bpp-phyl  2.2.0
 All Classes Namespaces Files Functions Variables Typedefs Friends Pages
bpp::RE08 Class Referenceabstract

The Rivas-Eddy substitution model with gap characters. More...

#include <Bpp/Phyl/Model/RE08.h>

+ Inheritance diagram for bpp::RE08:
+ Collaboration diagram for bpp::RE08:

Public Member Functions

 RE08 (ReversibleSubstitutionModel *simpleModel, double lambda=0, double mu=0)
 Build a new Rivas & Eddy model from a standard substitution model. More...
 
 RE08 (const RE08 &model)
 
RE08operator= (const RE08 &model)
 
virtual ~RE08 ()
 
RE08clone () const
 
double Pij_t (size_t i, size_t j, double d) const
 
double dPij_dt (size_t i, size_t j, double d) const
 
double d2Pij_dt2 (size_t i, size_t j, double d) const
 
const Matrix< double > & getPij_t (double d) const
 
const Matrix< double > & getdPij_dt (double d) const
 
const Matrix< double > & getd2Pij_dt2 (double d) const
 
std::string getName () const
 Get the name of the model. More...
 
void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
 This method is forwarded to the simple model. More...
 
void fireParameterChanged (const ParameterList &parameters)
 Tells the model that a parameter value has changed. More...
 
size_t getNumberOfStates () const
 Get the number of states. More...
 
double getInitValue (size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException)
 
void setNamespace (const std::string &prefix)
 
const SubstitutionModelgetNestedModel () const
 
const AlphabetgetAlphabet () const
 
const StateMapgetStateMap () const
 
const std::vector< int > & getAlphabetStates () const
 
std::string getAlphabetStateAsChar (size_t index) const
 
int getAlphabetStateAsInt (size_t index) const
 
std::vector< size_t > getModelStates (int code) const
 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
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
virtual const VdoublegetFrequencies () const
 
const Matrix< double > & getGenerator () const
 
const Matrix< double > & getExchangeabilityMatrix () const
 
double Sij (size_t i, size_t j) const
 
const VdoublegetEigenValues () const
 
const VdoublegetIEigenValues () const
 
bool isDiagonalizable () const
 
bool isNonSingular () const
 
const Matrix< double > & getRowLeftEigenVectors () const
 
const Matrix< double > & getColumnRightEigenVectors () const
 
virtual double freq (size_t i) const
 
virtual double Qij (size_t i, size_t j) const
 
virtual void setFreq (std::map< int, double > &)
 Set equilibrium frequencies. More...
 
void enableEigenDecomposition (bool yn)
 Set if eigenValues and Vectors must be computed. More...
 
bool enableEigenDecomposition ()
 Tell if eigenValues and Vectors must be computed. More...
 
void addRateParameter ()
 
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. More...
 
void setScale (double scale)
 Multiplies the current generator by the given scale. More...
 
virtual double getRate () const
 Get the rate. More...
 
virtual void setRate (double rate)
 Set the rate of the model (must be positive). More...
 
virtual const FrequenciesSetgetFrequenciesSet () const
 If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0. More...
 
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
 
ParameterList getAliasedParameters (const ParameterList &pl) const
 
std::string getFrom (const std::string &name) const
 
bool hasParameter (const std::string &name) const
 
const ParameterListgetParameters () const
 
const ParametergetParameter (const std::string &name) const
 
double getParameterValue (const std::string &name) const
 
void setAllParametersValues (const ParameterList &parameters)
 
void setParameterValue (const std::string &name, double value)
 
void setParametersValues (const ParameterList &parameters)
 
bool matchParametersValues (const ParameterList &parameters)
 
size_t getNumberOfParameters () const
 
std::string getNamespace () const
 
std::string getParameterNameWithoutNamespace (const std::string &name) const
 

Protected Member Functions

void updateMatrices ()
 Compute and diagonalize the $Q$ matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...
 
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

const Alphabetalphabet_
 The alphabet relevant to this model. More...
 
std::auto_ptr< StateMapstateMap_
 The map of model states with alphabet states. More...
 
size_t size_
 The size of the generator, i.e. the number of states. More...
 
double rate_
 The rate of the model (default: 1). The generator (and all its vectorial components) is independent of the rate, since it should be normalized. More...
 
RowMatrix< double > generator_
 The generator matrix $Q$ of the model. More...
 
Vdouble freq_
 The vector $\pi_e$ of equilibrium frequencies. More...
 
RowMatrix< double > exchangeability_
 The exchangeability matrix $S$ of the model, defined as $ S_{ij}=\frac{Q_{ij}}{\pi_j}$. When the model is reversible, this matrix is symetric. More...
 
RowMatrix< double > pijt_
 These ones are for bookkeeping: More...
 
RowMatrix< double > dpijt_
 
RowMatrix< double > d2pijt_
 
bool eigenDecompose_
 Tell if the eigen decomposition should be performed. More...
 
Vdouble eigenValues_
 The vector of eigen values. More...
 
Vdouble iEigenValues_
 The vector of the imaginary part of the eigen values. More...
 
bool isDiagonalizable_
 boolean value for diagonalizability in R of the generator_ More...
 
RowMatrix< double > rightEigenVectors_
 The $U^-1$ matrix made of right eigen vectors (by column). More...
 
bool isNonSingular_
 boolean value for non-singularity of rightEigenVectors_ More...
 
RowMatrix< double > leftEigenVectors_
 The $U$ matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular. More...
 
std::vector< RowMatrix< double > > vPowGen_
 vector of the powers of generator_ for Taylor development (if rightEigenVectors_ is singular). More...
 
RowMatrix< double > tmpMat_
 For computational issues. More...
 

Private Attributes

std::auto_ptr
< ReversibleSubstitutionModel
simpleModel_
 
RowMatrix< double > simpleGenerator_
 
RowMatrix< double > simpleExchangeabilities_
 
double exp_
 
RowMatrix< double > p_
 
double lambda_
 
double mu_
 
std::string nestedPrefix_
 

Detailed Description

The Rivas-Eddy substitution model with gap characters.

This model expends any reversible substitution model with gaps as an additional state. Although the conditionnal subtitution process is reversible, the insertion/deletion process needs not be. The model hence adds two parameters for insertion and deletions, $\lambda$ and $\mu$. If we note $Q$ the (simple) transition matrix (= Markov generator) and $Q^\epsilon$ the extended one, we have:

\[ Q^\epsilon = \left( \begin{array}{ccc|c} & & & \mu \\ & \rule{0cm}{1cm}\rule{1cm}{0cm}Q-\mu\delta_{ij} & & \vdots \\ & & & \mu \\ \hline \lambda\pi_1 & \ldots & \lambda\pi_n & -\lambda \\ \end{array} \right) \]

where $n$ is the number of states of the simple model (in most case equal to the size of the alphabet) and $(\pi_1,\ldots,\pi_n)$ is the vector of equilibrium frequencies of the conditional model. $\delta_{ij}$ is 1 if i=j, 0 otherwise. Note that in the original paper $Q$ is noted as $R$, and $Q_t$ is used for the probability matrix, which is referred here as $P^\epsilon(t)$ for consistency with the documentation of other models.

The extended Markov model is reversible, and the equilibrium frequencies are

\[ \pi^\epsilon = \left( \pi \cdot \frac{\lambda}{\lambda + \mu}, \frac{\mu}{\lambda + \mu}\right). \]

The corresponding exchangeability matrix is:

\[ S^\epsilon = \left( \begin{array}{ccc|c} & & & \lambda + \mu \\ & \rule{0cm}{1cm}\rule{1cm}{0cm}(S - \frac{\mu\delta_{ij}}{\pi_i})\frac{\lambda+\mu}{\lambda} & & \vdots \\ & & & \lambda + \mu \\ \hline \lambda + \mu & \ldots & \lambda + \mu & - (\lambda + \mu) \\ \end{array} \right) \]

The eigen values and vectors are computed numerically, but the transition probabilities are computed analytically from the simple substitution model, together with the first and second order derivatives according to time.

Please note that the original Rivas and Eddy method uses this substitution model with a modification of the Felsenstein algorithm.

Reference:

  • Rivas E and Eddy SR (2008), Probabilistic Phylogenetic Inference with Insertions and Deletions, 4(9):e1000172, in PLoS Computational Biology.

Definition at line 96 of file RE08.h.

Constructor & Destructor Documentation

RE08::RE08 ( ReversibleSubstitutionModel simpleModel,
double  lambda = 0,
double  mu = 0 
)

Build a new Rivas & Eddy model from a standard substitution model.

The alphabet and number of states for the extended model will be derived from the simple one.

Parameters
simpleModelThe simple model to use to build the extended one. THE RE08 class will own the simple one, meaning that it will be destroyed together with the RE08 instance, and cloned when cloning the RE08 instance. To prevent the original simple model to be destroyed, you should make a copy of it before creating the RE08 instance.
lambdaInsertion rate.
muDeletion rate.

Definition at line 50 of file RE08.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractSubstitutionModel::freq_, bpp::AbstractSubstitutionModel::generator_, bpp::SubstitutionModel::getNumberOfStates(), bpp::AbstractSubstitutionModel::leftEigenVectors_, nestedPrefix_, p_, bpp::RowMatrix< Scalar >::resize(), bpp::AbstractSubstitutionModel::rightEigenVectors_, simpleModel_, bpp::AbstractSubstitutionModel::size_, and updateMatrices().

Referenced by clone().

bpp::RE08::RE08 ( const RE08 model)
inline

Definition at line 123 of file RE08.h.

virtual bpp::RE08::~RE08 ( )
inlinevirtual

Definition at line 153 of file RE08.h.

Member Function Documentation

void AbstractSubstitutionModel::addRateParameter ( )
virtualinherited
RE08* bpp::RE08::clone ( ) const
inlinevirtual

Implements bpp::AbstractReversibleSubstitutionModel.

Definition at line 155 of file RE08.h.

References RE08().

double RE08::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const
virtual
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()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 181 of file RE08.cpp.

References bpp::AbstractSubstitutionModel::freq_, lambda_, mu_, simpleModel_, and bpp::AbstractSubstitutionModel::size_.

double RE08::dPij_dt ( size_t  i,
size_t  j,
double  t 
) const
virtual
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()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 150 of file RE08.cpp.

References bpp::AbstractSubstitutionModel::freq_, lambda_, mu_, simpleModel_, and bpp::AbstractSubstitutionModel::size_.

void bpp::AbstractSubstitutionModel::enableEigenDecomposition ( bool  yn)
inlinevirtualinherited

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 289 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

void bpp::RE08::fireParameterChanged ( const ParameterList parameters)
inlinevirtual

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 179 of file RE08.h.

References bpp::AbstractParameterAliasable::fireParameterChanged(), bpp::AbstractParameterAliasable::getParameter_(), lambda_, mu_, simpleModel_, and updateMatrices().

virtual double bpp::AbstractSubstitutionModel::freq ( size_t  i) const
inlinevirtualinherited
Returns
Equilibrium frequency associated to character i.
See Also
getFrequencies(), getStates()

Implements bpp::SubstitutionModel.

Definition at line 275 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

std::string bpp::AbstractSubstitutionModel::getAlphabetStateAsChar ( size_t  index) const
inlinevirtualinherited
Parameters
indexThe model state.
Returns
The corresponding alphabet state as character code.

Implements bpp::SubstitutionModel.

Definition at line 243 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::stateMap_.

int bpp::AbstractSubstitutionModel::getAlphabetStateAsInt ( size_t  index) const
inlinevirtualinherited
Parameters
indexThe model state.
Returns
The corresponding alphabet state as character code.

Implements bpp::SubstitutionModel.

Definition at line 245 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::stateMap_.

const std::vector<int>& bpp::AbstractSubstitutionModel::getAlphabetStates ( ) const
inlinevirtualinherited
Returns
The alphabet states of each state of the model, as a vector of int codes.
See Also
Alphabet

Implements bpp::SubstitutionModel.

Definition at line 241 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::stateMap_.

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

Implements bpp::SubstitutionModel.

Definition at line 273 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::rightEigenVectors_.

const Matrix< double > & RE08::getd2Pij_dt2 ( double  t) const
virtual
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()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 267 of file RE08.cpp.

References bpp::AbstractSubstitutionModel::freq_, lambda_, mu_, p_, simpleModel_, and bpp::AbstractSubstitutionModel::size_.

const Matrix< double > & RE08::getdPij_dt ( double  t) const
virtual
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()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 239 of file RE08.cpp.

References bpp::AbstractSubstitutionModel::freq_, lambda_, mu_, p_, simpleModel_, and bpp::AbstractSubstitutionModel::size_.

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

Implements bpp::SubstitutionModel.

Definition at line 263 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenValues_.

const Matrix<double>& bpp::AbstractSubstitutionModel::getExchangeabilityMatrix ( ) const
inlinevirtualinherited
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 255 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

virtual const Vdouble& bpp::AbstractSubstitutionModel::getFrequencies ( ) const
inlinevirtualinherited
Returns
A vector of all equilibrium frequencies.
See Also
freq()

Implements bpp::SubstitutionModel.

Definition at line 251 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

const Matrix<double>& bpp::AbstractSubstitutionModel::getGenerator ( ) const
inlinevirtualinherited
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 253 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

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

Implements bpp::SubstitutionModel.

Definition at line 265 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::iEigenValues_.

double RE08::getInitValue ( size_t  i,
int  state 
) const
throw (IndexOutOfBoundsException,
BadIntException
)
virtual

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();

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 297 of file RE08.cpp.

std::vector<size_t> bpp::AbstractSubstitutionModel::getModelStates ( int  code) const
inlinevirtualinherited

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::SubstitutionModel.

Definition at line 247 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::stateMap_.

std::vector<size_t> bpp::AbstractSubstitutionModel::getModelStates ( const std::string &  code) const
inlinevirtualinherited

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::SubstitutionModel.

Definition at line 249 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::stateMap_.

std::string bpp::RE08::getName ( ) const
inlinevirtual

Get the name of the model.

Returns
The name of this model.

Implements bpp::SubstitutionModel.

Definition at line 166 of file RE08.h.

const SubstitutionModel* bpp::RE08::getNestedModel ( ) const
inline

Definition at line 194 of file RE08.h.

References simpleModel_.

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

size_t bpp::RE08::getNumberOfStates ( ) const
inlinevirtual

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::SubstitutionModel.

Definition at line 188 of file RE08.h.

References bpp::AbstractSubstitutionModel::size_.

const Matrix< double > & RE08::getPij_t ( double  t) const
virtual
Returns
All probabilities of change from state i to state j during time t.
See Also
Pij_t()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 213 of file RE08.cpp.

References bpp::AbstractSubstitutionModel::freq_, lambda_, mu_, p_, simpleModel_, and bpp::AbstractSubstitutionModel::size_.

double AbstractSubstitutionModel::getRate ( ) const
virtualinherited

Get the rate.

Implements bpp::SubstitutionModel.

Definition at line 415 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::rate_.

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

Implements bpp::SubstitutionModel.

Definition at line 271 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::leftEigenVectors_.

double AbstractSubstitutionModel::getScale ( ) const
virtualinherited

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 400 of file AbstractSubstitutionModel.cpp.

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

Referenced by bpp::AbstractReversibleSubstitutionModel::updateMatrices().

const StateMap& bpp::AbstractSubstitutionModel::getStateMap ( ) const
inlinevirtualinherited
Returns
The mapping of model states with alphabet states.

Implements bpp::SubstitutionModel.

Definition at line 239 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::stateMap_.

bool bpp::AbstractSubstitutionModel::isDiagonalizable ( ) const
inlinevirtualinherited
Returns
True if the model is diagonalizable in R.

Implements bpp::SubstitutionModel.

Definition at line 267 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isDiagonalizable_.

bool bpp::AbstractSubstitutionModel::isNonSingular ( ) const
inlinevirtualinherited
Returns
True is the model is non-singular.

Implements bpp::SubstitutionModel.

Definition at line 269 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isNonSingular_.

double RE08::Pij_t ( size_t  i,
size_t  j,
double  t 
) const
virtual
Returns
The probability of change from state i to state j during time t.
See Also
getPij_t(), getStates()

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 120 of file RE08.cpp.

References bpp::AbstractSubstitutionModel::freq_, lambda_, mu_, simpleModel_, and bpp::AbstractSubstitutionModel::size_.

virtual double bpp::AbstractSubstitutionModel::Qij ( size_t  i,
size_t  j 
) const
inlinevirtualinherited
Returns
The rate in the generator of change from state i to state j.
See Also
getStates();

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel.

Definition at line 277 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

void bpp::RE08::setFreqFromData ( const SequenceContainer data,
double  pseudoCount = 0 
)
inlinevirtual

This method is forwarded to the simple model.

Parameters
dataThe data to be passed to the simple model (gaps will be ignored).
pseudoCountA (typically small) value to add to each count to avoid 0 estimates.

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 174 of file RE08.h.

References simpleModel_.

void RE08::setNamespace ( const std::string &  prefix)
void AbstractSubstitutionModel::setRate ( double  rate)
virtualinherited
void AbstractSubstitutionModel::setScale ( double  scale)
virtualinherited

Multiplies the current generator by the given scale.

Parameters
scalethe scale by which the generator is multiplied.

Implements bpp::SubstitutionModel.

Definition at line 409 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::generator_, and bpp::MatrixTools::scale().

double bpp::AbstractSubstitutionModel::Sij ( size_t  i,
size_t  j 
) const
inlinevirtualinherited
Returns
The exchangeability between state i and state j.

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

Implements bpp::SubstitutionModel.

Definition at line 257 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

void RE08::updateMatrices ( )
protectedvirtual

Compute and diagonalize the $Q$ matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices.

The exchangeability_ matrix and freq_ vector must be initialized. This function computes the generator_ matrix with the formula

\[ Q = S \times \pi \]

where $Q$ is the generator matrix, $S$ is the exchangeability matrix and $Pi$ the diagonal matrix with frequencies.

The generator is then scaled so that

\[ \sum_i Q_{i,i} \times \pi_i = -1 \]

( $\pi_i$ are the equilibrium frequencies).

Eigen values and vectors are computed from the scaled generator and assigned to the eigenValues_, rightEigenVectors_ and leftEigenVectors_ variables.

Reimplemented from bpp::AbstractReversibleSubstitutionModel.

Definition at line 78 of file RE08.cpp.

References bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractSubstitutionModel::freq_, bpp::AbstractSubstitutionModel::generator_, lambda_, mu_, simpleExchangeabilities_, simpleGenerator_, simpleModel_, bpp::AbstractSubstitutionModel::size_, and bpp::AbstractSubstitutionModel::updateMatrices().

Referenced by fireParameterChanged(), and RE08().

Member Data Documentation

bool bpp::AbstractSubstitutionModel::eigenDecompose_
protectedinherited
double bpp::RE08::exp_
mutableprivate

Definition at line 103 of file RE08.h.

Referenced by operator=().

Vdouble bpp::AbstractSubstitutionModel::freq_
protectedinherited

The vector $\pi_e$ of equilibrium frequencies.

Definition at line 113 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::AbstractSubstitutionModel(), bpp::WordSubstitutionModel::completeMatrices(), bpp::Coala::computeEquilibriumFrequencies(), d2Pij_dt2(), dPij_dt(), bpp::DSO78::DSO78(), bpp::LG08::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::WAG01::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::JCprot::fireParameterChanged(), bpp::AbstractSubstitutionModel::freq(), getd2Pij_dt2(), getdPij_dt(), bpp::AbstractSubstitutionModel::getFrequencies(), bpp::RN95s::getPij_t(), getPij_t(), bpp::RN95::getPij_t(), bpp::AbstractSubstitutionModel::getScale(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::AbstractSubstitutionModel::operator=(), bpp::RN95s::Pij_t(), Pij_t(), bpp::RN95::Pij_t(), RE08(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::AbstractSubstitutionModel::setFreq(), bpp::LG08::setFreqFromData(), bpp::DSO78::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::L95::updateMatrices(), bpp::SSR::updateMatrices(), bpp::MixtureOfASubstitutionModel::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::MixtureOfSubstitutionModels::updateMatrices(), bpp::YpR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().

double bpp::RE08::lambda_
private
double bpp::RE08::mu_
private
std::string bpp::RE08::nestedPrefix_
private

Definition at line 107 of file RE08.h.

Referenced by operator=(), RE08(), and setNamespace().

RowMatrix<double> bpp::RE08::p_
mutableprivate

Definition at line 104 of file RE08.h.

Referenced by getd2Pij_dt2(), getdPij_dt(), getPij_t(), operator=(), and RE08().

RowMatrix<double> bpp::AbstractSubstitutionModel::pijt_
mutableprotectedinherited
double bpp::AbstractSubstitutionModel::rate_
protectedinherited

The rate of the model (default: 1). The generator (and all its vectorial components) is independent of the rate, since it should be normalized.

Definition at line 103 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::addRateParameter(), bpp::RN95s::d2Pij_dt2(), bpp::JCnuc::d2Pij_dt2(), bpp::TN93::d2Pij_dt2(), bpp::RN95::d2Pij_dt2(), bpp::K80::d2Pij_dt2(), bpp::T92::d2Pij_dt2(), bpp::JCprot::d2Pij_dt2(), bpp::HKY85::d2Pij_dt2(), bpp::F84::d2Pij_dt2(), bpp::RN95s::dPij_dt(), bpp::JCnuc::dPij_dt(), bpp::TN93::dPij_dt(), bpp::RN95::dPij_dt(), bpp::K80::dPij_dt(), bpp::T92::dPij_dt(), bpp::JCprot::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::F84::dPij_dt(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::RN95s::getd2Pij_dt2(), bpp::JCnuc::getd2Pij_dt2(), bpp::TN93::getd2Pij_dt2(), bpp::RN95::getd2Pij_dt2(), bpp::K80::getd2Pij_dt2(), bpp::T92::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::F84::getd2Pij_dt2(), bpp::HKY85::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::RN95s::getdPij_dt(), bpp::JCnuc::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::RN95::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::WordSubstitutionModel::getPij_t(), bpp::RN95s::getPij_t(), bpp::JCnuc::getPij_t(), bpp::TN93::getPij_t(), bpp::RN95::getPij_t(), bpp::K80::getPij_t(), bpp::T92::getPij_t(), bpp::JCprot::getPij_t(), bpp::HKY85::getPij_t(), bpp::F84::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getRate(), bpp::AbstractMixedSubstitutionModel::normalizeVRates(), bpp::AbstractSubstitutionModel::operator=(), bpp::RN95s::Pij_t(), bpp::JCnuc::Pij_t(), bpp::TN93::Pij_t(), bpp::RN95::Pij_t(), bpp::K80::Pij_t(), bpp::T92::Pij_t(), bpp::JCprot::Pij_t(), bpp::HKY85::Pij_t(), bpp::F84::Pij_t(), bpp::AbstractMixedSubstitutionModel::setRate(), bpp::AbstractSubstitutionModel::setRate(), and bpp::BinarySubstitutionModel::updateMatrices().

RowMatrix<double> bpp::RE08::simpleExchangeabilities_
private

Definition at line 102 of file RE08.h.

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

RowMatrix<double> bpp::RE08::simpleGenerator_
private

Definition at line 101 of file RE08.h.

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


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