bpp-phyl  2.2.0
Public Member Functions | List of all members
bpp::SubstitutionModel Class Referenceabstract

Interface for all substitution models. More...

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

+ Inheritance diagram for bpp::SubstitutionModel:
+ Collaboration diagram for bpp::SubstitutionModel:

Public Member Functions

 SubstitutionModel ()
 
virtual ~SubstitutionModel ()
 
SubstitutionModel * clone () const =0
 
virtual std::string getName () const =0
 Get the name of the model. More...
 
virtual const std::vector< int > & getAlphabetStates () const =0
 
virtual const StateMap & getStateMap () const =0
 
virtual std::vector< size_t > getModelStates (int code) const =0
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
virtual std::vector< size_t > getModelStates (const std::string &code) const =0
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
virtual int getAlphabetStateAsInt (size_t index) const =0
 
virtual std::string getAlphabetStateAsChar (size_t index) const =0
 
virtual double freq (size_t i) const =0
 
virtual double Qij (size_t i, size_t j) const =0
 
virtual double Pij_t (size_t i, size_t j, double t) const =0
 
virtual double dPij_dt (size_t i, size_t j, double t) const =0
 
virtual double d2Pij_dt2 (size_t i, size_t j, double t) const =0
 
virtual const Vdouble & getFrequencies () const =0
 
virtual const Matrix< double > & getGenerator () const =0
 
virtual const Matrix< double > & getExchangeabilityMatrix () const =0
 
virtual double Sij (size_t i, size_t j) const =0
 
virtual const Matrix< double > & getPij_t (double t) const =0
 
virtual const Matrix< double > & getdPij_dt (double t) const =0
 
virtual const Matrix< double > & getd2Pij_dt2 (double t) const =0
 
virtual void enableEigenDecomposition (bool yn)=0
 Set if eigenValues and Vectors must be computed. More...
 
virtual bool enableEigenDecomposition ()=0
 Tell if eigenValues and Vectors must be computed. More...
 
virtual const Vdouble & getEigenValues () const =0
 
virtual const Vdouble & getIEigenValues () const =0
 
virtual bool isDiagonalizable () const =0
 
virtual bool isNonSingular () const =0
 
virtual const Matrix< double > & getRowLeftEigenVectors () const =0
 
virtual const Matrix< double > & getColumnRightEigenVectors () const =0
 
virtual const Alphabet * getAlphabet () const =0
 
virtual size_t getNumberOfStates () const =0
 Get the number of states. More...
 
virtual double getInitValue (size_t i, int state) const =0 throw (IndexOutOfBoundsException, BadIntException)
 
virtual double getScale () const =0
 Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale. More...
 
virtual void setScale (double scale)=0
 Multiplies the current generator by the given scale. More...
 
virtual double getRate () const =0
 Get the rate. More...
 
virtual void setRate (double rate)=0
 Set the rate of the model (must be positive). More...
 
virtual void addRateParameter ()=0
 
virtual void setFreqFromData (const SequenceContainer &data, double pseudoCount=0)=0
 Set equilibrium frequencies equal to the frequencies estimated from the data. More...
 
virtual void setFreq (std::map< int, double > &frequencies)
 Set equilibrium frequencies. More...
 
virtual const FrequenciesSet * getFrequenciesSet () const
 If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0. More...
 

Detailed Description

Interface for all substitution models.

A substitution model is based on a Markov generator $Q$, the size of which depends on the alphabet used (4 for nucleotides, 20 for proteins, etc.). Each SubstitutionModel object hence includes a pointer toward an alphabet, and provides a method to retrieve the alphabet used (getAlphabet() method).

What we want from a substitution model is to compute the probabilities of state j at time t geven state j at time 0 ( $P_{i,j}(t)$). Typically, this is computed using the formula

\[ P(t) = e^{r \times t \times Q}, \]

where $P(t)$ is the matrix with all probabilities $P_{i,j}(t)$, and $ r $ the rate. For some models, the $P_{i,j}(t)$'s can be computed analytically.

For more complex models, we need to use a eigen-decomposition of $Q$:

\[ Q = U^{-1} . D . U, \]

where $D = diag(\lambda_i)$ is a diagonal matrix. Hence

\[ P(t) = e^{r \times t \times Q} = U^{-1} . e^{r \times D \times t} . U, \]

where $e^{r \times D \times t} = diag\left(e^{r \times \lambda_i \times t}\right)$ is a diagonal matrix with all terms equal to exp the terms in $D$ multiplied per $ r \times t $. $U$ is the matrix of left eigen vectors (by row), and $U^{-1}$ is the matrix of right eigen vectors (by column). The values in $D$ are the eigen values of $Q$. All $Q,U,U^{-1}$ and $D$ (its diagonal) may be retrieved from the class (getEigenValues(), getRowRightEigenVectors() and getColumnLeftEigenVectors() functions).

First and second order derivatives of $P(t)$ with respect to $t$ can also be retrieved. These methods may be useful for optimization processes. Derivatives may be computed analytically, or using the general formulas:

\[ \frac{\partial P(t)}{\partial t} = U^{-1} . diag\left(r \times \lambda_i \times e^{r \times \lambda_i \times t}\right) . U \]

and

\[ \frac{\partial^2 P(t)}{\partial t^2} = U^{-1} . diag\left(r^2 \times \lambda_i^2 \times e^{r \times \lambda_i \times t}\right) . U \]

If Q is not symmetric, then the eigenvalue matrix D is block diagonal with the real eigenvalues in 1-by-1 blocks and any complex eigenvalues, a + i*b, in 2-by-2 blocks, [a, b; -b, a]. That is, if the complex eigenvalues look like 

          a + ib   .        .    .
          .        a - ib   .    .
          .        .        x    .
          .        .        .    y

 then D looks like 
          a          b      .    .
         -b          a      .    .
          .          .      x    .
          .          .      .    y

and exp(tD) equals 
          exp(ta)cos(tb)   exp(ta)sin(tb)  .        .
         -exp(ta)sin(tb)   exp(ta)cos(tb)  .        . 
          .                .               exp(tx)  .
          .                .               .        exp(ty)

If U is singular, it cannot be inverted. In this case exp(tQ) is approximated using Taylor decomposition:



\[ P(t) = Id + tQ + \frac{(tQ)^2}{2!} + ... + \frac{(tQ)^n}{n!} + ... \]



To prevent approximation issues, if \f$ max(tQ) \f$ is too high (currently above 0.5), \f$ t \f$ is divided in an ad hoc way (e.g. by \f$ N \f$), and we compute \f$ P(t) = (P(t/N))^N \f$ with a Taylor decomposition for \f$ P(t/N) \f$.


In this case, derivatives according to \f$ t \f$ are computed analytically too. 



Definition at line 199 of file SubstitutionModel.h.


Constructor & Destructor Documentation



◆ SubstitutionModel()








  

  
      

        

          bpp::SubstitutionModel::SubstitutionModel 
          (
          )
          
        

      

  		
  
inline  
  







Definition at line 203 of file SubstitutionModel.h.








◆ ~SubstitutionModel()








  

  
      

        

          virtual bpp::SubstitutionModel::~SubstitutionModel 
          (
          )
          
        

      

  		
  
inlinevirtual  
  







Definition at line 204 of file SubstitutionModel.h.







Member Function Documentation



◆ addRateParameter()








  

  
      

        

          virtual void bpp::SubstitutionModel::addRateParameter 
          (
          )
          
        

      

  		
  
pure virtual  
  







Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::G2001, and bpp::TS98.



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








◆ clone()








  

  
      

        

          SubstitutionModel* bpp::SubstitutionModel::clone 
          (
          )
           const
        

      

  		
  
pure virtual  
  







Implemented in bpp::ReversibleSubstitutionModel, bpp::AbstractReversibleSubstitutionModel, bpp::YpR_Gen, bpp::AbstractSubstitutionModel, bpp::YpR_Sym, bpp::HKY85, bpp::F84, bpp::JCprot, bpp::MarkovModulatedSubstitutionModel, bpp::T92, bpp::K80, bpp::GTR, bpp::RN95, bpp::MixtureOfSubstitutionModels, bpp::TN93, bpp::RE08, bpp::AbstractCodonSubstitutionModel, bpp::JCnuc, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::MixtureOfASubstitutionModel, bpp::WAG01, bpp::SSR, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::L95, bpp::DSO78, bpp::JTT92, bpp::LLG08_EX3, bpp::LG08, bpp::LLG08_EHO, bpp::LLG08_UL3, bpp::CodonRateFrequenciesSubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::G2001, bpp::LG10_EX_EHO, bpp::LGL08_CAT, bpp::LLG08_EX2, bpp::LLG08_UL2, bpp::AbstractMixedSubstitutionModel, bpp::gBGC, bpp::GY94, bpp::YN98, bpp::TS98, bpp::WordSubstitutionModel, bpp::TripletSubstitutionModel, bpp::MG94, bpp::YNGKP_M1, bpp::CodonRateSubstitutionModel, bpp::YNGKP_M8, bpp::Coala, bpp::YNGKP_M7, bpp::YNGKP_M3, bpp::LLG08_EX3::EmbeddedModel, bpp::YNGKP_M2, bpp::LLG08_EHO::EmbeddedModel, bpp::LLG08_UL3::EmbeddedModel, bpp::LG10_EX_EHO::EmbeddedModel, bpp::LGL08_CAT::EmbeddedModel, bpp::LLG08_EX2::EmbeddedModel, bpp::LLG08_UL2::EmbeddedModel, bpp::AbstractBiblioSubstitutionModel, bpp::AbstractBiblioMixedSubstitutionModel, bpp::CodonSubstitutionModel, bpp::MixedSubstitutionModel, bpp::NucleotideSubstitutionModel, and bpp::ProteinSubstitutionModel.



Referenced by bpp::SubstitutionModelSet::addModel(), bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator(), and bpp::YpR::operator=().








◆ d2Pij_dt2()








  

  
      

        

          virtual double bpp::SubstitutionModel::d2Pij_dt2 
          (
          size_t 
          i, 
        

        

          
          
          size_t 
          j, 
        

        

          
          
          double 
          t 
        

        

          
          )
           const
        

      

  		
  
pure 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() 



Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.



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








◆ dPij_dt()








  

  
      

        

          virtual double bpp::SubstitutionModel::dPij_dt 
          (
          size_t 
          i, 
        

        

          
          
          size_t 
          j, 
        

        

          
          
          double 
          t 
        

        

          
          )
           const
        

      

  		
  
pure 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() 



Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.



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








◆ enableEigenDecomposition() [1/2]








  

  
      

        

          virtual void bpp::SubstitutionModel::enableEigenDecomposition 
          (
          bool 
          yn)
          
        

      

  		
  
pure virtual  
  







Set if eigenValues and Vectors must be computed. 



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



Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition(), and bpp::YpR::YpR().








◆ enableEigenDecomposition() [2/2]








  

  
      

        

          virtual bool bpp::SubstitutionModel::enableEigenDecomposition 
          (
          )
          
        

      

  		
  
pure virtual  
  







Tell if eigenValues and Vectors must be computed. 



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








◆ freq()








  

  
      

        

          virtual double bpp::SubstitutionModel::freq 
          (
          size_t 
          i)
           const
        

      

  		
  
pure virtual  
  






Returns
Equilibrium frequency associated to character i. 


See also
getFrequencies(), getStates() 



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



Referenced by bpp::TwoTreeLikelihood::computeTreeD2Likelihood(), bpp::TwoTreeLikelihood::computeTreeDLikelihood(), and bpp::AbstractBiblioSubstitutionModel::freq().








◆ getAlphabet()








  

  
      

        

          virtual const Alphabet* bpp::SubstitutionModel::getAlphabet 
          (
          )
           const
        

      

  		
  
pure virtual  
  






Returns
Get the alphabet associated to this model. 



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



Referenced by bpp::AAExteriorSubstitutionRegister::AAExteriorSubstitutionRegister(), bpp::AAInteriorSubstitutionRegister::AAInteriorSubstitutionRegister(), bpp::SubstitutionModelSet::addModel(), bpp::DecompositionReward::alphabetIndexHasChanged(), bpp::ComprehensiveSubstitutionRegister::ComprehensiveSubstitutionRegister(), bpp::DecompositionReward::DecompositionReward(), bpp::DecompositionSubstitutionCount::DecompositionSubstitutionCount(), bpp::AbstractMutationProcess::detailedEvolve(), bpp::LaplaceSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::AbstractSubstitutionRegister::getAlphabet(), bpp::AbstractBiblioSubstitutionModel::getAlphabet(), bpp::MarkovModulatedSubstitutionModel::getAlphabet(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::DnDsSubstitutionRegister::getType(), bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister(), bpp::CategorySubstitutionRegister::setCategories(), bpp::LaplaceSubstitutionCount::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::DecompositionSubstitutionCount::setSubstitutionModel(), bpp::DecompositionReward::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::substitutionRegisterHasChanged(), bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), bpp::YpR::updateMatrices(), and bpp::BppOSubstitutionModelFormat::writeMixed_().








◆ getAlphabetStateAsChar()








  

  
      

        

          virtual std::string bpp::SubstitutionModel::getAlphabetStateAsChar 
          (
          size_t 
          index)
           const
        

      

  		
  
pure virtual  
  






Parameters

  

    
indexThe model state. 

  

  




Returns
The corresponding alphabet state as character code. 



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



Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetStateAsChar(), bpp::TwoTreeLikelihood::getAlphabetStateAsChar(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsChar(), and bpp::SubstitutionModelSet::getAlphabetStateAsChar().








◆ getAlphabetStateAsInt()








  

  
      

        

          virtual int bpp::SubstitutionModel::getAlphabetStateAsInt 
          (
          size_t 
          index)
           const
        

      

  		
  
pure virtual  
  






Parameters

  

    
indexThe model state. 

  

  




Returns
The corresponding alphabet state as character code. 



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



Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetStateAsInt(), bpp::TwoTreeLikelihood::getAlphabetStateAsInt(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsInt(), bpp::SubstitutionModelSet::getAlphabetStateAsInt(), bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(), bpp::CategorySubstitutionRegister::getCategory(), bpp::SiteSimulationResult::getSite(), bpp::CategorySubstitutionRegister::getType(), bpp::TsTvSubstitutionRegister::getType(), bpp::DnDsSubstitutionRegister::getType(), bpp::GCSynonymousSubstitutionRegister::getType(), and bpp::NonHomogeneousSequenceSimulator::multipleEvolve().








◆ getAlphabetStates()








  

  
      

        

          virtual const std::vector<int>& bpp::SubstitutionModel::getAlphabetStates 
          (
          )
           const
        

      

  		
  
pure virtual  
  






Returns
The alphabet states of each state of the model, as a vector of int codes.


See also
Alphabet 



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



Referenced by bpp::DecompositionReward::computeBMatrice_(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::AbstractBiblioSubstitutionModel::getAlphabetStates(), bpp::TwoTreeLikelihood::getAlphabetStates(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStates(), bpp::SubstitutionModelSet::getAlphabetStates(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::CategorySubstitutionRegister::setCategories(), bpp::NaiveSubstitutionCount::setSubstitutionModel(), and bpp::LabelSubstitutionCount::setSubstitutionModel().








◆ getColumnRightEigenVectors()








  

  
      

        

          virtual const Matrix<double>& bpp::SubstitutionModel::getColumnRightEigenVectors 
          (
          )
           const
        

      

  		
  
pure virtual  
  






Returns
A matrix with right eigen vectors. Each column in the matrix stands for an eigen vector. 



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



Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::DecompositionReward::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getColumnRightEigenVectors(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().








◆ getd2Pij_dt2()








  

  
      

        

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

      

  		
  
pure 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() 



Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::AbstractBiblioSubstitutionModel, and bpp::WordSubstitutionModel.



Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractBiblioSubstitutionModel::getd2Pij_dt2().








◆ getdPij_dt()








  

  
      

        

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

      

  		
  
pure 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() 



Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::AbstractBiblioSubstitutionModel, and bpp::WordSubstitutionModel.



Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractBiblioSubstitutionModel::getdPij_dt().








◆ getEigenValues()








  

  
      

        

          virtual const Vdouble& bpp::SubstitutionModel::getEigenValues 
          (
          )
           const
        

      

  		
  
pure virtual  
  






Returns
A vector with all real parts of the eigen values of the generator of this model; 



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



Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::DecompositionReward::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getEigenValues(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().








◆ getExchangeabilityMatrix()








  

  
      

        

          virtual const Matrix<double>& bpp::SubstitutionModel::getExchangeabilityMatrix 
          (
          )
           const
        

      

  		
  
pure virtual  
  






Returns
The matrix of exchangeability terms. It is recommended that exchangeability matrix be normalized so that the normalized generator be obtained directly by the dot product $S . \pi$. 



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



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








◆ getFrequencies()








  

  
      

        

          virtual const Vdouble& bpp::SubstitutionModel::getFrequencies 
          (
          )
           const
        

      

  		
  
pure virtual  
  






Returns
A vector of all equilibrium frequencies. 


See also
freq() 



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



Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::TwoTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioSubstitutionModel::getFrequencies(), bpp::TwoTreeLikelihood::getRootFrequencies(), bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies(), bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().








◆ getFrequenciesSet()








  

  
      

        

          virtual const FrequenciesSet* bpp::SubstitutionModel::getFrequenciesSet 
          (
          )
           const
        

      

  		
  
inlinevirtual  
  







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::YNGKP_M1, bpp::YNGKP_M8, bpp::YNGKP_M7, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::YNGKP_M3, bpp::YNGKP_M2, and bpp::AbstractCodonFrequenciesSubstitutionModel.



Definition at line 479 of file SubstitutionModel.h.



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








◆ getGenerator()








  

  
      

        

          virtual const Matrix<double>& bpp::SubstitutionModel::getGenerator 
          (
          )
           const
        

      

  		
  
pure virtual  
  






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


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



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



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








◆ getIEigenValues()








  

  
      

        

          virtual const Vdouble& bpp::SubstitutionModel::getIEigenValues 
          (
          )
           const
        

      

  		
  
pure virtual  
  






Returns
A vector with all imaginary parts of the eigen values of the generator of this model; 



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



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








◆ getInitValue()








  

  
      

        

          virtual double bpp::SubstitutionModel::getInitValue 
          (
          size_t 
          i, 
        

        

          
          
          int 
          state 
        

        

          
          )
           const
        

        

          throw (IndexOutOfBoundsException,
        

        

          BadIntException
        

        

          )
        

      

  		
  
pure 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(); 



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



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








◆ getModelStates() [1/2]








  

  
      

        

          virtual std::vector<size_t> bpp::SubstitutionModel::getModelStates 
          (
          int 
          code)
           const
        

      

  		
  
pure virtual  
  







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


Parameters

  

    
codeThe alphabet state to check. 

  

  




Returns
A vector of indices of model states. 



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



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








◆ getModelStates() [2/2]








  

  
      

        

          virtual std::vector<size_t> bpp::SubstitutionModel::getModelStates 
          (
          const std::string & 
          code)
           const
        

      

  		
  
pure virtual  
  







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


Parameters

  

    
codeThe alphabet state to check. 

  

  




Returns
A vector of indices of model states. 



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








◆ getName()








  

  
      

        

          virtual std::string bpp::SubstitutionModel::getName 
          (
          )
           const
        

      

  		
  
pure virtual  
  







Get the name of the model. 


Returns
The name of this model. 



Implemented in bpp::YpR_Gen, bpp::YpR_Sym, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::GTR, bpp::TN93, bpp::RE08, bpp::MixtureOfSubstitutionModels, bpp::JCnuc, bpp::RN95s, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::BinarySubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::MixtureOfASubstitutionModel, bpp::LLG08_EX3, bpp::WordSubstitutionModel, bpp::LLG08_EHO, bpp::LLG08_UL3, bpp::WAG01, bpp::SSR, bpp::LG10_EX_EHO, bpp::CodonDistanceSubstitutionModel, bpp::L95, bpp::LGL08_CAT, bpp::LLG08_EX2, bpp::LLG08_UL2, bpp::DSO78, bpp::JTT92, bpp::CodonRateFrequenciesSubstitutionModel, bpp::LG08, bpp::YNGKP_M1, bpp::G2001, bpp::gBGC, bpp::YNGKP_M8, bpp::GY94, bpp::YNGKP_M7, bpp::YN98, bpp::YNGKP_M3, bpp::TS98, bpp::TripletSubstitutionModel, bpp::YNGKP_M2, bpp::MG94, bpp::CodonRateSubstitutionModel, bpp::Coala, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_EHO::EmbeddedModel, bpp::LLG08_UL3::EmbeddedModel, bpp::LG10_EX_EHO::EmbeddedModel, bpp::LGL08_CAT::EmbeddedModel, bpp::LLG08_EX2::EmbeddedModel, and bpp::LLG08_UL2::EmbeddedModel.



Referenced by bpp::AbstractCodonFitnessSubstitutionModel::AbstractCodonFitnessSubstitutionModel(), bpp::AbstractSubstitutionModel::fireParameterChanged(), bpp::MixtureOfSubstitutionModels::getSubmodelNumbers(), bpp::BppOSubstitutionModelFormat::readMixed_(), bpp::AbstractBiblioSubstitutionModel::updateMatrices(), and bpp::BppOSubstitutionModelFormat::write().








◆ getNumberOfStates()








  

  
      

        

          virtual size_t bpp::SubstitutionModel::getNumberOfStates 
          (
          )
           const
        

      

  		
  
pure virtual  
  







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::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::YpR, bpp::AbstractBiblioSubstitutionModel, bpp::AbstractWordSubstitutionModel, bpp::BinarySubstitutionModel, bpp::gBGC, bpp::NucleotideSubstitutionModel, and bpp::ProteinSubstitutionModel.



Referenced by bpp::SubstitutionModelSet::addModel(), bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::TwoTreeLikelihood::getNumberOfStates(), bpp::AbstractBiblioSubstitutionModel::getNumberOfStates(), bpp::AbstractHomogeneousTreeLikelihood::getNumberOfStates(), bpp::BranchLikelihood::initModel(), bpp::RE08::RE08(), bpp::SimpleMutationProcess::SimpleMutationProcess(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().








◆ getPij_t()








  

  
      

        

          virtual const Matrix<double>& bpp::SubstitutionModel::getPij_t 
          (
          double 
          t)
           const
        

      

  		
  
pure virtual  
  






Returns
All probabilities of change from state i to state j during time t. 


See also
Pij_t() 



Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::AbstractBiblioSubstitutionModel, and bpp::WordSubstitutionModel.



Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeCounts_(), bpp::DecompositionReward::computeRewards_(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), and bpp::AbstractBiblioSubstitutionModel::getPij_t().








◆ getRate()








  

  
      

        

          virtual double bpp::SubstitutionModel::getRate 
          (
          )
           const
        

      

  		
  
pure virtual  
  







Get the rate. 



Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::G2001, and bpp::TS98.



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








◆ getRowLeftEigenVectors()








  

  
      

        

          virtual const Matrix<double>& bpp::SubstitutionModel::getRowLeftEigenVectors 
          (
          )
           const
        

      

  		
  
pure virtual  
  






Returns
A matrix with left eigen vectors. Each row in the matrix stands for an eigen vector. 



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



Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::DecompositionReward::computeEigen_(), and bpp::AbstractBiblioSubstitutionModel::getRowLeftEigenVectors().








◆ getScale()








  

  
      

        

          virtual double bpp::SubstitutionModel::getScale 
          (
          )
           const
        

      

  		
  
pure virtual  
  







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


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



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



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








◆ getStateMap()








  

  
      

        

          virtual const StateMap& bpp::SubstitutionModel::getStateMap 
          (
          )
           const
        

      

  		
  
pure virtual  
  






Returns
The mapping of model states with alphabet states. 



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



Referenced by bpp::AbstractBiblioSubstitutionModel::getStateMap(), bpp::SubstitutionModelSet::getStateMap(), and bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator().








◆ isDiagonalizable()








  

  
      

        

          virtual bool bpp::SubstitutionModel::isDiagonalizable 
          (
          )
           const
        

      

  		
  
pure virtual  
  






Returns
True if the model is diagonalizable in R. 



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



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








◆ isNonSingular()








  

  
      

        

          virtual bool bpp::SubstitutionModel::isNonSingular 
          (
          )
           const
        

      

  		
  
pure virtual  
  






Returns
True is the model is non-singular. 



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



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








◆ Pij_t()








  

  
      

        

          virtual double bpp::SubstitutionModel::Pij_t 
          (
          size_t 
          i, 
        

        

          
          
          size_t 
          j, 
        

        

          
          
          double 
          t 
        

        

          
          )
           const
        

      

  		
  
pure virtual  
  






Returns
The probability of change from state i to state j during time t. 


See also
getPij_t(), getStates() 



Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.



Referenced by bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::SimpleMutationProcess::evolve(), bpp::OneJumpSubstitutionCount::getNumberOfSubstitutions(), and bpp::AbstractBiblioSubstitutionModel::Pij_t().








◆ Qij()








  

  
      

        

          virtual double bpp::SubstitutionModel::Qij 
          (
          size_t 
          i, 
        

        

          
          
          size_t 
          j 
        

        

          
          )
           const
        

      

  		
  
pure virtual  
  






Returns
The rate in the generator of change from state i to state j.


See also
getStates(); 



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



Referenced by bpp::UniformizationSubstitutionCount::fillBMatrices_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::AbstractMutationProcess::getTimeBeforeNextMutationEvent(), bpp::AbstractBiblioSubstitutionModel::Qij(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), and bpp::YpR::updateMatrices().








◆ setFreq()








  

  
      

        

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

      

  		
  
inlinevirtual  
  







Set equilibrium frequencies. 


Parameters

  

    
frequenciesThe map of the frequencies to use. 

  

  





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



Definition at line 473 of file SubstitutionModel.h.



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








◆ setFreqFromData()








  

  
      

        

          virtual void bpp::SubstitutionModel::setFreqFromData 
          (
          const SequenceContainer & 
          data, 
        

        

          
          
          double 
          pseudoCount = 0 
        

        

          
          )
          
        

      

  		
  
pure virtual  
  







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


Parameters

  

    
dataThe sequences to use. 

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

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


 

  

  





Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::K80, bpp::RE08, bpp::JCnuc, bpp::UserProteinSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::WAG01, bpp::DSO78, bpp::JTT92, bpp::LG08, and bpp::Coala.



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








◆ setRate()








  

  
      

        

          virtual void bpp::SubstitutionModel::setRate 
          (
          double 
          rate)
          
        

      

  		
  
pure virtual  
  







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


Parameters

  

    
ratemust be positive. 

  

  





Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::G2001, and bpp::TS98.



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








◆ setScale()








  

  
      

        

          virtual void bpp::SubstitutionModel::setScale 
          (
          double 
          scale)
          
        

      

  		
  
pure virtual  
  







Multiplies the current generator by the given scale. 


Parameters

  

    
scalethe scale by which the generator is multiplied. 

  

  





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



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








◆ Sij()








  

  
      

        

          virtual double bpp::SubstitutionModel::Sij 
          (
          size_t 
          i, 
        

        

          
          
          size_t 
          j 
        

        

          
          )
           const
        

      

  		
  
pure virtual  
  






Returns
The exchangeability between state i and state j.


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



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



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







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