void CharacterDependentCladoBirthDeathProcess::computeNodeProbability(const RevBayesCore::TopologyNode &node, size_t node_index) const
{
// check for recomputation
if ( dirty_nodes[node_index] || true )
{
// mark as computed
dirty_nodes[node_index] = false;
// get cladogenesis event map (sparse speciation rate matrix)
const DeterministicNode<MatrixReal>* cpn = static_cast<const DeterministicNode<MatrixReal>* >( cladogenesis_matrix );
const TypedFunction<MatrixReal>& tf = cpn->getFunction();
const AbstractCladogenicStateFunction* csf = dynamic_cast<const AbstractCladogenicStateFunction*>( &tf );
std::map<std::vector<unsigned>, double> eventMap = csf->getEventMap();
state_type node_likelihood = std::vector<double>(2*num_states,0);
if ( node.isTip() )
{
// this is a tip node
double samplingProbability = rho->getValue();
const DiscreteCharacterState &state = static_cast<TreeDiscreteCharacterData*>( this->value )->getCharacterData().getTaxonData( node.getTaxon().getName() )[0];
const RbBitSet &obs_state = state.getState();
for (size_t j = 0; j < num_states; ++j)
{
node_likelihood[j] = 1.0 - samplingProbability;
if ( obs_state.isSet( j ) == true || state.isMissingState() == true || state.isGapState() == true )
{
node_likelihood[num_states+j] = samplingProbability;
}
else
{
node_likelihood[num_states+j] = 0.0;
}
}
}
else
{
// this is an internal node
const TopologyNode &left = node.getChild(0);
size_t left_index = left.getIndex();
computeNodeProbability( left, left_index );
const TopologyNode &right = node.getChild(1);
size_t right_index = right.getIndex();
computeNodeProbability( right, right_index );
// get the likelihoods of descendant nodes
const state_type &left_likelihoods = partial_likelihoods[left_index];
const state_type &right_likelihoods = partial_likelihoods[right_index];
// merge descendant likelihoods
for (size_t i=1; i<num_states; ++i)
{
node_likelihood[i] = left_likelihoods[i];
double like_sum = 0.0;
std::map<std::vector<unsigned>, double>::iterator it;
for (it = eventMap.begin(); it != eventMap.end(); it++)
{
const std::vector<unsigned>& states = it->first;
double speciation_rate = it->second;
if (i == states[0])
{
double likelihoods = left_likelihoods[num_states + states[1]] * right_likelihoods[num_states + states[2]];
like_sum += speciation_rate * likelihoods;
}
}
node_likelihood[num_states + i] = like_sum;
}
}
// calculate likelihood for this branch
CDCladoSE ode = CDCladoSE(extinction_rates, &Q->getValue(), eventMap, rate->getValue());
double beginAge = node.getAge();
double endAge = node.getParent().getAge();
double dt = root_age->getValue() / NUM_TIME_SLICES;
// boost::numeric::odeint::runge_kutta4< state_type > stepper;
// boost::numeric::odeint::integrate_const( stepper, ode , node_likelihood , beginAge , endAge, dt );
boost::numeric::odeint::bulirsch_stoer< state_type > stepper(1E-8, 0.0, 0.0, 0.0);
boost::numeric::odeint::integrate_adaptive( stepper, ode , node_likelihood , beginAge , endAge, dt );
// store the likelihoods
partial_likelihoods[node_index] = node_likelihood;
}
}
void StateDependentSpeciationExtinctionProcess::computeNodeProbability(const RevBayesCore::TopologyNode &node, size_t node_index) const
{
// check for recomputation
// if ( dirty_nodes[node_index] == true )
if ( true )
{
// mark as computed
dirty_nodes[node_index] = false;
std::vector<double> node_likelihood = std::vector<double>(2 * num_states, 0);
if ( node.isTip() == true )
{
// this is a tip node
double samplingProbability = rho->getValue();
const DiscreteCharacterState &state = static_cast<TreeDiscreteCharacterData*>( this->value )->getCharacterData().getTaxonData( node.getTaxon().getName() )[0];
const RbBitSet &obs_state = state.getState();
for (size_t j = 0; j < num_states; ++j)
{
node_likelihood[j] = 1.0 - samplingProbability;
if ( obs_state.isSet( j ) == true || state.isMissingState() == true || state.isGapState() == true )
{
node_likelihood[num_states+j] = samplingProbability;
}
else
{
node_likelihood[num_states+j] = 0.0;
}
}
}
else
{
// this is an internal node
const TopologyNode &left = node.getChild(0);
size_t left_index = left.getIndex();
computeNodeProbability( left, left_index );
const TopologyNode &right = node.getChild(1);
size_t right_index = right.getIndex();
computeNodeProbability( right, right_index );
// get the likelihoods of descendant nodes
const std::vector<double> &left_likelihoods = partial_likelihoods[left_index][active_likelihood[left_index]];
const std::vector<double> &right_likelihoods = partial_likelihoods[right_index][active_likelihood[right_index]];
std::map<std::vector<unsigned>, double> eventMap;
std::vector<double> speciation_rates;
if ( use_cladogenetic_events == true )
{
// get cladogenesis event map (sparse speciation rate matrix)
const DeterministicNode<MatrixReal>* cpn = static_cast<const DeterministicNode<MatrixReal>* >( cladogenesis_matrix );
const TypedFunction<MatrixReal>& tf = cpn->getFunction();
const AbstractCladogenicStateFunction* csf = dynamic_cast<const AbstractCladogenicStateFunction*>( &tf );
eventMap = csf->getEventMap();
}
else
{
speciation_rates = lambda->getValue();
}
// merge descendant likelihoods
for (size_t i=0; i<num_states; ++i)
{
node_likelihood[i] = left_likelihoods[i];
if ( use_cladogenetic_events == true )
{
double like_sum = 0.0;
std::map<std::vector<unsigned>, double>::iterator it;
for (it = eventMap.begin(); it != eventMap.end(); it++)
{
const std::vector<unsigned>& states = it->first;
double speciation_rate = it->second;
if (i == states[0])
{
double likelihoods = left_likelihoods[num_states + states[1]] * right_likelihoods[num_states + states[2]];
like_sum += speciation_rate * likelihoods;
}
}
node_likelihood[num_states + i] = like_sum;
}
else
{
node_likelihood[num_states + i] = left_likelihoods[num_states + i] * right_likelihoods[num_states + i] * speciation_rates[i];
}
}
}
// calculate likelihood for this branch
double begin_age = node.getAge();
double end_age = node.getParent().getAge();
numericallyIntegrateProcess(node_likelihood, begin_age, end_age, true, false);
// rescale the states
double max = 0.0;
for (size_t i=0; i<num_states; ++i)
{
if ( node_likelihood[num_states+i] > max )
{
max = node_likelihood[num_states+i];
}
}
for (size_t i=0; i<num_states; ++i)
{
node_likelihood[num_states+i] /= max;
}
scaling_factors[node_index][active_likelihood[node_index]] = log(max);
total_scaling += scaling_factors[node_index][active_likelihood[node_index]] - scaling_factors[node_index][active_likelihood[node_index]^1];
// store the likelihoods
partial_likelihoods[node_index][active_likelihood[node_index]] = node_likelihood;
}
}