void FONSEModel::calculateLogLikelihoodRatioForHyperParameters(Genome &genome, unsigned iteration, std::vector <double> & logProbabilityRatio)
{
double lpr = 0.0;
unsigned selectionCategory = getNumSynthesisRateCategories();
std::vector<double> currentStdDevSynthesisRate(selectionCategory, 0.0);
std::vector<double> currentMphi(selectionCategory, 0.0);
std::vector<double> proposedStdDevSynthesisRate(selectionCategory, 0.0);
std::vector<double> proposedMphi(selectionCategory, 0.0);
for (unsigned i = 0u; i < selectionCategory; i++)
{
currentStdDevSynthesisRate[i] = getStdDevSynthesisRate(i, false);
currentMphi[i] = -((currentStdDevSynthesisRate[i] * currentStdDevSynthesisRate[i]) / 2);
proposedStdDevSynthesisRate[i] = getStdDevSynthesisRate(i, true);
proposedMphi[i] = -((proposedStdDevSynthesisRate[i] * proposedStdDevSynthesisRate[i]) / 2);
// take the Jacobian into account for the non-linear transformation from logN to N distribution
lpr -= (std::log(currentStdDevSynthesisRate[i]) - std::log(proposedStdDevSynthesisRate[i]));
}
logProbabilityRatio.resize(1);
#ifdef _OPENMP
//#ifndef __APPLE__
#pragma omp parallel for reduction(+:lpr)
#endif
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
unsigned mixture = getMixtureAssignment(i);
mixture = getSynthesisRateCategory(mixture);
double phi = getSynthesisRate(i, mixture, false);
lpr += Parameter::densityLogNorm(phi, proposedMphi[mixture], proposedStdDevSynthesisRate[mixture], true)
- Parameter::densityLogNorm(phi, currentMphi[mixture], currentStdDevSynthesisRate[mixture], true);
}
logProbabilityRatio[0] = lpr;
}
void FONSEModel::printHyperParameters()
{
for (unsigned i = 0u; i < getNumSynthesisRateCategories(); i++)
{
my_print("stdDevSynthesisRate posterior estimate for selection category %: %\n", i, getStdDevSynthesisRate(i));
}
my_print("\t current stdDevSynthesisRate proposal width: %\n", getCurrentStdDevSynthesisRateProposalWidth());
}
void FONSEModel::printHyperParameters()
{
for(unsigned i = 0u; i < getNumSynthesisRateCategories(); i++)
{
std::cout << "stdDevSynthesisRate posterior estimate for selection category " << i << ": " << getStdDevSynthesisRate(i) << std::endl;
}
std::cout << "\t current stdDevSynthesisRate proposal width: " << getCurrentStdDevSynthesisRateProposalWidth() << std::endl;
}
