bpp-phyl  2.1.0
Public Member Functions | Protected Member Functions | Protected Attributes
bpp::TS98 Class Reference

Tuffley and Steel's 1998 covarion model. More...

#include <Bpp/Phyl/Model/TS98.h>

+ Inheritance diagram for bpp::TS98:
+ Collaboration diagram for bpp::TS98:

List of all members.

Public Member Functions

 TS98 (ReversibleSubstitutionModel *model, double s1=1., double s2=1., bool normalizeRateChanges=false)
 Build a new TS98 substitution model.
virtual ~TS98 ()
TS98 * clone () const
std::string getName () const
 Get the name of the model.
double getRate () const
 Get the rate.
void setRate (double rate)
 Set the rate of the model (must be positive).
void addRateParameter ()
const Alphabet * getAlphabet () const
size_t getNumberOfStates () const
 Get the number of states.
const Vdouble & getFrequencies () const
const Matrix< double > & getExchangeabilityMatrix () const
const Matrix< double > & getGenerator () const
const Matrix< double > & getPij_t (double t) const
const Matrix< double > & getdPij_dt (double t) const
const Matrix< double > & getd2Pij_dt2 (double t) const
const Vdouble & getEigenValues () const
const Vdouble & getIEigenValues () const
bool isDiagonalizable () const
bool isNonSingular () const
const Matrix< double > & getRowLeftEigenVectors () const
const Matrix< double > & getColumnRightEigenVectors () const
double freq (size_t i) const
double Sij (size_t i, size_t j) const
double Qij (size_t i, size_t j) const
double Pij_t (size_t i, size_t j, double t) const
double dPij_dt (size_t i, size_t j, double t) const
double d2Pij_dt2 (size_t i, size_t j, double t) const
double getInitValue (size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException)
void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
 Set equilibrium frequencies equal to the frequencies estimated from the data.
const std::vector< int > & getAlphabetChars () const
int getAlphabetChar (size_t i) const
 Get the char in the alphabet corresponding to a given state in the model.
std::vector< size_t > getModelStates (int i) const
 Get the state in the model corresponding to a particular char in the alphabet.
const ReversibleSubstitutionModel * getNestedModel () const
size_t getRate (size_t i) const
 Get the rate category corresponding to a particular state in the compound model.
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.
void setScale (double scale)
 Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.
void enableEigenDecomposition (bool yn)
 Set if eigenValues and Vectors must be computed.
bool enableEigenDecomposition ()
 Tell if eigenValues and Vectors must be computed.
virtual void fireParameterChanged (const ParameterList &parameters)
 Tells the model that a parameter value has changed.
void setNamespace (const std::string &prefix)
virtual void setFreq (std::map< int, double > &frequencies)
 Set equilibrium frequencies.
virtual const FrequenciesSet * getFrequenciesSet () const
 If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.
virtual size_t getNumberOfIndependentParameters () const =0
size_t getNumberOfIndependentParameters () const
virtual void aliasParameters (const std::string &p1, const std::string &p2)=0
void aliasParameters (const std::string &p1, const std::string &p2)
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
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 ParameterList & getParameters () const =0
const ParameterList & getParameters () const
virtual const Parameter & getParameter (const std::string &name) const =0
const Parameter & getParameter (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 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
std::string getFrom (const std::string &name) const

Protected Member Functions

void updateRatesModel ()
 Update the rates vector, generator and equilibrium frequencies.
virtual void updateMatrices ()
void addParameter_ (Parameter *parameter)
void addParameters_ (const ParameterList &parameters)
void deleteParameter_ (size_t index)
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
ParameterList & getParameters_ ()

Protected Attributes

ReversibleSubstitutionModel * model_
size_t nbStates_
size_t nbRates_
RowMatrix< double > ratesGenerator_
std::vector< int > chars_
 The list of supported chars.
RowMatrix< double > generator_
 The generator matrix $Q$ of the model.
RowMatrix< double > exchangeability_
 The exchangeability matrix $S$ of the model.
RowMatrix< double > leftEigenVectors_
 The $U$ matrix made of left eigen vectors (by row).
RowMatrix< double > rightEigenVectors_
 The $U^-1$ matrix made of right eigen vectors (by column).
Vdouble eigenValues_
 The vector of real parts of eigen values.
Vdouble iEigenValues_
 The vector of imaginary parts of the eigen values (zero in case of reversible pmodel).
bool eigenDecompose_
 Tell if the eigen decomposition should be performed.
RowMatrix< double > pijt_
 These ones are for bookkeeping:
RowMatrix< double > dpijt_
RowMatrix< double > d2pijt_
Vdouble freq_
 The vector of equilibrium frequencies.
bool normalizeRateChanges_
std::string nestedPrefix_
Rate generator.

These variables must be initialized in the constructor of the derived class.

RowMatrix< double > rates_
RowMatrix< double > ratesExchangeability_
Vdouble ratesFreq_

Detailed Description

Tuffley and Steel's 1998 covarion model.

This model is a subclass of the so-called Markov-modulated substitution models, with a rate matrix

\[ G = \begin{pmatrix} -s_1 & s_1\\ s_2 & -s_2 \end{pmatrix} \]

and

\[ D_R = \begin{pmatrix} 0 & 0\\ 0 & \dfrac{s_1+s_2}{s_1} \end{pmatrix}. \]

This model was originally designed for nucleotides sequences, but it can be used with other alphabets.

See also:
MarkovModulatedSubstitutionModel

Tuffley C. and Steel M. A., Modelling the covarion hypothesis of nucleotide substitution (1998), _Math. Biosci._, 147:63-91.

Definition at line 77 of file TS98.h.

Constructor & Destructor Documentation

bpp::TS98::TS98 ( ReversibleSubstitutionModel *  model,
double  s1 = 1.,
double  s2 = 1.,
bool  normalizeRateChanges = false 
) [inline]

Build a new TS98 substitution model.

Parameters:
modelThe substitution model to use. May be of any alphabet type.
s1First rate parameter.
s2Second rate parameter.
normalizeRateChangesTell if the rate transition matrix should be normalized.

Definition at line 89 of file TS98.h.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::MarkovModulatedSubstitutionModel::nbRates_, bpp::Parameter::R_PLUS_STAR, bpp::MarkovModulatedSubstitutionModel::rates_, bpp::MarkovModulatedSubstitutionModel::ratesExchangeability_, bpp::MarkovModulatedSubstitutionModel::ratesFreq_, bpp::RowMatrix< Scalar >::resize(), bpp::MarkovModulatedSubstitutionModel::updateMatrices(), and updateRatesModel().

Referenced by clone().

virtual bpp::TS98::~TS98 ( ) [inline, virtual]

Definition at line 102 of file TS98.h.

Member Function Documentation

void bpp::TS98::addRateParameter ( ) [inline, virtual]

Implements bpp::SubstitutionModel.

Definition at line 118 of file TS98.h.

TS98* bpp::TS98::clone ( ) const [inline, virtual]

Implements bpp::MarkovModulatedSubstitutionModel.

Definition at line 109 of file TS98.h.

References TS98().

double bpp::MarkovModulatedSubstitutionModel::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 220 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::getd2Pij_dt2().

double bpp::MarkovModulatedSubstitutionModel::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 219 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::getdPij_dt().

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

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 280 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::eigenDecompose_.

bool bpp::MarkovModulatedSubstitutionModel::enableEigenDecomposition ( ) [inline, virtual, inherited]

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 282 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::eigenDecompose_.

virtual void bpp::MarkovModulatedSubstitutionModel::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.

Reimplemented in bpp::G2001.

Definition at line 289 of file MarkovModulatedSubstitutionModel.h.

References bpp::ParameterAliasable::matchParametersValues(), bpp::MarkovModulatedSubstitutionModel::model_, bpp::MarkovModulatedSubstitutionModel::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateRatesModel().

double bpp::MarkovModulatedSubstitutionModel::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 214 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::freq_.

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

Implements bpp::SubstitutionModel.

Definition at line 191 of file MarkovModulatedSubstitutionModel.h.

References bpp::SubstitutionModel::getAlphabet(), and bpp::MarkovModulatedSubstitutionModel::model_.

int bpp::MarkovModulatedSubstitutionModel::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 235 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::chars_.

const std::vector<int>& bpp::MarkovModulatedSubstitutionModel::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 230 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::chars_.

const Matrix<double>& bpp::MarkovModulatedSubstitutionModel::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 212 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::rightEigenVectors_.

const Matrix< double > & MarkovModulatedSubstitutionModel::getd2Pij_dt2 ( double  t) const [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 196 of file MarkovModulatedSubstitutionModel.cpp.

References bpp::MarkovModulatedSubstitutionModel::d2pijt_, bpp::MarkovModulatedSubstitutionModel::eigenValues_, bpp::VectorTools::exp(), bpp::MarkovModulatedSubstitutionModel::leftEigenVectors_, bpp::MatrixTools::mult(), bpp::MarkovModulatedSubstitutionModel::rightEigenVectors_, and bpp::NumTools::sqr().

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

const Matrix< double > & MarkovModulatedSubstitutionModel::getdPij_dt ( double  t) const [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 190 of file MarkovModulatedSubstitutionModel.cpp.

References bpp::MarkovModulatedSubstitutionModel::dpijt_, bpp::MarkovModulatedSubstitutionModel::eigenValues_, bpp::VectorTools::exp(), bpp::MarkovModulatedSubstitutionModel::leftEigenVectors_, bpp::MatrixTools::mult(), and bpp::MarkovModulatedSubstitutionModel::rightEigenVectors_.

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

const Vdouble& bpp::MarkovModulatedSubstitutionModel::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 205 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::eigenValues_.

const Matrix<double>& bpp::MarkovModulatedSubstitutionModel::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 197 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::exchangeability_.

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

Implements bpp::SubstitutionModel.

Definition at line 195 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::freq_.

virtual const FrequenciesSet* bpp::SubstitutionModel::getFrequenciesSet ( ) const [inline, virtual, inherited]

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

Reimplemented in bpp::JCprot, bpp::AbstractBiblioSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::DSO78, bpp::JTT92, bpp::LG08, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, and bpp::AbstractCodonFrequenciesSubstitutionModel.

Definition at line 463 of file SubstitutionModel.h.

Referenced by bpp::AbstractBiblioSubstitutionModel::getFrequenciesSet(), and bpp::BppOSubstitutionModelFormat::write().

const Matrix<double>& bpp::MarkovModulatedSubstitutionModel::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 199 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::generator_.

const Vdouble& bpp::MarkovModulatedSubstitutionModel::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 206 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::iEigenValues_.

double MarkovModulatedSubstitutionModel::getInitValue ( size_t  i,
int  state 
) const throw (IndexOutOfBoundsException, BadIntException) [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 204 of file MarkovModulatedSubstitutionModel.cpp.

References bpp::Alphabet::getAlias(), and bpp::BadIntException::getAlphabet().

std::vector<size_t> bpp::MarkovModulatedSubstitutionModel::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 240 of file MarkovModulatedSubstitutionModel.h.

References bpp::SubstitutionModel::getModelStates(), bpp::MarkovModulatedSubstitutionModel::model_, bpp::MarkovModulatedSubstitutionModel::nbRates_, and bpp::MarkovModulatedSubstitutionModel::nbStates_.

std::string bpp::TS98::getName ( ) const [inline, virtual]

Get the name of the model.

Returns:
The name of this model.

Implements bpp::SubstitutionModel.

Definition at line 112 of file TS98.h.

const ReversibleSubstitutionModel* bpp::MarkovModulatedSubstitutionModel::getNestedModel ( ) const [inline, inherited]

Definition at line 250 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::model_.

Referenced by bpp::BppOSubstitutionModelFormat::write().

size_t bpp::MarkovModulatedSubstitutionModel::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 193 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::nbRates_, and bpp::MarkovModulatedSubstitutionModel::nbStates_.

const Matrix< double > & MarkovModulatedSubstitutionModel::getPij_t ( double  t) const [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 181 of file MarkovModulatedSubstitutionModel.cpp.

References bpp::MarkovModulatedSubstitutionModel::eigenValues_, bpp::VectorTools::exp(), bpp::MarkovModulatedSubstitutionModel::leftEigenVectors_, bpp::MatrixTools::mult(), bpp::MarkovModulatedSubstitutionModel::nbRates_, bpp::MarkovModulatedSubstitutionModel::nbStates_, bpp::MarkovModulatedSubstitutionModel::pijt_, and bpp::MarkovModulatedSubstitutionModel::rightEigenVectors_.

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

double bpp::TS98::getRate ( ) const [inline, virtual]

Get the rate.

Reimplemented from bpp::MarkovModulatedSubstitutionModel.

Definition at line 114 of file TS98.h.

size_t bpp::MarkovModulatedSubstitutionModel::getRate ( size_t  i) const [inline, inherited]

Get the rate category corresponding to a particular state in the compound model.

Parameters:
iThe state.
Returns:
The corresponding rate category.
See also:
getState;

Definition at line 259 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::nbStates_.

const Matrix<double>& bpp::MarkovModulatedSubstitutionModel::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 211 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::leftEigenVectors_.

double bpp::MarkovModulatedSubstitutionModel::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 268 of file MarkovModulatedSubstitutionModel.h.

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

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

Implements bpp::SubstitutionModel.

Definition at line 208 of file MarkovModulatedSubstitutionModel.h.

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

Implements bpp::SubstitutionModel.

Definition at line 209 of file MarkovModulatedSubstitutionModel.h.

double bpp::MarkovModulatedSubstitutionModel::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 218 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::getPij_t().

double bpp::MarkovModulatedSubstitutionModel::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 216 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::generator_.

virtual void bpp::SubstitutionModel::setFreq ( std::map< int, double > &  frequencies) [inline, virtual, inherited]

Set equilibrium frequencies.

Parameters:
frequenciesThe map of the frequencies to use.

Reimplemented in bpp::AbstractSubstitutionModel, bpp::F84, bpp::HKY85, bpp::MixtureOfSubstitutionModels, bpp::T92, bpp::AbstractWordSubstitutionModel, bpp::GTR, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::RN95, bpp::TN93, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::RN95s, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::MixtureOfASubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::BinarySubstitutionModel, bpp::SSR, bpp::L95, bpp::CodonRateFrequenciesSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, and bpp::AbstractCodonFitnessSubstitutionModel.

Definition at line 455 of file SubstitutionModel.h.

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

void bpp::MarkovModulatedSubstitutionModel::setFreqFromData ( const SequenceContainer &  data,
double  pseudoCount = 0 
) [inline, 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 224 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::model_, bpp::SubstitutionModel::setFreqFromData(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

void MarkovModulatedSubstitutionModel::setNamespace ( const std::string &  prefix) [virtual, inherited]

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::G2001.

Definition at line 221 of file MarkovModulatedSubstitutionModel.cpp.

References bpp::MarkovModulatedSubstitutionModel::model_, bpp::MarkovModulatedSubstitutionModel::nestedPrefix_, and bpp::ParameterAliasable::setNamespace().

void bpp::TS98::setRate ( double  rate) [inline, virtual]

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

Parameters:
ratemust be positive.

Reimplemented from bpp::MarkovModulatedSubstitutionModel.

Definition at line 116 of file TS98.h.

void bpp::MarkovModulatedSubstitutionModel::setScale ( double  scale) [inline, virtual, inherited]

Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.

When the generator is normalized, scale=1. Otherwise each element is multiplied such that the correct scale is set.

Implements bpp::SubstitutionModel.

Definition at line 275 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::model_, bpp::SubstitutionModel::setScale(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

double bpp::MarkovModulatedSubstitutionModel::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 215 of file MarkovModulatedSubstitutionModel.h.

References bpp::MarkovModulatedSubstitutionModel::exchangeability_.

void MarkovModulatedSubstitutionModel::updateMatrices ( ) [protected, virtual, inherited]

Definition at line 107 of file MarkovModulatedSubstitutionModel.cpp.

References bpp::MatrixTools::add(), bpp::MarkovModulatedSubstitutionModel::chars_, bpp::MarkovModulatedSubstitutionModel::d2pijt_, bpp::MatrixTools::diag(), bpp::MarkovModulatedSubstitutionModel::dpijt_, bpp::MarkovModulatedSubstitutionModel::eigenValues_, bpp::MarkovModulatedSubstitutionModel::exchangeability_, bpp::MarkovModulatedSubstitutionModel::freq_, bpp::MarkovModulatedSubstitutionModel::generator_, bpp::SubstitutionModel::getAlphabetChars(), bpp::SubstitutionModel::getColumnRightEigenVectors(), bpp::SubstitutionModel::getEigenValues(), bpp::SubstitutionModel::getExchangeabilityMatrix(), bpp::SubstitutionModel::getFrequencies(), bpp::SubstitutionModel::getGenerator(), bpp::RowMatrix< Scalar >::getNumberOfColumns(), bpp::SubstitutionModel::getNumberOfStates(), bpp::EigenValue< Real >::getRealEigenValues(), bpp::EigenValue< Real >::getV(), bpp::MarkovModulatedSubstitutionModel::iEigenValues_, bpp::MatrixTools::inv(), bpp::VectorTools::kroneckerMult(), bpp::MatrixTools::kroneckerMult(), bpp::MarkovModulatedSubstitutionModel::leftEigenVectors_, bpp::MarkovModulatedSubstitutionModel::model_, bpp::MatrixTools::mult(), bpp::MarkovModulatedSubstitutionModel::nbRates_, bpp::MarkovModulatedSubstitutionModel::nbStates_, bpp::MarkovModulatedSubstitutionModel::normalizeRateChanges_, bpp::MarkovModulatedSubstitutionModel::pijt_, bpp::MarkovModulatedSubstitutionModel::rates_, bpp::MarkovModulatedSubstitutionModel::ratesExchangeability_, bpp::MarkovModulatedSubstitutionModel::ratesFreq_, bpp::MarkovModulatedSubstitutionModel::ratesGenerator_, bpp::VectorTools::rep(), bpp::RowMatrix< Scalar >::resize(), bpp::MarkovModulatedSubstitutionModel::rightEigenVectors_, and bpp::MatrixTools::scale().

Referenced by bpp::MarkovModulatedSubstitutionModel::fireParameterChanged(), bpp::G2001::G2001(), bpp::MarkovModulatedSubstitutionModel::setFreqFromData(), bpp::MarkovModulatedSubstitutionModel::setScale(), and TS98().

void bpp::TS98::updateRatesModel ( ) [inline, protected, virtual]

Update the rates vector, generator and equilibrium frequencies.

This method must be implemented by the derived class. It is called by the fireParameterChanged() method.

Implements bpp::MarkovModulatedSubstitutionModel.

Definition at line 121 of file TS98.h.

References bpp::AbstractParameterAliasable::getParameterValue(), bpp::MarkovModulatedSubstitutionModel::rates_, bpp::MarkovModulatedSubstitutionModel::ratesExchangeability_, and bpp::MarkovModulatedSubstitutionModel::ratesFreq_.

Referenced by TS98().

Member Data Documentation

std::vector<int> bpp::MarkovModulatedSubstitutionModel::chars_ [protected, inherited]

The list of supported chars.

Definition at line 100 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::getAlphabetChar(), bpp::MarkovModulatedSubstitutionModel::getAlphabetChars(), bpp::MarkovModulatedSubstitutionModel::operator=(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::MarkovModulatedSubstitutionModel::d2pijt_ [mutable, protected, inherited]

Definition at line 143 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::getd2Pij_dt2(), bpp::MarkovModulatedSubstitutionModel::operator=(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::MarkovModulatedSubstitutionModel::dpijt_ [mutable, protected, inherited]

Definition at line 142 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::getdPij_dt(), bpp::MarkovModulatedSubstitutionModel::operator=(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

bool bpp::MarkovModulatedSubstitutionModel::eigenDecompose_ [protected, inherited]

Tell if the eigen decomposition should be performed.

Definition at line 136 of file MarkovModulatedSubstitutionModel.h.

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

Vdouble bpp::MarkovModulatedSubstitutionModel::eigenValues_ [protected, inherited]

The vector of real parts of eigen values.

Definition at line 125 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::getd2Pij_dt2(), bpp::MarkovModulatedSubstitutionModel::getdPij_dt(), bpp::MarkovModulatedSubstitutionModel::getEigenValues(), bpp::MarkovModulatedSubstitutionModel::getPij_t(), bpp::MarkovModulatedSubstitutionModel::operator=(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::MarkovModulatedSubstitutionModel::exchangeability_ [protected, inherited]

The exchangeability matrix $S$ of the model.

Definition at line 110 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::getExchangeabilityMatrix(), bpp::MarkovModulatedSubstitutionModel::operator=(), bpp::MarkovModulatedSubstitutionModel::Sij(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

Vdouble bpp::MarkovModulatedSubstitutionModel::freq_ [protected, inherited]

The vector of equilibrium frequencies.

Definition at line 148 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::freq(), bpp::MarkovModulatedSubstitutionModel::getFrequencies(), bpp::MarkovModulatedSubstitutionModel::getScale(), bpp::MarkovModulatedSubstitutionModel::operator=(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::MarkovModulatedSubstitutionModel::generator_ [protected, inherited]

The generator matrix $Q$ of the model.

Definition at line 105 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::getGenerator(), bpp::MarkovModulatedSubstitutionModel::getScale(), bpp::MarkovModulatedSubstitutionModel::operator=(), bpp::MarkovModulatedSubstitutionModel::Qij(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

Vdouble bpp::MarkovModulatedSubstitutionModel::iEigenValues_ [protected, inherited]

The vector of imaginary parts of the eigen values (zero in case of reversible pmodel).

Definition at line 131 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::getIEigenValues(), bpp::MarkovModulatedSubstitutionModel::operator=(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::MarkovModulatedSubstitutionModel::leftEigenVectors_ [protected, inherited]

The $U$ matrix made of left eigen vectors (by row).

Definition at line 115 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::getd2Pij_dt2(), bpp::MarkovModulatedSubstitutionModel::getdPij_dt(), bpp::MarkovModulatedSubstitutionModel::getPij_t(), bpp::MarkovModulatedSubstitutionModel::getRowLeftEigenVectors(), bpp::MarkovModulatedSubstitutionModel::operator=(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

ReversibleSubstitutionModel* bpp::MarkovModulatedSubstitutionModel::model_ [protected, inherited]

Definition at line 81 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::fireParameterChanged(), bpp::MarkovModulatedSubstitutionModel::getAlphabet(), bpp::MarkovModulatedSubstitutionModel::getModelStates(), bpp::MarkovModulatedSubstitutionModel::getNestedModel(), bpp::MarkovModulatedSubstitutionModel::getRate(), bpp::MarkovModulatedSubstitutionModel::MarkovModulatedSubstitutionModel(), bpp::MarkovModulatedSubstitutionModel::operator=(), bpp::MarkovModulatedSubstitutionModel::setFreqFromData(), bpp::MarkovModulatedSubstitutionModel::setNamespace(), bpp::MarkovModulatedSubstitutionModel::setRate(), bpp::MarkovModulatedSubstitutionModel::setScale(), bpp::MarkovModulatedSubstitutionModel::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::~MarkovModulatedSubstitutionModel().

size_t bpp::MarkovModulatedSubstitutionModel::nbRates_ [protected, inherited]

Definition at line 83 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::G2001::G2001(), bpp::MarkovModulatedSubstitutionModel::getModelStates(), bpp::MarkovModulatedSubstitutionModel::getNumberOfStates(), bpp::MarkovModulatedSubstitutionModel::getPij_t(), bpp::MarkovModulatedSubstitutionModel::operator=(), TS98(), bpp::MarkovModulatedSubstitutionModel::updateMatrices(), and bpp::G2001::updateRatesModel().

size_t bpp::MarkovModulatedSubstitutionModel::nbStates_ [protected, inherited]

Definition at line 82 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::getModelStates(), bpp::MarkovModulatedSubstitutionModel::getNumberOfStates(), bpp::MarkovModulatedSubstitutionModel::getPij_t(), bpp::MarkovModulatedSubstitutionModel::getRate(), bpp::MarkovModulatedSubstitutionModel::operator=(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

std::string bpp::MarkovModulatedSubstitutionModel::nestedPrefix_ [protected, inherited]

Definition at line 152 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::MarkovModulatedSubstitutionModel(), bpp::MarkovModulatedSubstitutionModel::operator=(), and bpp::MarkovModulatedSubstitutionModel::setNamespace().

bool bpp::MarkovModulatedSubstitutionModel::normalizeRateChanges_ [protected, inherited]

Definition at line 150 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::operator=(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::MarkovModulatedSubstitutionModel::pijt_ [mutable, protected, inherited]

These ones are for bookkeeping:

Definition at line 141 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::getPij_t(), bpp::MarkovModulatedSubstitutionModel::operator=(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::MarkovModulatedSubstitutionModel::rates_ [protected, inherited]

Definition at line 91 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::G2001::G2001(), bpp::MarkovModulatedSubstitutionModel::operator=(), TS98(), bpp::MarkovModulatedSubstitutionModel::updateMatrices(), updateRatesModel(), and bpp::G2001::updateRatesModel().

RowMatrix<double> bpp::MarkovModulatedSubstitutionModel::ratesExchangeability_ [protected, inherited]

Definition at line 92 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::G2001::G2001(), bpp::MarkovModulatedSubstitutionModel::operator=(), TS98(), bpp::MarkovModulatedSubstitutionModel::updateMatrices(), updateRatesModel(), and bpp::G2001::updateRatesModel().

Vdouble bpp::MarkovModulatedSubstitutionModel::ratesFreq_ [protected, inherited]

Definition at line 93 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::G2001::G2001(), bpp::MarkovModulatedSubstitutionModel::operator=(), TS98(), bpp::MarkovModulatedSubstitutionModel::updateMatrices(), and updateRatesModel().

RowMatrix<double> bpp::MarkovModulatedSubstitutionModel::ratesGenerator_ [protected, inherited]

Definition at line 95 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::operator=(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

RowMatrix<double> bpp::MarkovModulatedSubstitutionModel::rightEigenVectors_ [protected, inherited]

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

Definition at line 120 of file MarkovModulatedSubstitutionModel.h.

Referenced by bpp::MarkovModulatedSubstitutionModel::getColumnRightEigenVectors(), bpp::MarkovModulatedSubstitutionModel::getd2Pij_dt2(), bpp::MarkovModulatedSubstitutionModel::getdPij_dt(), bpp::MarkovModulatedSubstitutionModel::getPij_t(), bpp::MarkovModulatedSubstitutionModel::operator=(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

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