ParameterList SubstitutionProcessCollectionMember::getNonDerivableParameters() const { ParameterList pl = getSubstitutionModelParameters(true); pl.includeParameters(getRootFrequenciesParameters(true)); pl.includeParameters(getRateDistributionParameters(true)); // patch, to be fixed properly later pl.includeParameters(getBranchLengthParameters(true)); return pl; }
ParameterList SetOfAbstractPhyloLikelihood::getRootFrequenciesParameters() const { ParameterList pl; for (size_t i=0; i<nPhylo_.size(); i++) pl.includeParameters(getAbstractPhyloLikelihood(nPhylo_[i])->getRootFrequenciesParameters()); return pl; }
ParameterList SetOfAbstractPhyloLikelihood::getSubstitutionModelParameters() const { ParameterList pl; for (size_t i=0; i<nPhylo_.size(); i++) pl.includeParameters(getAbstractPhyloLikelihood(nPhylo_[i])->getSubstitutionModelParameters()); return pl; }
ParameterList SubstitutionProcessCollectionMember::getSubstitutionModelParameters(bool independent) const { ParameterList pl; // Then we update all models in the set: std::map<size_t, std::vector<int> >::const_iterator it; for (it = modelToNodes_.begin(); it != modelToNodes_.end(); it++) { pl.includeParameters(pSubProColl_->getSubstitutionModelParameters(it->first, independent)); } return pl; }