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;
}
