, bpp::YNGP_M3, bpp::YNGP_M2, bpp::YNGP_M10, bpp::YNGP_M1, bpp::YN98, bpp::TripletSubstitutionModel, bpp::SENCA, bpp::RELAX, bpp::MG94, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::GY94, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::DFP07, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AnonymousSubstitutionModel, bpp::AbstractWrappedModel, bpp::TwoParameterBinarySubstitutionModel, bpp::LG10_EX_EHO, bpp::LG10_EX_EHO::EmbeddedModel, bpp::HKY85, bpp::F84, bpp::CodonDistanceSubstitutionModel, and bpp::BinarySubstitutionModel.

Referenced by bpp::YpR::checkModel(), bpp::TransitionMatrixFromModel::compute(), bpp::AbstractWrappedModel::getName(), bpp::FromMixtureSubstitutionModel::getName(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::BppOSubstitutionModelFormat::initialize_(), bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(), bpp::MixtureOfATransitionModel::model(), bpp::LegacyPhylogeneticsApplicationTools::setSubstitutionModelParametersInitialValuesWithAliases(), bpp::ModelPath::toString(), and bpp::BppOSubstitutionModelFormat::write().

◆ getNumberOfStates()

virtual size_t bpp::BranchModelInterface::getNumberOfStates ( ) const
pure virtualinherited

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.

Implemented in bpp::RegisterRatesSubstitutionModel, bpp::RE08Codon, bpp::RE08Protein, bpp::RE08Nucleotide, bpp::YpR, bpp::gBGC, bpp::MarkovModulatedSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::AbstractWrappedModel, bpp::AbstractTransitionModel, bpp::TwoParameterBinarySubstitutionModel, and bpp::BinarySubstitutionModel.

Referenced by bpp::NonHomogeneousSubstitutionProcess::addModel(), bpp::SubstitutionModelSet::addModel(), bpp::AbstractWrappedModel::getNumberOfStates(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), and bpp::NonHomogeneousSubstitutionProcess::setModel().

◆ getPij_t()

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

Implemented in bpp::AbstractTransitionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), bpp::AbstractTotallyWrappedTransitionModel::getPij_t(), bpp::InMixedSubstitutionModel::getPij_t(), bpp::OneChangeRegisterTransitionModel::getPij_t(), and bpp::AbstractLkTransitionModel::Lik_t().

◆ getRate()

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

Get the rate.

Implemented in bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MultinomialFromTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::AbstractTotallyWrappedTransitionModel, and bpp::AbstractTransitionModel.

Referenced by bpp::AbstractFromSubstitutionModelTransitionModel::addRateParameter(), bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::dPij_dt(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), bpp::OneChangeRegisterTransitionModel::getPij_t(), bpp::AbstractTotallyWrappedTransitionModel::getRate(), bpp::InMixedSubstitutionModel::getRate(), bpp::MultinomialFromTransitionModel::getRate(), bpp::OneChangeRegisterTransitionModel::getRate(), bpp::OneChangeTransitionModel::getRate(), bpp::RegisterRatesSubstitutionModel::getRate(), and bpp::TransitionFromTransitionModel::getRate().

◆ getRowLeftEigenVectors()

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

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getRowLeftEigenVectors(), and bpp::InMixedSubstitutionModel::getRowLeftEigenVectors().

◆ getScale()

virtual double bpp::SubstitutionModelInterface::getScale ( ) const
pure virtual

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::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getScale(), and bpp::InMixedSubstitutionModel::getScale().

◆ getStateMap()

virtual std::shared_ptr<const StateMapInterface> bpp::BranchModelInterface::getStateMap ( ) const
pure virtualinherited
Returns
A shared_ptr to the mapping of model states with alphabet states.

Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractWrappedModel, and bpp::AbstractTransitionModel.

Referenced by bpp::SubstitutionModelSet::getStateMap(), bpp::SubstitutionProcessCollectionMember::getStateMap(), and bpp::AbstractWrappedModel::getStateMap().

◆ isDiagonalizable()

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

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::isDiagonalizable(), and bpp::InMixedSubstitutionModel::isDiagonalizable().

◆ isNonSingular()

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

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::isNonSingular(), and bpp::InMixedSubstitutionModel::isNonSingular().

◆ isScalable()

virtual bool bpp::SubstitutionModelInterface::isScalable ( ) const
pure virtual

returns if model is scalable

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::isScalable(), and bpp::InMixedSubstitutionModel::isScalable().

◆ Lik_t()

virtual const Eigen::VectorXd& bpp::TransitionModelInterface::Lik_t ( const Eigen::VectorXd &  values,
double  t 
) const
pure virtualinherited

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::BranchModelInterface.

Implemented in bpp::AbstractLkTransitionModel.

◆ normalize()

virtual void bpp::SubstitutionModelInterface::normalize ( )
pure virtual

Normalize the generator.

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::normalize(), and bpp::InMixedSubstitutionModel::normalize().

◆ Pij_t()

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

Implemented in bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::AbstractTotallyWrappedTransitionModel::Pij_t(), bpp::InMixedSubstitutionModel::Pij_t(), and bpp::OneChangeRegisterTransitionModel::Pij_t().

◆ Qij()

virtual double bpp::SubstitutionModelInterface::Qij ( size_t  i,
size_t  j 
) const
pure virtual

A method for computing all necessary matrices.

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

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::YpR::checkModel(), bpp::DFP07::DFP07(), bpp::AbstractTotallyWrappedSubstitutionModel::Qij(), bpp::InMixedSubstitutionModel::Qij(), bpp::RELAX::RELAX(), bpp::DFP07::updateMatrices_(), bpp::RELAX::updateMatrices_(), bpp::YNGP_M1::updateMatrices_(), bpp::YNGP_M10::updateMatrices_(), bpp::YNGP_M2::updateMatrices_(), bpp::YNGP_M3::updateMatrices_(), bpp::YNGP_M7::updateMatrices_(), bpp::YNGP_M8::updateMatrices_(), bpp::YNGP_M9::updateMatrices_(), bpp::YNGP_M1::YNGP_M1(), bpp::YNGP_M10::YNGP_M10(), bpp::YNGP_M2::YNGP_M2(), bpp::YNGP_M3::YNGP_M3(), bpp::YNGP_M7::YNGP_M7(), bpp::YNGP_M8::YNGP_M8(), and bpp::YNGP_M9::YNGP_M9().

◆ setDiagonal()

virtual void bpp::SubstitutionModelInterface::setDiagonal ( )
pure virtual

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

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::setDiagonal(), and bpp::InMixedSubstitutionModel::setDiagonal().

◆ setFreq()

virtual void bpp::TransitionModelInterface::setFreq ( std::map< int, double > &  frequencies)
pure virtualinherited

Set equilibrium frequencies.

Parameters
frequenciesThe map of the frequencies to use.

Implemented in bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::RE08Codon, bpp::RE08, bpp::POMO, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::YN98, bpp::SENCA, bpp::MG94, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractBiblioTransitionModel, bpp::TN93, bpp::T92, bpp::GTR, bpp::F81, bpp::AbstractTransitionModel, bpp::HKY85, bpp::BinarySubstitutionModel, bpp::AbstractWordSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, bpp::SSR, bpp::RN95s, bpp::RN95, bpp::L95, bpp::MixtureOfTransitionModels, bpp::MixtureOfATransitionModel, and bpp::F84.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::setFreq(), bpp::InMixedSubstitutionModel::setFreq(), bpp::RE08Codon::setFreq(), bpp::MultinomialFromTransitionModel::setFreq(), bpp::TransitionFromTransitionModel::setFreq(), bpp::OneChangeRegisterTransitionModel::setFreq(), bpp::OneChangeTransitionModel::setFreq(), and bpp::AbstractTotallyWrappedTransitionModel::setFreqFromData().

◆ setFreqFromData()

virtual void bpp::TransitionModelInterface::setFreqFromData ( const SequenceDataInterface &  data,
double  pseudoCount = 0 
)
pure virtualinherited

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

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

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

Implemented in bpp::RE08, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::Coala, bpp::K80, bpp::JCnuc, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::AbstractBiblioTransitionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, and bpp::AbstractMixedTransitionModel.

Referenced by bpp::TransitionFromTransitionModel::setFreqFromData(), bpp::OneChangeRegisterTransitionModel::setFreqFromData(), bpp::OneChangeTransitionModel::setFreqFromData(), bpp::MultinomialFromTransitionModel::setFreqFromData(), and bpp::InMixedSubstitutionModel::setFreqFromData().

◆ setRate()

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

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

Parameters
ratemust be positive.

Implemented in bpp::TS98, bpp::TransitionFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::MultinomialFromTransitionModel, bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::G2001, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, and bpp::AbstractMixedTransitionModel.

Referenced by bpp::AbstractBiblioTransitionModel::fireParameterChanged(), bpp::AbstractTotallyWrappedTransitionModel::setRate(), bpp::InMixedSubstitutionModel::setRate(), bpp::MultinomialFromTransitionModel::setRate(), bpp::OneChangeRegisterTransitionModel::setRate(), bpp::OneChangeTransitionModel::setRate(), bpp::RegisterRatesSubstitutionModel::setRate(), and bpp::TransitionFromTransitionModel::setRate().

◆ setScalable()

virtual void bpp::SubstitutionModelInterface::setScalable ( bool  scalable)
pure virtual

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

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::setScalable(), and bpp::InMixedSubstitutionModel::setScalable().

◆ setScale()

virtual void bpp::SubstitutionModelInterface::setScale ( double  scale)
pure virtual

Multiplies the current generator by the given scale.

Parameters
scalethe scale by which the generator is multiplied.

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::setScale(), and bpp::InMixedSubstitutionModel::setScale().

◆ Sij()

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

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

Implemented in bpp::MarkovModulatedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::Sij(), and bpp::InMixedSubstitutionModel::Sij().

◆ stateMap()

virtual const StateMapInterface& bpp::BranchModelInterface::stateMap ( ) const
pure virtualinherited
Returns
The mapping of model states with alphabet states.

Implemented in bpp::RegisterRatesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractWrappedModel, and bpp::AbstractTransitionModel.

Referenced by bpp::SubstitutionModelSet::stateMap(), bpp::SubstitutionProcessCollectionMember::stateMap(), and bpp::AbstractWrappedModel::stateMap().

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