void HeterogeneousRateBirthDeath::executeMethod(const std::string &n, const std::vector<const DagNode *> &args, RbVector<int> &rv) const
{
if ( n == "numberEvents" )
{
size_t num_branches = branch_histories.getNumberBranches();
rv.clear();
rv.resize( num_branches );
for (size_t i = 0; i < num_branches; ++i)
{
rv[i] = int(branch_histories[i].getNumberEvents());
}
}
else
{
throw RbException("The heterogeneous rate birth-death process does not have a member method called '" + n + "'.");
}
}
void HeterogeneousRateBirthDeath::executeMethod(const std::string &n, const std::vector<const DagNode *> &args, RbVector<double> &rv) const
{
if ( n == "averageSpeciationRate" )
{
size_t num_branches = branch_histories.getNumberBranches();
const RbVector<double> &lambda = speciation->getValue();
rv.clear();
rv.resize( num_branches );
for (size_t i = 0; i < num_branches; ++i)
{
const TopologyNode &node = this->value->getNode( i );
const BranchHistory& bh = branch_histories[ i ];
const std::multiset<CharacterEvent*,CharacterEventCompare>& hist = bh.getHistory();
size_t state_index_rootwards = computeStartIndex( node.getParent().getIndex() );
double rate = 0;
double begin_time = 0.0;
double branch_length = node.getBranchLength();
for (std::multiset<CharacterEvent*,CharacterEventCompare>::const_iterator it=hist.begin(); it!=hist.end(); ++it)
{
CharacterEvent* event = *it;
double end_time = event->getTime();
double time_interval = (end_time - begin_time) / branch_length;
// we need to set the current rate caterogy
size_t current_state = event->getState();
rate += time_interval * lambda[current_state];
begin_time = end_time;
}
rate += (branch_length-begin_time)/branch_length * lambda[state_index_rootwards];
rv[i] = rate;
}
}
else if ( n == "averageExtinctionRate" )
{
size_t num_branches = branch_histories.getNumberBranches();
const RbVector<double> &mu = extinction->getValue();
rv.clear();
rv.resize( num_branches );
for (size_t i = 0; i < num_branches; ++i)
{
const TopologyNode &node = this->value->getNode( i );
const BranchHistory& bh = branch_histories[ i ];
const std::multiset<CharacterEvent*,CharacterEventCompare>& hist = bh.getHistory();
size_t state_index_rootwards = computeStartIndex( node.getParent().getIndex() );
double rate = 0;
double begin_time = 0.0;
double branch_length = node.getBranchLength();
for (std::multiset<CharacterEvent*,CharacterEventCompare>::const_iterator it=hist.begin(); it!=hist.end(); ++it)
{
CharacterEvent* event = *it;
double end_time = event->getTime();
double time_interval = (end_time - begin_time) / branch_length;
// we need to set the current rate caterogy
size_t current_state = event->getState();
rate += time_interval * mu[current_state];
begin_time = end_time;
}
rate += (branch_length-begin_time)/branch_length * mu[state_index_rootwards];
rv[i] = rate;
}
}
else
{
throw RbException("The heterogeneous rate birth-death process does not have a member method called '" + n + "'.");
}
}