bpp-phyl  2.1.0
bpp::YNGKP_M8 Class Reference

The Yang et al (2000) M8 substitution model for codons. More...

#include <Bpp/Phyl/Model/Codon/YNGKP_M8.h>

+ Inheritance diagram for bpp::YNGKP_M8:
+ Collaboration diagram for bpp::YNGKP_M8:

List of all members.

Public Member Functions

 YNGKP_M8 (const GeneticCode *gc, FrequenciesSet *codonFreqs, unsigned int nbclass)
 ~YNGKP_M8 ()
YNGKP_M8clone () const
 YNGKP_M8 (const YNGKP_M8 &)
YNGKP_M8operator= (const YNGKP_M8 &)
const SubstitutionModelgetModel () const
const MixedSubstitutionModelgetMixedModel () const
std::string getName () const
 Get the name of the model.
const SubstitutionModelgetNModel (size_t i) const
 Returns a specific model from the mixture.
SubstitutionModelgetNModel (size_t i)
double getNProbability (size_t i) const
 Returns the probability of a specific model from the mixture.
const std::vector< double > & getProbabilities () const
 Returns the vector of the probabilities of the submodels of the mixture.
void setNProbability (size_t i, double prob)
 Sets the probabilities of the submodels of the mixture.
size_t getNumberOfModels () const
 Returns the number of submodels.
void setVRates (const Vdouble &vd)
 sets the rates of the submodels.
void normalizeVRates ()
 normalizes the rates of the submodels.
const std::vector< double > & getVRates () const
 Returns the vector of all the rates of the mixture.
double getNRate (size_t i) const
 Returns the rate of a specific model from the mixture.
Vint getSubmodelNumbers (std::string &desc) const
virtual const std::vector< int > & getAlphabetChars () const =0
const std::vector< int > & getAlphabetChars () const
virtual int getAlphabetChar (size_t i) const =0
 Get the char in the alphabet corresponding to a given state in the model.
int getAlphabetChar (size_t i) const
 Get the char in the alphabet corresponding to a given state in the model.
virtual std::vector< size_t > getModelStates (int i) const =0
 Get the state in the model corresponding to a particular char in the alphabet.
std::vector< size_t > getModelStates (int i) const
 Get the state in the model corresponding to a particular char in the alphabet.
virtual double freq (size_t i) const =0
virtual double freq (size_t i) const
virtual double Qij (size_t i, size_t j) const =0
virtual double Qij (size_t i, size_t j) const
virtual double Pij_t (size_t i, size_t j, double t) const =0
virtual double Pij_t (size_t i, size_t j, double t) const
virtual double dPij_dt (size_t i, size_t j, double t) const =0
virtual double dPij_dt (size_t i, size_t j, double t) const
virtual double d2Pij_dt2 (size_t i, size_t j, double t) const =0
virtual double d2Pij_dt2 (size_t i, size_t j, double t) const
virtual const VdoublegetFrequencies () const =0
virtual const VdoublegetFrequencies () const
virtual const Matrix< double > & getGenerator () const =0
const Matrix< double > & getGenerator () const
virtual const Matrix< double > & getExchangeabilityMatrix () const =0
const Matrix< double > & getExchangeabilityMatrix () const
virtual double Sij (size_t i, size_t j) const =0
double Sij (size_t i, size_t j) const
virtual const Matrix< double > & getPij_t (double t) const =0
const Matrix< double > & getPij_t (double t) const
virtual const Matrix< double > & getdPij_dt (double t) const =0
const Matrix< double > & getdPij_dt (double t) const
virtual const Matrix< double > & getd2Pij_dt2 (double t) const =0
const Matrix< double > & getd2Pij_dt2 (double t) const
virtual void enableEigenDecomposition (bool yn)=0
 Set if eigenValues and Vectors must be computed.
virtual bool enableEigenDecomposition ()=0
 Tell if eigenValues and Vectors must be computed.
void enableEigenDecomposition (bool yn)
 Set if eigenValues and Vectors must be computed.
bool enableEigenDecomposition ()
 Tell if eigenValues and Vectors must be computed.
virtual const VdoublegetEigenValues () const =0
const VdoublegetEigenValues () const
virtual const VdoublegetIEigenValues () const =0
const VdoublegetIEigenValues () const
virtual bool isDiagonalizable () const =0
bool isDiagonalizable () const
virtual bool isNonSingular () const =0
bool isNonSingular () const
virtual const Matrix< double > & getRowLeftEigenVectors () const =0
const Matrix< double > & getRowLeftEigenVectors () const
virtual const Matrix< double > & getColumnRightEigenVectors () const =0
const Matrix< double > & getColumnRightEigenVectors () const
virtual const AlphabetgetAlphabet () const =0
const AlphabetgetAlphabet () const
virtual size_t getNumberOfStates () const =0
 Get the number of states.
size_t getNumberOfStates () const
 Get the number of states.
virtual double getInitValue (size_t i, int state) const =0 throw (IndexOutOfBoundsException, BadIntException)
double getInitValue (size_t i, int state) const throw (BadIntException)
virtual double getScale () const =0
 Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.
double getScale () const
 Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.
virtual void setScale (double scale)=0
 Multiplies the current generator by the given scale.
void setScale (double scale)
 Multiplies the current generator by the given scale.
virtual double getRate () const =0
 Get the rate.
double getRate () const
 Get the rate.
virtual void setRate (double rate)=0
 Set the rate of the model (must be positive).
void setRate (double rate)
 Set the rate of the model (must be positive).
virtual void addRateParameter ()=0
void addRateParameter ()
virtual void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)=0
 Set equilibrium frequencies equal to the frequencies estimated from the data.
void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
 Set equilibrium frequencies equal to the frequencies estimated from the data.
virtual void setFreq (std::map< int, double > &frequencies)
 Set equilibrium frequencies.
void setFreq (std::map< int, double > &frequ)
 Set equilibrium frequencies.
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 ParameterListgetIndependentParameters () const =0
const ParameterListgetIndependentParameters () const
virtual std::vector< std::string > getAlias (const std::string &name) const =0
std::vector< std::string > getAlias (const std::string &name) const
virtual bool hasParameter (const std::string &name) const =0
bool hasParameter (const std::string &name) const
virtual const ParameterListgetParameters () const =0
const ParameterListgetParameters () const
virtual const ParametergetParameter (const std::string &name) const =0
const ParametergetParameter (const std::string &name) const
virtual double getParameterValue (const std::string &name) const =0
double getParameterValue (const std::string &name) const
virtual void setAllParametersValues (const ParameterList &parameters)=0
void setAllParametersValues (const ParameterList &parameters)
virtual void setParameterValue (const std::string &name, double value)=0
void setParameterValue (const std::string &name, double value)
virtual void setParametersValues (const ParameterList &parameters)=0
void setParametersValues (const ParameterList &parameters)
virtual bool matchParametersValues (const ParameterList &parameters)=0
bool matchParametersValues (const ParameterList &parameters)
virtual size_t getNumberOfParameters () const =0
size_t getNumberOfParameters () const
virtual void setNamespace (const std::string &prefix)=0
void setNamespace (const std::string &prefix)
virtual std::string getNamespace () const =0
std::string getNamespace () const
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const =0
std::string getParameterNameWithoutNamespace (const std::string &name) const
virtual void fireParameterChanged (const ParameterList &parameters)
 Tells the model that a parameter value has changed.
ParameterList getAliasedParameters (const ParameterList &pl) const
std::string getFrom (const std::string &name) const

Protected Member Functions

void updateMatrices ()
void addParameter_ (Parameter *parameter)
void addParameters_ (const ParameterList &parameters)
void deleteParameter_ (size_t index)
void deleteParameter_ (std::string &name)
void deleteParameters_ (const std::vector< std::string > &names)
void resetParameters_ ()
ParametergetParameter_ (const std::string &name)
ParametergetParameter_ (size_t index)
const ParametergetParameter_ (size_t index) const
ParametergetParameterWithNamespace_ (const std::string &name)
const ParametergetParameterWithNamespace_ (const std::string &name) const
ParameterListgetParameters_ ()

Protected Attributes

std::map< std::string,
std::string > 
mapParNamesFromPmodel_
 Tools to make the link between the Parameters of the object and those of pmixmodel_.
ParameterList lParPmodel_

Private Member Functions

SubstitutionModelgetModel ()
MixedSubstitutionModelgetMixedModel ()
const FrequenciesSetgetFrequenciesSet () const
 If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.

Private Attributes

std::auto_ptr
< MixtureOfASubstitutionModel
pmixmodel_
int synfrom_
int synto_

Detailed Description

The Yang et al (2000) M8 substitution model for codons.

Author:
Laurent Gu├ęguen

This model is a mixture of models as described in YN98 class, the mixture being defined on the selection parameter oomega to allow it to vary among sites, following a mixture of a Beta distribution and of another value above 1.

This model includes 5 parameters ( $\kappa$, $ \alpha $ and $\beta$) of the Beta distribution, $p0$ the weight of the Beta distribution and $\omega $ the selection parameter above 1 (with weight $ 1-p0 $). The codon frequencies $ \pi_j $ are either observed or infered.

References:

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

Definition at line 73 of file YNGKP_M8.h.


Constructor & Destructor Documentation

Definition at line 154 of file YNGKP_M8.cpp.

YNGKP_M8::YNGKP_M8 ( const YNGKP_M8 mod2)

Definition at line 137 of file YNGKP_M8.cpp.


Member Function Documentation

YNGKP_M8* bpp::YNGKP_M8::clone ( ) const [inline, virtual]

Implements bpp::AbstractBiblioMixedSubstitutionModel.

Definition at line 99 of file YNGKP_M8.h.

References YNGKP_M8().

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

Implements bpp::SubstitutionModel.

Definition at line 106 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::d2Pij_dt2(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

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

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

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

Implements bpp::SubstitutionModel.

Definition at line 105 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::dPij_dt(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

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

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

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

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 122 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::enableEigenDecomposition(), and bpp::AbstractBiblioSubstitutionModel::getModel().

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 124 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::enableEigenDecomposition(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

Tell if eigenValues and Vectors must be computed.

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

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

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 171 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractParameterAliasable::getNamespace(), bpp::ParameterList::size(), and bpp::AbstractBiblioSubstitutionModel::updateMatrices().

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

Implements bpp::SubstitutionModel.

Definition at line 100 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::freq(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

Implements bpp::SubstitutionModel.

Definition at line 147 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getAlphabet(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

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

In most cases, this method will return i.

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

Implements bpp::SubstitutionModel.

Definition at line 96 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getAlphabetChar(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

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

In most cases, this method will return i.

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

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

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

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

Implements bpp::SubstitutionModel.

Definition at line 94 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getAlphabetChars(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

Implements bpp::SubstitutionModel.

Definition at line 135 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getColumnRightEigenVectors(), and bpp::AbstractBiblioSubstitutionModel::getModel().

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::getd2Pij_dt2 ( double  t) const [inline, virtual, inherited]
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::SubstitutionModel.

Definition at line 120 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getd2Pij_dt2(), and bpp::AbstractBiblioSubstitutionModel::getModel().

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::getdPij_dt ( double  t) const [inline, virtual, inherited]
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::SubstitutionModel.

Definition at line 118 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getdPij_dt(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

Implements bpp::SubstitutionModel.

Definition at line 130 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getEigenValues(), and bpp::AbstractBiblioSubstitutionModel::getModel().

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix ( ) const [inline, virtual, inherited]
Returns:
The matrix of exchangeability terms. It is recommended that exchangeability matrix be normalized so that the normalized generator be obtained directly by the dot product $S . \pi$.

Implements bpp::SubstitutionModel.

Definition at line 112 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getExchangeabilityMatrix(), and bpp::AbstractBiblioSubstitutionModel::getModel().

virtual const Matrix<double>& bpp::SubstitutionModel::getExchangeabilityMatrix ( ) const [pure virtual, inherited]
Returns:
The matrix of exchangeability terms. It is recommended that exchangeability matrix be normalized so that the normalized generator be obtained directly by the dot product $S . \pi$.

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

Referenced by bpp::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix(), bpp::RE08::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

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

Implements bpp::SubstitutionModel.

Definition at line 108 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getFrequencies(), and bpp::AbstractBiblioSubstitutionModel::getModel().

const FrequenciesSet* bpp::YNGKP_M8::getFrequenciesSet ( ) const [inline, private, virtual]

If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.

Reimplemented from bpp::AbstractBiblioSubstitutionModel.

Definition at line 120 of file YNGKP_M8.h.

References pmixmodel_.

Referenced by YNGKP_M8().

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

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

See also:
Qij()

Implements bpp::SubstitutionModel.

Definition at line 110 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getGenerator(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

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

See also:
Qij()

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

Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::AbstractBiblioSubstitutionModel::getGenerator(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::RE08::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

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

Implements bpp::SubstitutionModel.

Definition at line 132 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getIEigenValues(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

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

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

double bpp::AbstractBiblioSubstitutionModel::getInitValue ( size_t  i,
int  state 
) const throw (BadIntException) [inline, virtual, inherited]

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

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

Implements bpp::SubstitutionModel.

Definition at line 151 of file AbstractBiblioSubstitutionModel.h.

References bpp::SubstitutionModel::getInitValue(), and bpp::AbstractBiblioSubstitutionModel::getModel().

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

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

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

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

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

const MixedSubstitutionModel& bpp::YNGKP_M8::getMixedModel ( ) const [inline, virtual]

Implements bpp::AbstractBiblioMixedSubstitutionModel.

Definition at line 111 of file YNGKP_M8.h.

References pmixmodel_.

MixedSubstitutionModel& bpp::YNGKP_M8::getMixedModel ( ) [inline, private, virtual]

Implements bpp::AbstractBiblioMixedSubstitutionModel.

Definition at line 118 of file YNGKP_M8.h.

References pmixmodel_.

const SubstitutionModel& bpp::YNGKP_M8::getModel ( ) const [inline, virtual]

Implements bpp::AbstractBiblioSubstitutionModel.

Definition at line 109 of file YNGKP_M8.h.

References pmixmodel_.

SubstitutionModel& bpp::YNGKP_M8::getModel ( ) [inline, private, virtual]

Implements bpp::AbstractBiblioSubstitutionModel.

Definition at line 116 of file YNGKP_M8.h.

References pmixmodel_.

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

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

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

Implements bpp::SubstitutionModel.

Definition at line 98 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getModelStates().

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

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

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

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

Referenced by bpp::AbstractBiblioSubstitutionModel::getModelStates(), bpp::MarkovModulatedSubstitutionModel::getModelStates(), and bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates().

std::string bpp::YNGKP_M8::getName ( ) const [inline, virtual]

Get the name of the model.

Returns:
The name of this model.

Implements bpp::SubstitutionModel.

Definition at line 113 of file YNGKP_M8.h.

const SubstitutionModel* bpp::AbstractBiblioMixedSubstitutionModel::getNModel ( size_t  i) const [inline, virtual, inherited]
double bpp::AbstractBiblioMixedSubstitutionModel::getNProbability ( size_t  i) const [inline, virtual, inherited]

Returns the probability of a specific model from the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 91 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getNProbability().

double bpp::AbstractBiblioMixedSubstitutionModel::getNRate ( size_t  i) const [inline, virtual, inherited]

Returns the rate of a specific model from the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 155 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getNRate().

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

Get the number of states.

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

Returns:
The number of different states in the model.

Implements bpp::SubstitutionModel.

Definition at line 149 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getNumberOfStates().

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::getPij_t ( double  t) const [inline, virtual, inherited]
Returns:
All probabilities of change from state i to state j during time t.
See also:
Pij_t()

Implements bpp::SubstitutionModel.

Definition at line 116 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getPij_t().

const std::vector<double>& bpp::AbstractBiblioMixedSubstitutionModel::getProbabilities ( ) const [inline, virtual, inherited]

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

Implements bpp::MixedSubstitutionModel.

Definition at line 102 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getProbabilities().

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

Implements bpp::SubstitutionModel.

Definition at line 134 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getRowLeftEigenVectors().

double bpp::AbstractBiblioSubstitutionModel::getScale ( ) const [inline, virtual, inherited]

Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.

Returns:
Minus the scalar product of diagonal elements and the frequencies vector.

Implements bpp::SubstitutionModel.

Definition at line 184 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getScale().

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

Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.

Returns:
Minus the scalar product of diagonal elements and the frequencies vector.

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

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

const std::vector<double>& bpp::AbstractBiblioMixedSubstitutionModel::getVRates ( ) const [inline, virtual, inherited]

Returns the vector of all the rates of the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 147 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getVRates().

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

Implements bpp::SubstitutionModel.

Definition at line 126 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::isDiagonalizable().

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

Implements bpp::SubstitutionModel.

Definition at line 128 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::isNonSingular().

virtual bool bpp::SubstitutionModel::isNonSingular ( ) const [pure virtual, inherited]
YNGKP_M8 & YNGKP_M8::operator= ( const YNGKP_M8 mod2)

Definition at line 143 of file YNGKP_M8.cpp.

References pmixmodel_, synfrom_, and synto_.

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

Implements bpp::SubstitutionModel.

Definition at line 104 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::Pij_t().

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

Implements bpp::SubstitutionModel.

Definition at line 102 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::Qij().

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

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

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

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

Implements bpp::SubstitutionModel.

Definition at line 110 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractBiblioSubstitutionModel::getModel(), bpp::AbstractParameterAliasable::getNamespace(), bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(), bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_, bpp::AbstractParameterAliasable::matchParametersValues(), and bpp::SubstitutionModel::setFreqFromData().

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

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

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

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

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

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

void bpp::AbstractBiblioMixedSubstitutionModel::setNProbability ( size_t  i,
double  prob 
) [inline, virtual, inherited]

Sets the probabilities of the submodels of the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 111 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::setNProbability().

void bpp::AbstractBiblioSubstitutionModel::setRate ( double  rate) [inline, virtual, inherited]

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

Parameters:
ratemust be positive.

Implements bpp::SubstitutionModel.

Definition at line 139 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::setRate().

virtual void bpp::SubstitutionModel::setRate ( double  rate) [pure virtual, inherited]
void bpp::AbstractBiblioSubstitutionModel::setScale ( double  scale) [inline, virtual, inherited]

Multiplies the current generator by the given scale.

Parameters:
scalethe scale by which the generator is multiplied.

Implements bpp::SubstitutionModel.

Definition at line 186 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::setScale().

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

Multiplies the current generator by the given scale.

Parameters:
scalethe scale by which the generator is multiplied.

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

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

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

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

Implements bpp::SubstitutionModel.

Definition at line 114 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::Sij().

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

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

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

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

void YNGKP_M8::updateMatrices ( ) [protected, virtual]

Reimplemented from bpp::AbstractBiblioSubstitutionModel.

Definition at line 156 of file YNGKP_M8.cpp.

References pmixmodel_, synfrom_, and synto_.

Referenced by YNGKP_M8().


Member Data Documentation

int bpp::YNGKP_M8::synfrom_ [private]

Definition at line 86 of file YNGKP_M8.h.

Referenced by operator=(), updateMatrices(), and YNGKP_M8().

int bpp::YNGKP_M8::synto_ [private]

Definition at line 86 of file YNGKP_M8.h.

Referenced by operator=(), updateMatrices(), and YNGKP_M8().


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