bpp-phyl3  3.0.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::YNGP_M1 Class Referenceabstract

The Yang et al (2000) M1 substitution model for codons, with the more realistic modification in Wong & al (2004). More...

#include <Bpp/Phyl/Model/Codon/YNGP_M1.h>

+ Inheritance diagram for bpp::YNGP_M1:
+ Collaboration diagram for bpp::YNGP_M1:

Public Member Functions

 YNGP_M1 (std::shared_ptr< const GeneticCode > gc, std::unique_ptr< CodonFrequencySetInterface > codonFreqs)
 
YNGP_M1 * clone () const override
 
std::string getName () const override
 Get the name of the model. More...
 
const TransitionModelInterface & nModel (size_t i) const override
 Returns the submodel from the mixture. More...
 
std::shared_ptr< const TransitionModelInterface > getNModel (size_t i) const override
 
double getNProbability (size_t i) const override
 Returns the probability of a specific model from the mixture. More...
 
const std::vector< double > & getProbabilities () const override
 Returns the vector of the probabilities of the submodels of the mixture. More...
 
void setNProbability (size_t i, double prob) override
 Sets the probabilities of the submodels of the mixture. More...
 
size_t getNumberOfModels () const override
 Returns the number of submodels. More...
 
void setVRates (const Vdouble &vd) override
 sets the rates of the submodels. More...
 
void normalizeVRates () override
 normalizes the rates of the submodels. More...
 
const std::vector< double > & getVRates () const override
 Returns the vector of all the rates of the mixture. More...
 
double getNRate (size_t i) const override
 Returns the rate of a specific model from the mixture. More...
 
const TransitionModelInterface & model (const std::string &name) const override
 Access the submodel with the given name. More...
 
const BranchModelInterface & model () const override
 
Vuint getSubmodelNumbers (const std::string &desc) const override
 Returns the vector of numbers of the submodels in the mixture that match a description. More...
 
const TransitionModelInterface & transitionModel () const override
 
const MixedTransitionModelInterface & mixedModel () const
 
const FrequencySetInterface & frequencySet () const override
 
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
 
const Eigen::VectorXd & Lik_t (const Eigen::VectorXd &values, double t) const override
 
virtual const Eigen::VectorXd & dLik_dt (const Eigen::VectorXd &values, double t) const =0
 
const Eigen::VectorXd & dLik_dt (const Eigen::VectorXd &values, double t) const override
 
virtual const Eigen::VectorXd & d2Lik_dt2 (const Eigen::VectorXd &values, double t) const =0
 
const Eigen::VectorXd & d2Lik_dt2 (const Eigen::VectorXd &values, double t) const override
 
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 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 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
 
size_t getNumberOfIndependentParameters () const
 
virtual void aliasParameters (const std::string &p1, const std::string &p2)=0
 
virtual void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0
 
void aliasParameters (const std::string &p1, const std::string &p2)
 
void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
 
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
 
void unaliasParameters (const std::string &p1, const std::string &p2)
 
virtual const ParameterList & getIndependentParameters () const=0
 
const ParameterList & getIndependentParameters () const
 
virtual std::vector< std::string > getAlias (const std::string &name) const=0
 
virtual std::vector< std::string > getAlias (const std::string &name) const
 
virtual std::map< std::string, std::string > getAliases () const=0
 
virtual std::map< std::string, std::string > getAliases () const
 
virtual bool hasParameter (const std::string &name) const=0
 
bool hasParameter (const std::string &name) const override
 
virtual const ParameterList & getParameters () const=0
 
const ParameterList & getParameters () const override
 
virtual const Parameter & parameter (const std::string &name) const=0
 
const Parameter & parameter (const std::string &name) const override
 
virtual double getParameterValue (const std::string &name) const=0
 
double getParameterValue (const std::string &name) const override
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 
void setAllParametersValues (const ParameterList &parameters) override
 
virtual void setParameterValue (const std::string &name, double value)=0
 
void setParameterValue (const std::string &name, double value) override
 
virtual void setParametersValues (const ParameterList &parameters)=0
 
void setParametersValues (const ParameterList &parameters) override
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 
bool matchParametersValues (const ParameterList &parameters) override
 
virtual void removeConstraint (const std::string &name)=0
 
void removeConstraint (const std::string &name) override
 
virtual void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
 
void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
 
virtual size_t getNumberOfParameters () const=0
 
size_t getNumberOfParameters () const override
 
virtual void setNamespace (const std::string &prefix)=0
 
virtual std::string getNamespace () const=0
 
std::string getNamespace () const override
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const=0
 
std::string getParameterNameWithoutNamespace (const std::string &name) const override
 
std::string getParNameFromPmodel (const std::string &name) const
 get the name of a parameter from its name in a submodel More...
 
std::string getPmodelParName (const std::string &name) const
 get the name of a parameter in the submodel from its apparent name More...
 
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
 
double freq (size_t i) const override
 Methods to supersede TransitionModel methods. More...
 
double Pij_t (size_t i, size_t j, double t) const override
 
double dPij_dt (size_t i, size_t j, double t) const override
 
double d2Pij_dt2 (size_t i, size_t j, double t) const override
 
const Vdouble & getFrequencies () const override
 
bool computeFrequencies () const override
 
void computeFrequencies (bool yn) override
 
const Matrix< double > & getPij_t (double t) const override
 
const Matrix< double > & getdPij_dt (double t) const override
 
const Matrix< double > & getd2Pij_dt2 (double t) const override
 
double getInitValue (size_t i, int state) const override
 
double getRate () const override
 Get the rate. More...
 
void setRate (double rate) override
 Set the rate of the model (must be positive). More...
 
void setFreqFromData (const SequenceDataInterface &data, double pseudoCount=0) override
 Set equilibrium frequencies equal to the frequencies estimated from the data. More...
 
void setFreq (std::map< int, double > &frequ) override
 Set equilibrium frequencies. More...
 
void addRateParameter () override
 Methods to supersede TransitionModel methods. More...
 
void setNamespace (const std::string &name) override
 
virtual void fireParameterChanged (const ParameterList &parameters) override
 Methods to supersede AbstractTransitionModel methods. More...
 
const std::vector< int > & getAlphabetStates () const override
 
const StateMapInterface & stateMap () const override
 
std::shared_ptr< const StateMapInterface > getStateMap () 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...
 
int getAlphabetStateAsInt (size_t i) const override
 
std::string getAlphabetStateAsChar (size_t i) const override
 
const Alphabet & alphabet () const override
 
std::shared_ptr< const Alphabet > getAlphabet () const override
 
size_t getNumberOfStates () const override
 Get the number of states. More...
 

Protected Member Functions

void updateMatrices_ () override
 
TransitionModelInterface & transitionModel_ () override
 
MixedTransitionModelInterface & mixedModel_ ()
 
TransitionModelInterface & nModel_ (size_t i) override
 
virtual Vdouble & getFrequencies_ ()=0
 
Vdouble & getFrequencies_ () override
 
virtual ParameterList & getParameters_ ()=0
 
ParameterList & getParameters_ () override
 
BranchModelInterface & model_ ()
 
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

const MixtureOfASubstitutionModel * mixedSubModelPtr_
 
size_t synfrom_
 indexes of 2 codons states between which the substitution is synonymous, to set a basis to the homogeneization of the rates. More...
 
size_t synto_
 
std::unique_ptr< MixedTransitionModelInterface > mixedModelPtr_
 
std::map< std::string, std::string > mapParNamesFromPmodel_
 Tools to make the link between the Parameters of the object and those of pmixmodel_. More...
 
ParameterList lParPmodel_
 

Private Attributes

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

Detailed Description

The Yang et al (2000) M1 substitution model for codons, with the more realistic modification in Wong & al (2004).

Author
Laurent Guéguen

This model is a mixture of models as described in YN98 class, the mixture being defined on the selection parameter to allow it to vary among sites. A site is either negatively selected $ 0 < \omega_0 < 1 $ (with probability $p_0 $), or neutral ( $ \omega_1 = 1 $) with probability $1-p_0 $.

The synonymous rates must be the same between both models, so the overall rates of the models are modified to respect this constraint and such that the mean rate of the mixed model equals one.

This model includes 3 parameters ( $\kappa$, $ p0 $ and $\omega$). The codon frequencies $\pi_j$ are either observed or inferred.

References:

Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000) Genetics 155:431-449.

Wong, W. S. W., Z. Yang, N. Goldman, and R. Nielsen. (2004) Genetics 168:1041–1051.

Definition at line 40 of file YNGP_M1.h.

Constructor & Destructor Documentation

◆ YNGP_M1()

YNGP_M1::YNGP_M1 ( std::shared_ptr< const GeneticCode >  gc,
std::unique_ptr< CodonFrequencySetInterface >  codonFreqs 
)

Definition at line 17 of file YNGP_M1.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::ParameterList::addParameters(), bpp::TransitionModelInterface::computeFrequencies(), bpp::AbstractBiblioMixedTransitionModel::frequencySet(), bpp::ParameterList::getParameterNames(), bpp::ParameterAliasable::getParameters(), bpp::AbstractBiblioTransitionModel::lParPmodel_, bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_, bpp::AbstractBiblioMixedTransitionModel::mixedModel(), bpp::AbstractBiblioMixedTransitionModel::mixedModelPtr_, bpp::YNGP_M::mixedSubModelPtr_, bpp::SubstitutionModelInterface::Qij(), bpp::MixtureOfASubstitutionModel::subNModel(), bpp::YNGP_M::synfrom_, bpp::YNGP_M::synto_, and updateMatrices_().

Referenced by clone().

Member Function Documentation

◆ addRateParameter() [1/2]

void AbstractBiblioTransitionModel::addRateParameter ( )
overridevirtualinherited

Methods to supersede TransitionModel methods.

Implements bpp::BranchModelInterface.

Definition at line 76 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::ParameterList::addParameters(), bpp::BranchModelInterface::addRateParameter(), bpp::AbstractParameterAliasable::getNamespace(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractTotallyWrappedTransitionModel::getRate(), bpp::AbstractBiblioTransitionModel::lParPmodel_, bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_, bpp::AbstractWrappedTransitionModel::model(), bpp::AbstractWrappedTransitionModel::model_(), bpp::Parameter::R_PLUS_STAR, and bpp::ParameterList::reset().

◆ 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::AbstractWrappedModel::alphabet ( ) const
inlineoverridevirtualinherited
Returns
A reference to the alphabet associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 53 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::alphabet(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::alphabet(), and bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel().

◆ clone()

YNGP_M1* bpp::YNGP_M1::clone ( ) const
inlineoverridevirtual

Implements bpp::YNGP_M.

Definition at line 48 of file YNGP_M1.h.

References YNGP_M1().

◆ computeFrequencies() [1/4]

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(), 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() [2/4]

bool bpp::AbstractTotallyWrappedTransitionModel::computeFrequencies ( ) const
inlineoverridevirtualinherited
Returns
Says if equilibrium frequencies should be computed

Implements bpp::TransitionModelInterface.

Definition at line 162 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::computeFrequencies(), and bpp::WrappedTransitionModelInterface::transitionModel().

Referenced by bpp::DFP07::DFP07(), and bpp::YN98::YN98().

◆ computeFrequencies() [3/4]

void bpp::AbstractTotallyWrappedTransitionModel::computeFrequencies ( bool  yn)
inlineoverridevirtualinherited
Returns
Set if equilibrium frequencies should be computed from the generator

Implements bpp::TransitionModelInterface.

Definition at line 171 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::computeFrequencies(), and bpp::AbstractWrappedTransitionModel::transitionModel_().

◆ computeFrequencies() [4/4]

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() [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]

double bpp::AbstractTotallyWrappedTransitionModel::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.

Definition at line 124 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::d2Pij_dt2(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ 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]

double bpp::AbstractTotallyWrappedTransitionModel::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.

Definition at line 123 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::dPij_dt(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ fireParameterChanged()

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

Methods to supersede AbstractTransitionModel methods.

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 86 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractParameterAliasable::getNamespace(), bpp::ParameterList::getParameterValue(), bpp::ParameterList::hasParameter(), bpp::AbstractWrappedTransitionModel::model_(), bpp::BranchModelInterface::setRate(), bpp::ParameterList::size(), and bpp::AbstractBiblioTransitionModel::updateMatrices_().

◆ 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]

double bpp::AbstractTotallyWrappedTransitionModel::freq ( size_t  i) const
inlineoverridevirtualinherited

Methods to supersede TransitionModel methods.

Implements bpp::TransitionModelInterface.

Definition at line 120 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::freq(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ frequencySet()

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

Implements bpp::BranchModelInterface.

Definition at line 138 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModelPtr_.

Referenced by bpp::RELAX::RELAX(), 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().

◆ 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::AbstractWrappedModel::getAlphabet ( ) const
inlineoverridevirtualinherited
Returns
A pointer toward the alphabet associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 55 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabet(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabet(), and bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel().

◆ getAlphabetStateAsChar() [1/2]

std::string bpp::AbstractWrappedModel::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 46 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStateAsChar(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStateAsChar().

◆ getAlphabetStateAsChar() [2/2]

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().

◆ getAlphabetStateAsInt() [1/2]

int bpp::AbstractWrappedModel::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 44 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStateAsInt(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStateAsInt().

◆ getAlphabetStateAsInt() [2/2]

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().

◆ 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::AbstractWrappedModel::getAlphabetStates ( ) const
inlineoverridevirtualinherited

@ brief Methods to supersede TransitionModel methods.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 38 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStates(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStates().

◆ getd2Pij_dt2() [1/2]

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().

◆ getd2Pij_dt2() [2/2]

const Matrix<double>& bpp::AbstractTotallyWrappedTransitionModel::getd2Pij_dt2 ( double  t) const
inlineoverridevirtualinherited
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::TransitionModelInterface.

Definition at line 132 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getd2Pij_dt2(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ getdPij_dt() [1/2]

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().

◆ getdPij_dt() [2/2]

const Matrix<double>& bpp::AbstractTotallyWrappedTransitionModel::getdPij_dt ( double  t) const
inlineoverridevirtualinherited
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::TransitionModelInterface.

Definition at line 130 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getdPij_dt(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ 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::AbstractTotallyWrappedTransitionModel::getFrequencies ( ) const
inlineoverridevirtualinherited
Returns
A vector of all equilibrium frequencies.
See also
freq()

Implements bpp::TransitionModelInterface.

Definition at line 126 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getFrequencies(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ getFrequencies_() [1/2]

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

Implements bpp::TransitionModelInterface.

Definition at line 181 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getFrequencies_(), and bpp::AbstractWrappedTransitionModel::transitionModel_().

◆ 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 bpp::AbstractTotallyWrappedTransitionModel::getInitValue ( size_t  i,
int  state 
) const
inlineoverridevirtualinherited

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.

Definition at line 134 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getInitValue(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ 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::AbstractWrappedModel::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 50 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getModelStates(), and bpp::WrappedModelInterface::model().

◆ 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::AbstractWrappedModel::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 48 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getModelStates(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getModelStates().

◆ getName()

std::string bpp::YNGP_M1::getName ( ) const
inlineoverridevirtual

Get the name of the model.

Returns
The name of this model.

Implements bpp::BranchModelInterface.

Definition at line 51 of file YNGP_M1.h.

◆ getNModel()

std::shared_ptr<const TransitionModelInterface> bpp::AbstractBiblioMixedTransitionModel::getNModel ( size_t  i) const
inlineoverridevirtualinherited

Implements bpp::MixedTransitionModelInterface.

Definition at line 43 of file AbstractBiblioMixedTransitionModel.h.

References bpp::MixedTransitionModelInterface::getNModel(), and bpp::AbstractBiblioMixedTransitionModel::mixedModel().

◆ getNProbability()

double bpp::AbstractBiblioMixedTransitionModel::getNProbability ( size_t  i) const
inlineoverridevirtualinherited

Returns the probability of a specific model from the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 51 of file AbstractBiblioMixedTransitionModel.h.

References bpp::MixedTransitionModelInterface::getNProbability(), and bpp::AbstractBiblioMixedTransitionModel::mixedModel().

◆ getNRate()

double bpp::AbstractBiblioMixedTransitionModel::getNRate ( size_t  i) const
inlineoverridevirtualinherited

Returns the rate of a specific model from the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 112 of file AbstractBiblioMixedTransitionModel.h.

References bpp::MixedTransitionModelInterface::getNRate(), and bpp::AbstractBiblioMixedTransitionModel::mixedModel().

◆ getNumberOfModels()

size_t bpp::AbstractBiblioMixedTransitionModel::getNumberOfModels ( ) const
inlineoverridevirtualinherited

Returns the number of submodels.

Implements bpp::MixedTransitionModelInterface.

Definition at line 78 of file AbstractBiblioMixedTransitionModel.h.

References bpp::MixedTransitionModelInterface::getNumberOfModels(), and bpp::AbstractBiblioMixedTransitionModel::mixedModel().

◆ 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::AbstractWrappedModel::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.

Definition at line 57 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getNumberOfStates(), and bpp::WrappedModelInterface::model().

◆ getParNameFromPmodel()

std::string AbstractBiblioTransitionModel::getParNameFromPmodel ( const std::string &  name) const
inherited

get the name of a parameter from its name in a submodel

Parameters
namethe name of the parameter in the submodel

Definition at line 37 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_.

◆ getPij_t() [1/2]

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().

◆ getPij_t() [2/2]

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

Implements bpp::TransitionModelInterface.

Definition at line 128 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::getPij_t(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ getPmodelParName()

std::string AbstractBiblioTransitionModel::getPmodelParName ( const std::string &  name) const
inherited

get the name of a parameter in the submodel from its apparent name

Parameters
namethe name of the parameter

Definition at line 47 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_.

◆ getProbabilities()

const std::vector<double>& bpp::AbstractBiblioMixedTransitionModel::getProbabilities ( ) const
inlineoverridevirtualinherited

Returns the vector of the probabilities of the submodels of the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 61 of file AbstractBiblioMixedTransitionModel.h.

References bpp::MixedTransitionModelInterface::getProbabilities(), and bpp::AbstractBiblioMixedTransitionModel::mixedModel().

◆ 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 bpp::AbstractTotallyWrappedTransitionModel::getRate ( ) const
inlineoverridevirtualinherited

Get the rate.

Implements bpp::BranchModelInterface.

Definition at line 139 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getRate(), and bpp::WrappedTransitionModelInterface::transitionModel().

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), and bpp::FromMixtureSubstitutionModel::addRateParameter().

◆ 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::AbstractWrappedModel::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 42 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getStateMap(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getStateMap().

◆ getSubmodelNumbers()

Vuint AbstractBiblioMixedTransitionModel::getSubmodelNumbers ( const std::string &  desc) const
overridevirtualinherited

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

Implements bpp::MixedTransitionModelInterface.

Definition at line 32 of file AbstractBiblioMixedTransitionModel.cpp.

References bpp::ParameterAliasable::getParameterNameWithoutNamespace(), bpp::MixedTransitionModelInterface::getSubmodelNumbers(), bpp::StringTokenizer::hasMoreToken(), bpp::AbstractBiblioMixedTransitionModel::mixedModel(), and bpp::StringTokenizer::nextToken().

◆ getVRates()

const std::vector<double>& bpp::AbstractBiblioMixedTransitionModel::getVRates ( ) const
inlineoverridevirtualinherited

Returns the vector of all the rates of the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 104 of file AbstractBiblioMixedTransitionModel.h.

References bpp::MixedTransitionModelInterface::getVRates(), and bpp::AbstractBiblioMixedTransitionModel::mixedModel().

◆ 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_.

◆ mixedModel()

const MixedTransitionModelInterface& bpp::AbstractBiblioMixedTransitionModel::mixedModel ( ) const
inlineinherited

Definition at line 136 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModelPtr_.

Referenced by bpp::DFP07::DFP07(), bpp::AbstractBiblioMixedTransitionModel::getNModel(), bpp::AbstractBiblioMixedTransitionModel::getNProbability(), bpp::AbstractBiblioMixedTransitionModel::getNRate(), bpp::AbstractBiblioMixedTransitionModel::getNumberOfModels(), bpp::AbstractBiblioMixedTransitionModel::getProbabilities(), bpp::AbstractBiblioMixedTransitionModel::getSubmodelNumbers(), bpp::AbstractBiblioMixedTransitionModel::getVRates(), bpp::AbstractBiblioMixedTransitionModel::model(), bpp::AbstractBiblioMixedTransitionModel::nModel(), bpp::YNGP_M::operator=(), bpp::RELAX::RELAX(), bpp::YNGP_M::YNGP_M(), 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().

◆ mixedModel_()

MixedTransitionModelInterface& bpp::AbstractBiblioMixedTransitionModel::mixedModel_ ( )
inlineprotectedinherited

Definition at line 149 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModelPtr_.

Referenced by bpp::AbstractBiblioMixedTransitionModel::nModel_(), bpp::AbstractBiblioMixedTransitionModel::normalizeVRates(), bpp::AbstractBiblioMixedTransitionModel::setNProbability(), and bpp::AbstractBiblioMixedTransitionModel::setVRates().

◆ model() [1/2]

const BranchModelInterface& bpp::AbstractWrappedTransitionModel::model ( ) const
inlineoverridevirtualinherited

Implements bpp::WrappedModelInterface.

Definition at line 98 of file AbstractWrappedModel.h.

References bpp::WrappedTransitionModelInterface::transitionModel().

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), bpp::InMixedSubstitutionModel::getInitValue(), bpp::FromMixtureSubstitutionModel::getName(), bpp::RegisterRatesSubstitutionModel::getRate(), bpp::AbstractBiblioSubstitutionModel::operator=(), bpp::AbstractBiblioTransitionModel::operator=(), bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel(), bpp::AbstractBiblioTransitionModel::setFreq(), bpp::AbstractBiblioTransitionModel::setNamespace(), and bpp::BppOSubstitutionModelFormat::write().

◆ model() [2/2]

const TransitionModelInterface& bpp::AbstractBiblioMixedTransitionModel::model ( const std::string &  name) const
inlineoverridevirtualinherited

Access the submodel with the given name.

Exceptions
NullPointerExceptionif no model with the given name is found.

Implements bpp::MixedTransitionModelInterface.

Definition at line 123 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModel(), and bpp::MixedTransitionModelInterface::model().

◆ model_()

BranchModelInterface& bpp::AbstractWrappedTransitionModel::model_ ( )
inlineprotectedinherited

Definition at line 85 of file AbstractWrappedModel.h.

References bpp::AbstractWrappedTransitionModel::transitionModel_().

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), bpp::AbstractBiblioTransitionModel::fireParameterChanged(), bpp::FromMixtureSubstitutionModel::fireParameterChanged(), bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel(), bpp::AbstractBiblioTransitionModel::setNamespace(), bpp::FromMixtureSubstitutionModel::setNamespace(), bpp::RegisterRatesSubstitutionModel::setRate(), and bpp::AbstractBiblioTransitionModel::updateMatrices_().

◆ nModel()

const TransitionModelInterface& bpp::AbstractBiblioMixedTransitionModel::nModel ( size_t  i) const
inlineoverridevirtualinherited

Returns the submodel from the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 38 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModel(), and bpp::MixedTransitionModelInterface::nModel().

Referenced by bpp::DFP07::proteinModel().

◆ nModel_()

TransitionModelInterface& bpp::AbstractBiblioMixedTransitionModel::nModel_ ( size_t  i)
inlineoverrideprotectedvirtualinherited

Implements bpp::MixedTransitionModelInterface.

Definition at line 151 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModel_(), and bpp::MixedTransitionModelInterface::nModel_().

◆ normalizeVRates()

void bpp::AbstractBiblioMixedTransitionModel::normalizeVRates ( )
inlineoverridevirtualinherited

normalizes the rates of the submodels.

Implements bpp::MixedTransitionModelInterface.

Definition at line 96 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModel_(), and bpp::MixedTransitionModelInterface::normalizeVRates().

◆ 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]

double bpp::AbstractTotallyWrappedTransitionModel::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.

Definition at line 122 of file AbstractWrappedModel.h.

References bpp::TransitionModelInterface::Pij_t(), and bpp::WrappedTransitionModelInterface::transitionModel().

◆ setFreq() [1/2]

void AbstractBiblioTransitionModel::setFreq ( std::map< int, double > &  frequencies)
overridevirtualinherited

Set equilibrium frequencies.

Parameters
frequenciesThe map of the frequencies to use.

Implements bpp::TransitionModelInterface.

Reimplemented in bpp::YN98, bpp::MG94, and bpp::KCM.

Definition at line 111 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::getNamespace(), bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(), bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_, bpp::AbstractParameterAliasable::matchParametersValues(), bpp::AbstractWrappedTransitionModel::model(), and bpp::AbstractTotallyWrappedTransitionModel::setFreq().

Referenced by bpp::KCM::setFreq(), bpp::MG94::setFreq(), bpp::YN98::setFreq(), and bpp::AbstractBiblioTransitionModel::setFreqFromData().

◆ setFreq() [2/2]

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() [1/2]

void AbstractBiblioTransitionModel::setFreqFromData ( const SequenceDataInterface &  data,
double  pseudoCount = 0 
)
overridevirtualinherited

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 125 of file AbstractBiblioSubstitutionModel.cpp.

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

◆ setFreqFromData() [2/2]

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().

◆ setNamespace()

void AbstractBiblioTransitionModel::setNamespace ( const std::string &  name)
overridevirtualinherited

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 88 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::ParameterList::addParameters(), bpp::ParameterAliasable::getParameterNameWithoutNamespace(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractBiblioTransitionModel::lParPmodel_, bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_, bpp::AbstractWrappedTransitionModel::model(), bpp::AbstractWrappedTransitionModel::model_(), bpp::ParameterList::reset(), bpp::AbstractParameterAliasable::setNamespace(), and bpp::ParameterAliasable::setNamespace().

◆ setNProbability()

void bpp::AbstractBiblioMixedTransitionModel::setNProbability ( size_t  i,
double  prob 
)
inlineoverridevirtualinherited

Sets the probabilities of the submodels of the mixture.

Implements bpp::MixedTransitionModelInterface.

Definition at line 70 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModel_(), and bpp::MixedTransitionModelInterface::setNProbability().

◆ setRate() [1/2]

void bpp::AbstractTotallyWrappedTransitionModel::setRate ( double  rate)
inlineoverridevirtualinherited

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

Parameters
ratemust be positive.

Implements bpp::BranchModelInterface.

Definition at line 144 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::setRate(), and bpp::AbstractWrappedTransitionModel::transitionModel_().

◆ setRate() [2/2]

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().

◆ setVRates()

void bpp::AbstractBiblioMixedTransitionModel::setVRates ( const Vdouble &  vd)
inlineoverridevirtualinherited

sets the rates of the submodels.

Implements bpp::MixedTransitionModelInterface.

Definition at line 87 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModel_(), and bpp::MixedTransitionModelInterface::setVRates().

◆ 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::AbstractWrappedModel::stateMap ( ) const
inlineoverridevirtualinherited
Returns
The mapping of model states with alphabet states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 40 of file AbstractWrappedModel.h.

References bpp::WrappedModelInterface::model(), and bpp::BranchModelInterface::stateMap().

Referenced by bpp::RegisterRatesSubstitutionModel::stateMap().

◆ transitionModel()

const TransitionModelInterface& bpp::AbstractBiblioMixedTransitionModel::transitionModel ( ) const
inlineoverridevirtualinherited

Implements bpp::WrappedTransitionModelInterface.

Definition at line 134 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModelPtr_.

◆ transitionModel_()

TransitionModelInterface& bpp::AbstractBiblioMixedTransitionModel::transitionModel_ ( )
inlineoverrideprotectedvirtualinherited

Implements bpp::AbstractWrappedTransitionModel.

Definition at line 144 of file AbstractBiblioMixedTransitionModel.h.

References bpp::AbstractBiblioMixedTransitionModel::mixedModelPtr_.

◆ updateMatrices_()

void YNGP_M1::updateMatrices_ ( )
overrideprotectedvirtual

Reimplemented from bpp::AbstractBiblioTransitionModel.

Definition at line 97 of file YNGP_M1.cpp.

References bpp::AbstractBiblioMixedTransitionModel::mixedModelPtr_, bpp::YNGP_M::mixedSubModelPtr_, bpp::SubstitutionModelInterface::Qij(), bpp::MixtureOfASubstitutionModel::subNModel(), bpp::YNGP_M::synfrom_, bpp::YNGP_M::synto_, and bpp::AbstractBiblioTransitionModel::updateMatrices_().

Referenced by YNGP_M1().

Member Data Documentation

◆ 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().

◆ lParPmodel_

ParameterList bpp::AbstractBiblioTransitionModel::lParPmodel_
protectedinherited

Definition at line 30 of file AbstractBiblioSubstitutionModel.h.

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::DFP07::DFP07(), bpp::GY94::GY94(), bpp::KCM::KCM(), bpp::LG10_EX_EHO::LG10_EX_EHO(), bpp::LGL08_CAT::LGL08_CAT(), bpp::LLG08_EHO::LLG08_EHO(), bpp::LLG08_EX2::LLG08_EX2(), bpp::LLG08_EX3::LLG08_EX3(), bpp::LLG08_UL2::LLG08_UL2(), bpp::LLG08_UL3::LLG08_UL3(), bpp::MG94::MG94(), bpp::AbstractBiblioTransitionModel::operator=(), bpp::RELAX::RELAX(), bpp::AbstractBiblioTransitionModel::setNamespace(), bpp::AbstractBiblioTransitionModel::updateMatrices_(), bpp::RELAX::updateMatrices_(), bpp::YNGP_M3::updateMatrices_(), bpp::YN98::YN98(), 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().

◆ mapParNamesFromPmodel_

std::map<std::string, std::string> bpp::AbstractBiblioTransitionModel::mapParNamesFromPmodel_
protectedinherited

Tools to make the link between the Parameters of the object and those of pmixmodel_.

Definition at line 28 of file AbstractBiblioSubstitutionModel.h.

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::DFP07::DFP07(), bpp::AbstractBiblioTransitionModel::getParNameFromPmodel(), bpp::AbstractBiblioTransitionModel::getPmodelParName(), bpp::GY94::GY94(), bpp::KCM::KCM(), bpp::LG10_EX_EHO::LG10_EX_EHO(), bpp::LGL08_CAT::LGL08_CAT(), bpp::LLG08_EHO::LLG08_EHO(), bpp::LLG08_EX2::LLG08_EX2(), bpp::LLG08_EX3::LLG08_EX3(), bpp::LLG08_UL2::LLG08_UL2(), bpp::LLG08_UL3::LLG08_UL3(), bpp::MG94::MG94(), bpp::AbstractBiblioTransitionModel::operator=(), bpp::RELAX::RELAX(), bpp::AbstractBiblioTransitionModel::setFreq(), bpp::AbstractBiblioTransitionModel::setNamespace(), bpp::AbstractBiblioTransitionModel::updateMatrices_(), bpp::RELAX::updateMatrices_(), bpp::YNGP_M3::updateMatrices_(), bpp::YN98::YN98(), 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().

◆ mixedModelPtr_

std::unique_ptr<MixedTransitionModelInterface> bpp::AbstractBiblioMixedTransitionModel::mixedModelPtr_
protectedinherited

Definition at line 23 of file AbstractBiblioMixedTransitionModel.h.

Referenced by bpp::DFP07::DFP07(), bpp::AbstractBiblioMixedTransitionModel::frequencySet(), bpp::LGL08_CAT::getNumberOfCategories(), bpp::LG10_EX_EHO::LG10_EX_EHO(), bpp::LGL08_CAT::LGL08_CAT(), bpp::LLG08_EHO::LLG08_EHO(), bpp::LLG08_EX2::LLG08_EX2(), bpp::LLG08_EX3::LLG08_EX3(), bpp::LLG08_UL2::LLG08_UL2(), bpp::LLG08_UL3::LLG08_UL3(), bpp::AbstractBiblioMixedTransitionModel::mixedModel(), bpp::AbstractBiblioMixedTransitionModel::mixedModel_(), bpp::AbstractBiblioMixedTransitionModel::operator=(), bpp::RELAX::RELAX(), bpp::AbstractBiblioMixedTransitionModel::transitionModel(), bpp::AbstractBiblioMixedTransitionModel::transitionModel_(), bpp::DFP07::updateMatrices_(), bpp::RELAX::updateMatrices_(), 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_(), 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().

◆ mixedSubModelPtr_

const MixtureOfASubstitutionModel* bpp::YNGP_M::mixedSubModelPtr_
protectedinherited

redefined mixed model pointer

Definition at line 37 of file YNGP_M.h.

Referenced by bpp::YNGP_M::operator=(), bpp::RELAX::RELAX(), bpp::RELAX::updateMatrices_(), 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_M::YNGP_M(), 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().

◆ synfrom_

size_t bpp::YNGP_M::synfrom_
protectedinherited

indexes of 2 codons states between which the substitution is synonymous, to set a basis to the homogeneization of the rates.

Definition at line 43 of file YNGP_M.h.

Referenced by bpp::YNGP_M::operator=(), bpp::RELAX::RELAX(), bpp::RELAX::updateMatrices_(), 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_(), 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().

◆ synto_

size_t bpp::YNGP_M::synto_
protectedinherited

Definition at line 43 of file YNGP_M.h.

Referenced by bpp::YNGP_M::operator=(), bpp::RELAX::RELAX(), bpp::RELAX::updateMatrices_(), 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_(), 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().

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