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

Partial implementation for Mixed Transition models, defined as a mixture of "simple" substitution models. Each model has a specific probability and rate, with the constraint that the expectation (on the distribution of the models) of the rate of all the models equals one. More...

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

+ Inheritance diagram for bpp::AbstractMixedTransitionModel:
+ Collaboration diagram for bpp::AbstractMixedTransitionModel:

Public Member Functions

 AbstractMixedTransitionModel (std::shared_ptr< const Alphabet >, std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix)
 
 AbstractMixedTransitionModel (const AbstractMixedTransitionModel &)
 
AbstractMixedTransitionModel & operator= (const AbstractMixedTransitionModel &)
 
virtual AbstractMixedTransitionModel * clone () const override=0
 
virtual size_t getNumberOfModels () const override
 returns the number of models in the mixture More...
 
const TransitionModelInterface & nModel (size_t i) const override
 Returns a specific model from the mixture. More...
 
std::shared_ptr< const TransitionModelInterface > getNModel (size_t i) const override
 
double getNRate (size_t i) const override
 Returns the rate of a specific model from the mixture. More...
 
virtual void setRate (double rate) override
 Set the rate of the model and the submodels. More...
 
virtual void setVRates (const Vdouble &vd) override
 Sets the rates of the submodels to be proportional to a given vector, with the constraint that the mean rate of the mixture equals rate_. More...
 
virtual void normalizeVRates () override
 Normalizes the rates of the submodels so that the mean rate of the mixture equals rate_. More...
 
const std::vector< double > & getVRates () const override
 Returns the vector of all the rates of the mixture. More...
 
virtual double getNProbability (size_t i) const override
 Returns the probability of a specific model from the mixture. More...
 
virtual const std::vector< double > & getProbabilities () const override
 Returns the vector of probabilities. More...
 
virtual void setNProbability (size_t i, double prob) override
 Sets the probability of a specific model from the mixture. More...
 
virtual const Matrix< double > & getPij_t (double t) const override
 From TransitionModel interface. More...
 
virtual const Matrix< double > & getdPij_dt (double t) const override
 
virtual const Matrix< double > & getd2Pij_dt2 (double t) const override
 
bool computeFrequencies () const override
 
void computeFrequencies (bool yn) override
 
void setFreq (std::map< int, double > &frequ) override
 Set equilibrium frequencies. More...
 
void setFreqFromData (const SequenceDataInterface &data, double pseudoCount) override
 Set equilibrium frequencies equal to the frequencies estimated from the data. More...
 
virtual const TransitionModelInterface & model (const std::string &name) const =0
 Access the submodel with the given name. More...
 
virtual Vuint getSubmodelNumbers (const std::string &desc) const =0
 Returns the vector of numbers of the submodels in the mixture that match a description. 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 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 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 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
 
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
 
virtual double Pij_t (size_t i, size_t j, double t) const override
 
virtual double dPij_dt (size_t i, size_t j, double t) const override
 
virtual double d2Pij_dt2 (size_t i, size_t j, double t) const override
 
double getInitValue (size_t i, int state) const override
 
const FrequencySetInterface & frequencySet () const override
 
virtual void fireParameterChanged (const ParameterList &parameters) override
 Tells the model that a parameter value has changed. More...
 
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...
 
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
 
size_t getNumberOfIndependentParameters () const
 
void aliasParameters (const std::string &p1, const std::string &p2)
 
void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
 
void unaliasParameters (const std::string &p1, const std::string &p2)
 
const ParameterList & getIndependentParameters () const
 
virtual std::vector< std::string > getAlias (const std::string &name) const
 
virtual std::map< std::string, std::string > getAliases () const
 
bool hasParameter (const std::string &name) const override
 
const ParameterList & getParameters () const override
 
const Parameter & parameter (const std::string &name) const override
 
double getParameterValue (const std::string &name) const override
 
void setAllParametersValues (const ParameterList &parameters) override
 
void setParameterValue (const std::string &name, double value) override
 
void setParametersValues (const ParameterList &parameters) override
 
bool matchParametersValues (const ParameterList &parameters) override
 
void removeConstraint (const std::string &name) override
 
void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
 
size_t getNumberOfParameters () const override
 
void setNamespace (const std::string &prefix)
 
std::string getNamespace () const override
 
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

TransitionModelInterface & nModel_ (size_t i) override
 
virtual Vdouble & getFrequencies_ ()=0
 
virtual ParameterList & getParameters_ ()=0
 
virtual void updateMatrices_ ()=0
 Diagonalize the $Q$ matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...
 
Vdouble & getFrequencies_ () override
 
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

std::vector< std::shared_ptr< TransitionModelInterface > > modelsContainer_
 vector of pointers to TransitionModels. More...
 
std::vector< double > vProbas_
 vector of the probabilities of the models More...
 
std::vector< double > vRates_
 vector of the rates of the models. 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

Eigen::VectorXd lik_
 
ParameterList independentParameters_
 
std::map< std::string, std::shared_ptr< AliasParameterListener > > aliasListenersRegister_
 
ParameterList parameters_
 
std::string prefix_
 

Detailed Description

Partial implementation for Mixed Transition models, defined as a mixture of "simple" substitution models. Each model has a specific probability and rate, with the constraint that the expectation (on the distribution of the models) of the rate of all the models equals one.

In this kind of model, there is no generator.

Author
Laurent Guéguen

Definition at line 30 of file AbstractMixedTransitionModel.h.

Constructor & Destructor Documentation

◆ AbstractMixedTransitionModel() [1/2]

AbstractMixedTransitionModel::AbstractMixedTransitionModel ( std::shared_ptr< const Alphabet >  alpha,
std::shared_ptr< const StateMapInterface >  stateMap,
const std::string &  prefix 
)

Definition at line 13 of file AbstractMixedTransitionModel.cpp.

◆ AbstractMixedTransitionModel() [2/2]

AbstractMixedTransitionModel::AbstractMixedTransitionModel ( const AbstractMixedTransitionModel &  msm)

Definition at line 24 of file AbstractMixedTransitionModel.cpp.

References modelsContainer_, vProbas_, and vRates_.

Member Function Documentation

◆ addRateParameter() [1/2]

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_.

◆ addRateParameter() [2/2]

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() [1/2]

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().

◆ alphabet() [2/2]

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()

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

Implements bpp::MixedTransitionModelInterface.

Implemented in bpp::MixtureOfTransitionModels, bpp::MixtureOfSubstitutionModels, bpp::MixtureOfATransitionModel, and bpp::MixtureOfASubstitutionModel.

◆ computeFrequencies() [1/2]

bool bpp::AbstractMixedTransitionModel::computeFrequencies ( ) const
inlineoverridevirtual
Returns
Says if equilibrium frequencies should be computed (all models are likewise, may be refined)

Implements bpp::TransitionModelInterface.

Definition at line 176 of file AbstractMixedTransitionModel.h.

References modelsContainer_.

◆ computeFrequencies() [2/2]

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

Implements bpp::TransitionModelInterface.

Definition at line 184 of file AbstractMixedTransitionModel.h.

References modelsContainer_.

◆ d2Lik_dt2() [1/2]

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

Implements bpp::BranchModelInterface.

Implemented in bpp::AbstractLkTransitionModel.

◆ d2Lik_dt2() [2/2]

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() [1/2]

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().

◆ d2Pij_dt2() [2/2]

virtual double bpp::AbstractTransitionModel::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const
inlineoverridevirtualinherited
Returns
The second order derivative of the probability of change from state i to state j with respect to time t, at time t.
See also
getd2Pij_dt2(), getStates()

Implements bpp::TransitionModelInterface.

Reimplemented in 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.

Definition at line 199 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::getd2Pij_dt2().

Referenced by bpp::JCprot::d2Pij_dt2().

◆ dLik_dt() [1/2]

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

Implements bpp::BranchModelInterface.

Implemented in bpp::AbstractLkTransitionModel.

◆ dLik_dt() [2/2]

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() [1/2]

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().

◆ dPij_dt() [2/2]

virtual double bpp::AbstractTransitionModel::dPij_dt ( size_t  i,
size_t  j,
double  t 
) const
inlineoverridevirtualinherited
Returns
The first order derivative of the probability of change from state i to state j with respect to time t, at time t.
See also
getdPij_dt(), getStates()

Implements bpp::TransitionModelInterface.

Reimplemented in 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.

Definition at line 198 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::getdPij_dt().

Referenced by bpp::JCprot::dPij_dt().

◆ fireParameterChanged()

virtual void bpp::AbstractTransitionModel::fireParameterChanged ( const ParameterList &  parameters)
inlineoverridevirtualinherited

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::RegisterRatesSubstitutionModel, bpp::RE08, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::POMO, bpp::YpR, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::SENCA, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::CodonDistanceSubstitutionModel, and bpp::gBGC.

Definition at line 217 of file AbstractSubstitutionModel.h.

References bpp::AbstractParameterAliasable::fireParameterChanged(), bpp::AbstractParameterAliasable::getNamespace(), bpp::ParameterList::getParameterValue(), bpp::ParameterList::hasParameter(), bpp::AbstractTransitionModel::rate_, bpp::ParameterList::size(), and bpp::AbstractTransitionModel::updateMatrices_().

Referenced by bpp::gBGC::fireParameterChanged(), bpp::CodonDistanceSubstitutionModel::fireParameterChanged(), bpp::CodonAdHocSubstitutionModel::fireParameterChanged(), bpp::CodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::fireParameterChanged(), bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), bpp::KroneckerCodonDistanceSubstitutionModel::fireParameterChanged(), bpp::SENCA::fireParameterChanged(), bpp::D1WalkSubstitutionModel::fireParameterChanged(), bpp::EquiprobableSubstitutionModel::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::JCprot::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::LG08::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), and bpp::WAG01::fireParameterChanged().

◆ freq() [1/2]

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().

◆ freq() [2/2]

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() [1/2]

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().

◆ frequencySet() [2/2]

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.

◆ getAlphabet() [1/2]

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_().

◆ getAlphabet() [2/2]

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 bpp::RE08::getInitValue().

◆ getAlphabetStateAsChar() [1/2]

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().

◆ getAlphabetStateAsChar() [2/2]

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() [1/2]

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().

◆ getAlphabetStateAsInt() [2/2]

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() [1/2]

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().

◆ getAlphabetStates() [2/2]

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().

◆ getd2Pij_dt2()

const Matrix< double > & AbstractMixedTransitionModel::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()

Implements bpp::AbstractTransitionModel.

Definition at line 110 of file AbstractMixedTransitionModel.cpp.

References bpp::AbstractTransitionModel::d2pijt_, bpp::AbstractTransitionModel::getNumberOfStates(), modelsContainer_, and vProbas_.

◆ getdPij_dt()

const Matrix< double > & AbstractMixedTransitionModel::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()

Implements bpp::AbstractTransitionModel.

Definition at line 84 of file AbstractMixedTransitionModel.cpp.

References bpp::AbstractTransitionModel::dpijt_, bpp::AbstractTransitionModel::getNumberOfStates(), modelsContainer_, and vProbas_.

◆ getFrequencies() [1/2]

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() [2/2]

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_() [1/2]

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().

◆ getFrequencies_() [2/2]

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_().

◆ getInitValue() [1/2]

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().

◆ getInitValue() [2/2]

double AbstractTransitionModel::getInitValue ( size_t  i,
int  state 
) const
overridevirtualinherited

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();

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RE08.

Definition at line 70 of file AbstractSubstitutionModel.cpp.

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

◆ getModelStates() [1/4]

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() [2/4]

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() [3/4]

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().

◆ getModelStates() [4/4]

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()

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().

◆ getNModel()

std::shared_ptr<const TransitionModelInterface> bpp::AbstractMixedTransitionModel::getNModel ( size_t  i) const
inlineoverridevirtual

Implements bpp::MixedTransitionModelInterface.

Definition at line 91 of file AbstractMixedTransitionModel.h.

References modelsContainer_.

Referenced by bpp::MixtureOfTransitionModels::getSubmodelNumbers().

◆ getNProbability()

virtual double bpp::AbstractMixedTransitionModel::getNProbability ( size_t  i) const
inlineoverridevirtual

Returns the probability of a specific model from the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 138 of file AbstractMixedTransitionModel.h.

References vProbas_.

◆ getNRate()

double bpp::AbstractMixedTransitionModel::getNRate ( size_t  i) const
inlineoverridevirtual

Returns the rate of a specific model from the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 99 of file AbstractMixedTransitionModel.h.

References vRates_.

◆ getNumberOfModels()

virtual size_t bpp::AbstractMixedTransitionModel::getNumberOfModels ( ) const
inlineoverridevirtual

returns the number of models in the mixture

Implements bpp::MixedTransitionModelInterface.

Definition at line 78 of file AbstractMixedTransitionModel.h.

References modelsContainer_.

Referenced by bpp::MixtureOfTransitionModels::getSubmodelNumbers(), bpp::MixtureOfATransitionModel::model(), and bpp::MixtureOfTransitionModels::model().

◆ getNumberOfStates() [1/2]

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().

◆ getNumberOfStates() [2/2]

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(), getd2Pij_dt2(), bpp::WordSubstitutionModel::getdPij_dt(), getdPij_dt(), bpp::RE08Nucleotide::getNumberOfStates(), bpp::RE08Protein::getNumberOfStates(), bpp::RE08Codon::getNumberOfStates(), bpp::WordSubstitutionModel::getPij_t(), getPij_t(), bpp::AbstractWordSubstitutionModel::setFreq(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::MixtureOfATransitionModel::updateMatrices_(), and bpp::MixtureOfTransitionModels::updateMatrices_().

◆ getPij_t()

const Matrix< double > & AbstractMixedTransitionModel::getPij_t ( double  t) const
overridevirtual

From TransitionModel interface.

Implements bpp::AbstractTransitionModel.

Definition at line 58 of file AbstractMixedTransitionModel.cpp.

References bpp::AbstractTransitionModel::getNumberOfStates(), modelsContainer_, bpp::AbstractTransitionModel::pijt_, and vProbas_.

◆ getProbabilities()

virtual const std::vector<double>& bpp::AbstractMixedTransitionModel::getProbabilities ( ) const
inlineoverridevirtual

Returns the vector of probabilities.

Implements bpp::MixedTransitionModelInterface.

Definition at line 147 of file AbstractMixedTransitionModel.h.

References vProbas_.

◆ getRate() [1/2]

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().

◆ getRate() [2/2]

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_.

◆ getStateMap() [1/2]

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().

◆ getStateMap() [2/2]

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().

◆ getSubmodelNumbers()

virtual Vuint bpp::MixedTransitionModelInterface::getSubmodelNumbers ( const std::string &  desc) const
pure virtualinherited

Returns the vector of numbers of the submodels in the mixture that match a description.

Implemented in bpp::MixtureOfTransitionModels, bpp::MixtureOfATransitionModel, and bpp::AbstractBiblioMixedTransitionModel.

Referenced by bpp::AbstractBiblioMixedTransitionModel::getSubmodelNumbers().

◆ getVRates()

const std::vector<double>& bpp::AbstractMixedTransitionModel::getVRates ( ) const
inlineoverridevirtual

Returns the vector of all the rates of the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 129 of file AbstractMixedTransitionModel.h.

References vRates_.

◆ Lik_t() [1/2]

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.

◆ Lik_t() [2/2]

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_.

◆ model()

virtual const TransitionModelInterface& bpp::MixedTransitionModelInterface::model ( const std::string &  name) const
pure virtualinherited

Access the submodel with the given name.

Exceptions
NullPointerExceptionif no model with the given name is found.

Implemented in bpp::MixtureOfTransitionModels, bpp::MixtureOfATransitionModel, and bpp::AbstractBiblioMixedTransitionModel.

Referenced by bpp::FromMixtureSubstitutionModel::FromMixtureSubstitutionModel(), bpp::AbstractBiblioMixedTransitionModel::model(), and operator=().

◆ nModel()

const TransitionModelInterface& bpp::AbstractMixedTransitionModel::nModel ( size_t  i) const
inlineoverridevirtual

Returns a specific model from the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 86 of file AbstractMixedTransitionModel.h.

References modelsContainer_.

Referenced by bpp::MixtureOfATransitionModel::model(), bpp::MixtureOfTransitionModels::model(), and bpp::MixtureOfASubstitutionModel::subNModel().

◆ nModel_()

TransitionModelInterface& bpp::AbstractMixedTransitionModel::nModel_ ( size_t  i)
inlineoverrideprotectedvirtual

Implements bpp::MixedTransitionModelInterface.

Definition at line 208 of file AbstractMixedTransitionModel.h.

References modelsContainer_.

◆ normalizeVRates()

void AbstractMixedTransitionModel::normalizeVRates ( )
overridevirtual

Normalizes the rates of the submodels so that the mean rate of the mixture equals rate_.

Implements bpp::MixedTransitionModelInterface.

Definition at line 169 of file AbstractMixedTransitionModel.cpp.

References modelsContainer_, bpp::AbstractTransitionModel::rate_, vProbas_, and vRates_.

Referenced by setVRates().

◆ operator=()

AbstractMixedTransitionModel & AbstractMixedTransitionModel::operator= ( const AbstractMixedTransitionModel &  model)

Definition at line 39 of file AbstractMixedTransitionModel.cpp.

References bpp::TransitionModelInterface::clone(), bpp::MixedTransitionModelInterface::model(), modelsContainer_, bpp::AbstractTransitionModel::operator=(), vProbas_, and vRates_.

Referenced by bpp::MixtureOfATransitionModel::operator=(), and bpp::MixtureOfTransitionModels::operator=().

◆ Pij_t() [1/2]

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().

◆ Pij_t() [2/2]

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

Implements bpp::TransitionModelInterface.

Reimplemented in 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.

Definition at line 197 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::getPij_t().

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

◆ setFreq()

void bpp::AbstractMixedTransitionModel::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::MixtureOfTransitionModels, and bpp::MixtureOfATransitionModel.

Definition at line 192 of file AbstractMixedTransitionModel.h.

References modelsContainer_.

Referenced by setFreqFromData().

◆ setFreqFromData()

void bpp::AbstractMixedTransitionModel::setFreqFromData ( const SequenceDataInterface &  data,
double  pseudoCount 
)
inlineoverridevirtual

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

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

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

Implements bpp::TransitionModelInterface.

Definition at line 200 of file AbstractMixedTransitionModel.h.

References bpp::SequenceContainerTools::getFrequencies(), and setFreq().

◆ setNProbability()

virtual void bpp::AbstractMixedTransitionModel::setNProbability ( size_t  i,
double  prob 
)
inlineoverridevirtual

Sets the probability of a specific model from the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 155 of file AbstractMixedTransitionModel.h.

References vProbas_.

◆ setRate()

void AbstractMixedTransitionModel::setRate ( double  rate)
overridevirtual

Set the rate of the model and the submodels.

Parameters
ratemust be positive.

Reimplemented from bpp::AbstractTransitionModel.

Definition at line 136 of file AbstractMixedTransitionModel.cpp.

References modelsContainer_, bpp::AbstractTransitionModel::rate_, bpp::AbstractTransitionModel::setRate(), vProbas_, and vRates_.

◆ setVerboseLevel()

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

Definition at line 239 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::verboseLevel_.

◆ setVRates()

void AbstractMixedTransitionModel::setVRates ( const Vdouble &  vd)
overridevirtual

Sets the rates of the submodels to be proportional to a given vector, with the constraint that the mean rate of the mixture equals rate_.

Parameters
vda vector of positive values such that the rates of the respective submodels are in the same proportions (ie this vector does not need to be normalized).

Implements bpp::MixedTransitionModelInterface.

Reimplemented in bpp::MixtureOfTransitionModels.

Definition at line 156 of file AbstractMixedTransitionModel.cpp.

References modelsContainer_, normalizeVRates(), and vRates_.

Referenced by bpp::MixtureOfTransitionModels::setVRates(), and bpp::MixtureOfASubstitutionModel::updateMatrices_().

◆ stateMap() [1/2]

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().

◆ stateMap() [2/2]

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_()

virtual void bpp::AbstractTransitionModel::updateMatrices_ ( )
protectedpure virtualinherited

Diagonalize the $Q$ matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices.

The generator_ matrix and freq_ vector must be initialized.

Eigen values and vectors are computed from the generator and assigned to the eigenValues_ for the real part, iEigenValues_ for the imaginary part, rightEigenVectors_ and leftEigenVectors_ variables. isDiagonalizable_ checks if the generator_ is diagonalizable in R.

The optional rate parameter is not taken into account in this method to prevent unnecessary computation.

!! Here there is no normalization of the generator.

Implemented in bpp::WordSubstitutionModel, bpp::RegisterRatesSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::Coala, bpp::POMO, bpp::YpR_Gen, bpp::YpR_Sym, bpp::YpR, bpp::TN93, bpp::T92, bpp::SSR, bpp::RN95s, bpp::RN95, bpp::L95, bpp::K80, bpp::JCnuc, bpp::GTR, bpp::gBGC, bpp::F81, bpp::MixtureOfTransitionModels, bpp::MixtureOfATransitionModel, bpp::MixtureOfASubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::AbstractCodonSubstitutionModel, bpp::AbstractReversibleSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, bpp::BinarySubstitutionModel, bpp::AbstractWordSubstitutionModel, and bpp::AbstractSubstitutionModel.

Referenced by bpp::AbstractTransitionModel::fireParameterChanged(), and bpp::AbstractTransitionModel::setFreq().

◆ 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(), bpp::RE08::getInitValue(), bpp::AbstractNucleotideSubstitutionModel::getNucleicAlphabet(), bpp::AbstractReversibleNucleotideSubstitutionModel::getNucleicAlphabet(), bpp::RE08Nucleotide::getNucleicAlphabet(), bpp::AbstractProteinSubstitutionModel::getProteicAlphabet(), bpp::AbstractReversibleProteinSubstitutionModel::getProteicAlphabet(), bpp::RE08Protein::getProteicAlphabet(), and bpp::AbstractWordSubstitutionModel::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 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 getdPij_dt().

◆ 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(), bpp::RE08::d2Pij_dt2(), bpp::RE08::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(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::AbstractTransitionModel::getFrequencies(), bpp::AbstractTransitionModel::getFrequencies_(), bpp::RE08::getPij_t(), bpp::AbstractSubstitutionModel::getScale(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::RE08::Pij_t(), bpp::RE08::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_(), bpp::RE08::updateMatrices_(), bpp::YpR::updateMatrices_(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().

◆ 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().

◆ modelsContainer_

std::vector< std::shared_ptr<TransitionModelInterface> > bpp::AbstractMixedTransitionModel::modelsContainer_
protected

vector of pointers to TransitionModels.

Beware: these TransitionModels are owned by the object, so will be deleted at destruction

Definition at line 41 of file AbstractMixedTransitionModel.h.

Referenced by AbstractMixedTransitionModel(), computeFrequencies(), getd2Pij_dt2(), getdPij_dt(), getNModel(), getNumberOfModels(), getPij_t(), bpp::MixtureOfATransitionModel::getSubmodelNumbers(), bpp::MixtureOfATransitionModel::MixtureOfATransitionModel(), bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(), bpp::MixtureOfTransitionModels::MixtureOfTransitionModels(), nModel(), nModel_(), normalizeVRates(), operator=(), bpp::MixtureOfATransitionModel::setFreq(), bpp::MixtureOfTransitionModels::setFreq(), setFreq(), setRate(), setVRates(), bpp::MixtureOfTransitionModels::setVRates(), bpp::MixtureOfASubstitutionModel::updateMatrices_(), bpp::MixtureOfATransitionModel::updateMatrices_(), and bpp::MixtureOfTransitionModels::updateMatrices_().

◆ 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 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(), 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(), setRate(), bpp::AbstractTransitionModel::setRate(), bpp::BinarySubstitutionModel::updateMatrices_(), bpp::TwoParameterBinarySubstitutionModel::updateMatrices_(), and bpp::MixtureOfTransitionModels::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(), bpp::RE08::d2Pij_dt2(), bpp::EquiprobableSubstitutionModel::dPij_dt(), bpp::RE08::dPij_dt(), bpp::EquiprobableSubstitutionModel::getd2Pij_dt2(), bpp::JCnuc::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::RE08::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::EquiprobableSubstitutionModel::getdPij_dt(), bpp::JCnuc::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::RE08::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractTransitionModel::getInitValue(), bpp::RE08::getInitValue(), bpp::EquiprobableSubstitutionModel::getPij_t(), bpp::JCnuc::getPij_t(), bpp::JCprot::getPij_t(), bpp::RE08::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::EquiprobableSubstitutionModel::Pij_t(), bpp::RE08::Pij_t(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::setDiagonal(), bpp::T92::T92(), bpp::TN93::TN93(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::EquiprobableSubstitutionModel::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::RE08::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().

◆ 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().

◆ vProbas_

std::vector<double> bpp::AbstractMixedTransitionModel::vProbas_
protected

vector of the probabilities of the models

Definition at line 46 of file AbstractMixedTransitionModel.h.

Referenced by AbstractMixedTransitionModel(), getd2Pij_dt2(), getdPij_dt(), getNProbability(), getPij_t(), getProbabilities(), bpp::MixtureOfATransitionModel::MixtureOfATransitionModel(), bpp::MixtureOfTransitionModels::MixtureOfTransitionModels(), normalizeVRates(), operator=(), setNProbability(), setRate(), bpp::MixtureOfATransitionModel::updateMatrices_(), and bpp::MixtureOfTransitionModels::updateMatrices_().

◆ vRates_

std::vector<double> bpp::AbstractMixedTransitionModel::vRates_
protected

vector of the rates of the models.

For the computation of the transition probabilities, the rates are included in the submodels while updating the mixture, so there is no need to multiply here the transition times with the rates.

The mean (on the distribution of the models) of the elements of this vector equals the overall rate of the mixture model, that is rate_;

Definition at line 60 of file AbstractMixedTransitionModel.h.

Referenced by AbstractMixedTransitionModel(), getNRate(), getVRates(), bpp::MixtureOfATransitionModel::MixtureOfATransitionModel(), bpp::MixtureOfTransitionModels::MixtureOfTransitionModels(), normalizeVRates(), operator=(), setRate(), setVRates(), bpp::MixtureOfTransitionModels::setVRates(), and bpp::MixtureOfTransitionModels::updateMatrices_().

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