bpp-phyl  2.4.0
bpp::RN95s Class Referenceabstract

Intersection of models RN95 and L95. More...

#include <Bpp/Phyl/Model/Nucleotide/RN95s.h>

+ Inheritance diagram for bpp::RN95s:
+ Collaboration diagram for bpp::RN95s:

Public Member Functions

 RN95s (const NucleicAlphabet *alphabet, double alpha=1, double beta=1, double gamma=1, double delta=1)
 
virtual ~RN95s ()
 
RN95sclone () 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 updateMatrices ()
 Diagonalize the $Q$ matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...
 
void setFreq (std::map< int, double > &)
 This method takes the average value between observed $\pi_A$ and $\pi_T$. More...
 
const NucleicAlphabetgetAlphabet () 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...
 
const VdoublegetFrequencies () const
 
bool computeFrequencies () const
 
void computeFrequencies (bool yn)
 
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
 
double getInitValue (size_t i, int state) const
 
void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
 Set equilibrium frequencies equal to the frequencies estimated from the data. 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...
 
virtual void fireParameterChanged (const ParameterList &parameters)
 Tells the model that a parameter value has changed. More...
 
void addRateParameter ()
 add a "rate" parameter to the model, that handles the overall rate of the process. More...
 
void setScalable (bool scalable)
 sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example. More...
 
virtual bool isScalable () const
 returns if model is scalable More...
 
double getScale () const
 return scale More...
 
void setScale (double scale)
 Multiplies the current generator by the given scale. More...
 
void normalize ()
 normalize the generator More...
 
void setDiagonal ()
 set the diagonal of the generator such that sum on each line equals 0. More...
 
virtual double getRate () const
 The rate of the substitution process. More...
 
virtual void setRate (double rate)
 Set the rate of the model (must be positive). More...
 
virtual size_t getNumberOfStates () const =0
 Get the number of states. More...
 
size_t getNumberOfStates () const
 Get the number of states. 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
 
virtual std::vector< std::string > getAlias (const std::string &name) const
 
virtual std::map< std::string, std::string > getAliases () const =0
 
virtual std::map< std::string, std::string > getAliases () const
 
virtual bool hasParameter (const std::string &name) const =0
 
bool hasParameter (const std::string &name) const
 
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
 
bool hasIndependentParameter (const std::string &name) const
 
ParameterList getAliasedParameters (const ParameterList &pl) const
 
ParameterList getFromParameters (const ParameterList &pl) const
 
std::string getFrom (const std::string &name) const
 
const std::shared_ptr< Parameter > & getSharedParameter (const std::string &name) const
 

Protected Member Functions

VdoublegetFrequencies_ ()
 
const std::shared_ptr< Parameter > & getSharedParameter (size_t i) const
 
std::shared_ptr< Parameter > & getSharedParameter (size_t i)
 
void addParameter_ (Parameter *parameter)
 
void addParameters_ (const ParameterList &parameters)
 
void includeParameters_ (const ParameterList &parameters)
 
void deleteParameter_ (size_t index)
 
void deleteParameter_ (std::string &name)
 
void deleteParameters_ (const std::vector< std::string > &names)
 
void resetParameters_ ()
 
void shareParameter_ (const std::shared_ptr< Parameter > &parameter)
 
void shareParameters_ (const ParameterList &parameters)
 
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::shared_ptr< const 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...
 
bool isScalable_
 If the model is scalable (ie generator can be normalized automatically). 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...
 
bool computeFreq_
 if the Frequencies must be computed from the generator 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

double alpha_
 
double beta_
 
double gamma_
 
double delta_
 
double r_
 
double c3_
 
double c4_
 
double c8_
 
RowMatrix< double > p_
 
double exp1_
 
double exp3_
 
double l_
 

Detailed Description

Intersection of models RN95 and L95.

The two hypotheses are that the transversion rates are only dependent of the target nucleotide, and strand symmetry.

After normalization this model has 3 parameters:

\[ Q= \frac 1P \begin{pmatrix} . & \gamma & \alpha & \delta \\ \delta & . & \gamma & \beta \\ \beta & \gamma & . & \delta \\ \delta & \alpha & \gamma & .\\ \end{pmatrix}\]

so in the parametrization process we set:

\[\gamma+\delta=\frac 12\]

The stationnary distribution

\[ \pi = \left(\pi_A, \pi_C, \pi_G, \pi_T\right) \]

is such as

\[\pi_A=\pi_T\]

and

\[\pi_C=\pi_G\]

It can be computed analytically.

We use as parameters:

\[ \begin{cases} \theta_A (=\pi_A) \in ]0;1/2[\\ \gamma \in ]0;1/2[\\ \alpha' > 1 \end{cases} \]

where

\[\alpha'=\frac{2\alpha\pi_A+min(0.5-\pi_A,\gamma)}{0.5-\pi_A}\]

.

The generator is then computed as:

\[ \begin{cases} \delta=\frac 12-\gamma\\ \alpha=\frac{\alpha'(0.5-\pi_A)-min(0.5-\pi_A,\gamma)}{2\pi_A}\\ \beta=\frac{2*\pi_A*(\alpha+\frac 12)-\delta}{1-2*\pi_A}\\ \end{cases} \]

and $P$ is set for normalization.

The parameters are named "thetaA", "gamma", "alphaP".

References:

  • Rhetsky A. & Ney M. (1995) MBE 12(1) 131-151.
  • Lobry J R (1995), Journal_ Of Molecular Evolution_ 40 326-330.
  • Schadt, Sinsheimer & Lange (1998) Genome Research 8 222-233.

Definition at line 110 of file RN95s.h.

Constructor & Destructor Documentation

RN95s::RN95s ( const NucleicAlphabet alphabet,
double  alpha = 1,
double  beta = 1,
double  gamma = 1,
double  delta = 1 
)
virtual bpp::RN95s::~RN95s ( )
inlinevirtual

Definition at line 130 of file RN95s.h.

Member Function Documentation

void AbstractSubstitutionModel::addRateParameter ( )
virtualinherited
RN95s* bpp::RN95s::clone ( ) const
inlinevirtual
void bpp::AbstractSubstitutionModel::computeFrequencies ( bool  yn)
inlinevirtualinherited
Returns
Set if equilibrium frequencies should be computed from the generator

Implements bpp::TransitionModel.

Definition at line 269 of file AbstractSubstitutionModel.h.

double RN95s::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 322 of file RN95s.cpp.

References alpha_, beta_, c3_, c4_, c8_, delta_, exp1_, exp3_, gamma_, l_, r_, and bpp::AbstractSubstitutionModel::rate_.

Referenced by clone().

double RN95s::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 267 of file RN95s.cpp.

References alpha_, beta_, c3_, c4_, c8_, delta_, exp1_, exp3_, gamma_, l_, r_, and bpp::AbstractSubstitutionModel::rate_.

Referenced by clone().

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

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 307 of file AbstractSubstitutionModel.h.

virtual void bpp::AbstractSubstitutionModel::fireParameterChanged ( const ParameterList parameters)
inlinevirtualinherited

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

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

Definition at line 316 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::addRateParameter(), bpp::AbstractParameterAliasable::fireParameterChanged(), bpp::AbstractParameterAliasable::getNamespace(), bpp::ParameterList::getParameterValue(), bpp::ParameterList::hasParameter(), bpp::ParameterList::size(), and bpp::AbstractSubstitutionModel::updateMatrices().

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

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

Implements bpp::TransitionModel.

Definition at line 293 of file AbstractSubstitutionModel.h.

const NucleicAlphabet* bpp::AbstractNucleotideSubstitutionModel::getAlphabet ( ) const
inlinevirtualinherited
Returns
Get the alphabet associated to this model.

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 108 of file NucleotideSubstitutionModel.h.

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

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 257 of file AbstractSubstitutionModel.h.

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

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 259 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices(), and bpp::AbstractSubstitutionModel::getInitValue().

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::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 255 of file AbstractSubstitutionModel.h.

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 291 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::rightEigenVectors_.

const Matrix< double > & RN95s::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 441 of file RN95s.cpp.

References alpha_, beta_, c3_, c4_, c8_, delta_, exp1_, exp3_, gamma_, l_, p_, r_, and bpp::AbstractSubstitutionModel::rate_.

Referenced by clone().

const Matrix< double > & RN95s::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 410 of file RN95s.cpp.

References alpha_, beta_, c3_, c4_, c8_, delta_, exp1_, exp3_, gamma_, l_, p_, r_, and bpp::AbstractSubstitutionModel::rate_.

Referenced by clone().

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 281 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 273 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

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

Implements bpp::TransitionModel.

Definition at line 265 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

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

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 271 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

Referenced by bpp::AbstractKroneckerWordSubstitutionModel::fillBasicGenerator().

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 283 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::iEigenValues_.

double AbstractSubstitutionModel::getInitValue ( size_t  i,
int  state 
) const
virtualinherited

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::TransitionModel.

Reimplemented in bpp::RE08.

Definition at line 541 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::alphabet_, bpp::Alphabet::getAlias(), bpp::AbstractSubstitutionModel::getAlphabetStateAsInt(), bpp::Alphabet::intToChar(), and bpp::AbstractSubstitutionModel::size_.

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

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::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 261 of file AbstractSubstitutionModel.h.

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::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 263 of file AbstractSubstitutionModel.h.

std::string bpp::RN95s::getName ( ) const
inlinevirtual

Get the name of the model.

Returns
The name of this model.

Implements bpp::TransitionModel.

Definition at line 142 of file RN95s.h.

References setFreq(), and updateMatrices().

size_t bpp::NucleotideSubstitutionModel::getNumberOfStates ( ) const
inlinevirtualinherited

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::TransitionModel.

Reimplemented in bpp::RE08Nucleotide.

Definition at line 64 of file NucleotideSubstitutionModel.h.

References bpp::NucleotideSubstitutionModel::getAlphabet().

virtual size_t bpp::TransitionModel::getNumberOfStates ( ) const
pure virtualinherited

Get the number of states.

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

See also
getAlphabetChars for the list of supported states.
Returns
The number of different states in the model.

Implemented in bpp::RE08Codon, bpp::RE08Protein, bpp::RE08Nucleotide, bpp::AbstractWordSubstitutionModel, bpp::RegisterRatesSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::YpR, bpp::BinarySubstitutionModel, bpp::gBGC, bpp::AbstractWrappedModel, bpp::AnonymousSubstitutionModel, bpp::NucleotideSubstitutionModel, and bpp::ProteinSubstitutionModel.

Referenced by bpp::SubstitutionModelSet::addModel(), bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::AbstractWrappedModel::getNumberOfStates(), bpp::TwoTreeLikelihood::getNumberOfStates(), bpp::AbstractHomogeneousTreeLikelihood::getNumberOfStates(), bpp::RegisterRatesSubstitutionModel::getNumberOfStates(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::BranchLikelihood::initModel(), bpp::RE08::RE08(), bpp::AbstractHomogeneousTreeLikelihood::setModel(), bpp::CategorySubstitutionRegister::setModelCategories(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::DecompositionMethods::setSubstitutionModel(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::TwoTreeLikelihood::TwoTreeLikelihood(), bpp::MarkovModulatedSubstitutionModel::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().

const Matrix< double > & RN95s::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 378 of file RN95s.cpp.

References alpha_, beta_, c3_, c4_, c8_, delta_, exp1_, exp3_, bpp::AbstractSubstitutionModel::freq_, gamma_, l_, p_, r_, and bpp::AbstractSubstitutionModel::rate_.

Referenced by clone().

double AbstractSubstitutionModel::getRate ( ) const
virtualinherited

The rate of the substitution process.

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 643 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::rate_.

Referenced by bpp::AbstractSubstitutionModel::isScalable().

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 289 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::leftEigenVectors_.

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

Implements bpp::TransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 253 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 285 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 287 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isNonSingular_.

double RN95s::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 212 of file RN95s.cpp.

References alpha_, beta_, c3_, c4_, c8_, delta_, exp1_, exp3_, bpp::AbstractSubstitutionModel::freq_, gamma_, l_, r_, and bpp::AbstractSubstitutionModel::rate_.

Referenced by clone().

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 295 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

void RN95s::setFreq ( std::map< int, double > &  freqs)
virtual

This method takes the average value between observed $\pi_A$ and $\pi_T$.

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 472 of file RN95s.cpp.

References bpp::AbstractParameterAliasable::setParameterValue(), and updateMatrices().

Referenced by getName().

void AbstractSubstitutionModel::setFreqFromData ( const SequenceContainer data,
double  pseudoCount = 0 
)
virtualinherited

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

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

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

Implements bpp::TransitionModel.

Reimplemented in bpp::JCprot, bpp::K80, bpp::RE08, bpp::JCnuc, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::JTT92, bpp::DSO78, bpp::LG08, and bpp::Coala.

Definition at line 559 of file AbstractSubstitutionModel.cpp.

References bpp::SequenceContainerTools::getCounts(), bpp::AbstractSubstitutionModel::setFreq(), and bpp::AbstractSubstitutionModel::size_.

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

void AbstractSubstitutionModel::setRate ( double  rate)
virtualinherited
void bpp::AbstractSubstitutionModel::setScalable ( bool  scalable)
inlinevirtualinherited

sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example.

Implements bpp::SubstitutionModel.

Definition at line 376 of file AbstractSubstitutionModel.h.

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 275 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), and bpp::AbstractSubstitutionModel::getPij_t().

void RN95s::updateMatrices ( )
virtual

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

The generator_ matrix and freq_ vector must be initialized.

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

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

!! Here there is no normalization of the generator.

Now check inversion and diagonalization

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 93 of file RN95s.cpp.

References alpha_, beta_, c3_, c4_, c8_, delta_, bpp::ApplicationTools::displayMessage(), bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::enableEigenDecomposition(), bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractSubstitutionModel::freq_, gamma_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractSubstitutionModel::iEigenValues_, bpp::MatrixTools::inv(), bpp::AbstractSubstitutionModel::isDiagonalizable_, bpp::AbstractSubstitutionModel::isNonSingular_, bpp::AbstractSubstitutionModel::isScalable(), bpp::AbstractSubstitutionModel::leftEigenVectors_, r_, bpp::AbstractSubstitutionModel::rightEigenVectors_, bpp::AbstractSubstitutionModel::setScale(), bpp::AbstractSubstitutionModel::size_, bpp::MatrixTools::Taylor(), bpp::NumConstants::TINY(), and bpp::AbstractSubstitutionModel::vPowGen_.

Referenced by getName(), RN95s(), and setFreq().

Member Data Documentation

double bpp::RN95s::alpha_
private

Definition at line 114 of file RN95s.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), Pij_t(), RN95s(), and updateMatrices().

double bpp::RN95s::beta_
private

Definition at line 114 of file RN95s.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), Pij_t(), RN95s(), and updateMatrices().

double bpp::RN95s::c3_
private

For calculation purposes as in Schadt & al. (with c1_=1)

Definition at line 119 of file RN95s.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), Pij_t(), and updateMatrices().

double bpp::RN95s::c4_
private

Definition at line 119 of file RN95s.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), Pij_t(), and updateMatrices().

double bpp::RN95s::c8_
private

Definition at line 119 of file RN95s.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), Pij_t(), and updateMatrices().

bool bpp::AbstractSubstitutionModel::computeFreq_
protectedinherited
double bpp::RN95s::delta_
private

Definition at line 114 of file RN95s.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), Pij_t(), RN95s(), and updateMatrices().

bool bpp::AbstractSubstitutionModel::eigenDecompose_
protectedinherited
double bpp::RN95s::exp1_
mutableprivate

Definition at line 121 of file RN95s.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), and Pij_t().

double bpp::RN95s::exp3_
mutableprivate

Definition at line 121 of file RN95s.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), and Pij_t().

Vdouble bpp::AbstractSubstitutionModel::freq_
protectedinherited

The vector $\pi_e$ of equilibrium frequencies.

Definition at line 121 of file AbstractSubstitutionModel.h.

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

double bpp::RN95s::gamma_
private

Definition at line 114 of file RN95s.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), Pij_t(), RN95s(), and updateMatrices().

bool bpp::AbstractSubstitutionModel::isScalable_
protectedinherited
double bpp::RN95s::l_
mutableprivate

Definition at line 121 of file RN95s.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), and Pij_t().

RowMatrix<double> bpp::RN95s::p_
mutableprivate

Definition at line 120 of file RN95s.h.

Referenced by getd2Pij_dt2(), getdPij_dt(), and getPij_t().

RowMatrix<double> bpp::AbstractSubstitutionModel::pijt_
mutableprotectedinherited
double bpp::RN95s::r_
private

Definition at line 115 of file RN95s.h.

Referenced by d2Pij_dt2(), dPij_dt(), getd2Pij_dt2(), getdPij_dt(), getPij_t(), Pij_t(), and updateMatrices().

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 111 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::addRateParameter(), bpp::BinarySubstitutionModel::d2Pij_dt2(), 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::F84::d2Pij_dt2(), bpp::HKY85::d2Pij_dt2(), bpp::BinarySubstitutionModel::dPij_dt(), 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::F84::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::BinarySubstitutionModel::getd2Pij_dt2(), 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::BinarySubstitutionModel::getdPij_dt(), 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::F84::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::WordSubstitutionModel::getPij_t(), bpp::BinarySubstitutionModel::getPij_t(), 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::F84::getPij_t(), bpp::HKY85::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getRate(), bpp::AbstractMixedSubstitutionModel::normalizeVRates(), bpp::AbstractSubstitutionModel::operator=(), bpp::BinarySubstitutionModel::Pij_t(), 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::F84::Pij_t(), bpp::HKY85::Pij_t(), bpp::AbstractMixedSubstitutionModel::setRate(), bpp::AbstractSubstitutionModel::setRate(), bpp::BinarySubstitutionModel::updateMatrices(), and bpp::MixtureOfSubstitutionModels::updateMatrices().

std::shared_ptr<const StateMap> bpp::AbstractSubstitutionModel::stateMap_
protectedinherited
std::vector< RowMatrix<double> > bpp::AbstractSubstitutionModel::vPowGen_
protectedinherited

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