void AdmixtureEdgeReplaceResidualsFNPR::storeAdmixtureEventsForLineage(AdmixtureNode* p)
{
AdmixtureTree& tau = variable->getValue();
AdmixtureNode* q_it = &p->getParent();
while (q_it->getNumberOfChildren() == 1)
{
AdmixtureNode* qp = q_it;
// adm parent
if (&q_it->getAdmixtureChild() != NULL)
;
// adm child
else if (&q_it->getAdmixtureParent() != NULL)
qp = &q_it->getAdmixtureParent();
// divergence
else
break;
AdmixtureNode* qc = &qp->getAdmixtureChild();
AdmixtureNode* qpc = &qp->getChild(0);
AdmixtureNode* qcc = &qc->getChild(0);
//std::cout << "rem " << qp << " " << qc << " " << qpc << " " << qcc << "\n";
AdmixtureEdgePosition ap(qp, qc, qpc, qcc, qc->getAge(), qc->getWeight());
storedAdmixtureEdges.push_front(ap);
tau.removeAdmixtureEdge(qp);
tau.eraseAdmixtureNode(qp);
tau.eraseAdmixtureNode(qc);
q_it = &p->getParent();
}
}
/** Perform the move */
double AdmixtureShiftNodeAgeAndRate::performSimpleMove( void ) {
failed = false;
//std::cout << "\nAge-Rate Shift\n";
// clear old rates
storedRates.clear();
// Get random number generator
RandomNumberGenerator* rng = GLOBAL_RNG;
AdmixtureTree& tau = variable->getValue();
AdmixtureNode* node = &tau.getNode(nodeIndex);
AdmixtureNode& parent = node->getParent();
// we need to work with the times
double parent_age = parent.getAge();
double my_age = node->getAge();
double child_Age = node->getChild( 0 ).getAge();
if ( node->getNumberOfChildren() > 1 && child_Age < node->getChild( 1 ).getAge()) {
child_Age = node->getChild( 1 ).getAge();
}
// admixture node ages are further constrained by their partner's time
if (&node->getAdmixtureChild() != NULL)
{
AdmixtureNode& admixtureChild = node->getAdmixtureChild();
double other_parent_age = admixtureChild.getParent().getAge();
if (parent_age > other_parent_age)
parent_age = other_parent_age;
double other_child_age = admixtureChild.getChild(0).getAge();
if (child_Age < other_child_age)
child_Age = other_child_age;
}
else if (&node->getAdmixtureParent() != NULL)
{
AdmixtureNode& admixtureParent = node->getAdmixtureParent();
double other_parent_age = admixtureParent.getParent().getAge();
if (parent_age > other_parent_age)
parent_age = other_parent_age;
double other_child_age = admixtureParent.getChild(0).getAge();
if (child_Age < other_child_age)
child_Age = other_child_age;
}
// now we store all necessary values
storedNode = node;
storedAge = my_age;
// draw new age
double ageRange = parent_age - child_Age;
double unitAge = (storedAge - child_Age) / ageRange;
double a = delta * unitAge + 1.0;
double b = delta * (1.0 - unitAge) + 1.0;
double newUnitAge = RbStatistics::Beta::rv(a, b, *rng);
double fwdProposal = RbStatistics::Beta::lnPdf(a, b, newUnitAge);
double my_new_age = newUnitAge * ageRange + child_Age;
double new_a = delta * newUnitAge + 1.0;
double new_b = delta * (1.0 - newUnitAge) + 1.0;
double bwdProposal = RbStatistics::Beta::lnPdf(new_a, new_b, unitAge);
// double get branch length
double old_brlen = node->getTopologyParent().getAge() - my_age;
double new_brlen = node->getTopologyParent().getAge() - my_new_age;
double brlen_ratio = old_brlen / new_brlen;
// update branch rate leading to node
double node_rate = branchRates[node->getIndex()]->getValue();
//branchRates[node->getIndex()]->touch();
//std::cout << "br_name" << branchRates[node->getIndex()]->getName() << "\n";
storedRates[node] = node_rate;
//std::cout << "brlen\t" << old_brlen << " -> " << new_brlen << " " << brlen_ratio << "\n";
//std::cout << "node_rate " << node_rate << " -> " << node_rate * brlen_ratio <<"\n";
node_rate = node_rate * brlen_ratio;
branchRates[node->getIndex()]->setValue(new double(node_rate));
// update branch rates following from node
for (size_t i = 0; i < storedNode->getNumberOfChildren(); i++)
{
AdmixtureNode* ch = &storedNode->getTopologyChild(i);
//AdmixtureNode* ch = &storedNode->getChild(i);
//double ch_ratio = (storedAge - ch->getAge()) / (my_new_age - ch->getAge());
double ch_ratio = (storedAge - ch->getAge()) / (my_new_age - ch->getAge());
double ch_rate = branchRates[ch->getIndex()]->getValue();
// branchRates[ch->getIndex()]->touch();
storedRates[ch] = ch_rate;
//branchRates[node->getIndex()]->setValue(new double(ch_rate * ch_ratio));
//std::cout << "ch_brlen " << i << " " << (storedAge - ch->getAge()) << " -> " << (my_new_age - ch->getAge()) << " " << ch_ratio << "\n";
//std::cout << "ch_rate " << i << " " << ch_rate << " -> " << ch_rate * ch_ratio << "\n";
ch_rate = ch_rate * ch_ratio;
branchRates[ch->getIndex()]->setValue(new double(ch_rate));
}
// set the age
node->setAge( my_new_age );
// set age of admixture partner
if (&node->getAdmixtureParent() != NULL)
node->getAdmixtureParent().setAge( my_new_age );
else if (&node->getAdmixtureChild() != NULL)
node->getAdmixtureChild().setAge( my_new_age );
return bwdProposal - fwdProposal;
}
/** Perform the move */
double AdmixtureEdgeRemoveResidualWeights::performSimpleMove( void ) {
//std::cout << "\nAdmix Node Rem RW\n";
// Get random number generator
failed = false;
RandomNumberGenerator* rng = GLOBAL_RNG;
AdmixtureTree& tau = variable->getValue();
std::vector<AdmixtureNode*> admixtureParents = tau.getAdmixtureParents();
// if no admixtureParent exists, the proposal fails
if (admixtureParents.size() == 0)
{
failed = true;
return RbConstants::Double::neginf;
}
// otherwise, proceed
else
{
failed = false;
// sample a random admixture parent node
double u = rng->uniform01();
size_t index = std::floor(admixtureParents.size() * u);
AdmixtureNode* admixtureParent = admixtureParents[index];
AdmixtureNode* admixtureChild = &admixtureParent->getAdmixtureChild();
//double w = admixtureChild->getWeight();
// get all nodes adjacent to proposal
storedAdmixtureChild = admixtureChild;
storedAdmixtureChildChild = &admixtureChild->getChild(0);
storedAdmixtureChildParent = &admixtureChild->getParent();
storedAdmixtureParent = admixtureParent;
storedAdmixtureParentChild = &admixtureParent->getChild(0);
storedAdmixtureParentParent = &admixtureParent->getParent();
// update edges to remove admixtureChild in graph
storedAdmixtureChildChild->setParent(storedAdmixtureChildParent);
storedAdmixtureChildParent->removeChild(admixtureChild);
storedAdmixtureChildParent->addChild(storedAdmixtureChildChild);
// update edges to remove admixtureParent in graph
storedAdmixtureParentParent->removeChild(admixtureParent);
storedAdmixtureParentParent->addChild(storedAdmixtureParentChild);
storedAdmixtureParentChild->setParent(storedAdmixtureParentParent);
/*
// get set of tips descendant from AC and AP
//std::cout << "tips_ap\n";
std::set<AdmixtureNode*> tips_ap;
findDescendantTips(tips_ap, storedAdmixtureParent);
//std::cout << "tips_ac\n";
std::set<AdmixtureNode*> tips_ac;
findDescendantTips(tips_ac, storedAdmixtureChild);
*/
// remove nodes from admixtureTree vector
tau.eraseAdmixtureNode(storedAdmixtureParent);
tau.eraseAdmixtureNode(storedAdmixtureChild);
// get sum of positive residuals for each taxon against all other taxa
storedResiduals = residuals->getValue();
size_t numTaxa = tau.getNumberOfTips();
double bwdProposal = 0.0;
double maxStoredResidual = 0.0;
for (size_t i = 0; i < storedResiduals.size(); i++)
if (storedResiduals[i] > maxStoredResidual)
maxStoredResidual = storedResiduals[i];
double lambda = delta / maxStoredResidual;
// get sum of positive residuals for each taxon against all other taxa
std::vector<double> residualWeights_a(numTaxa,0.0);
double sumResidualWeights_a = 0.0;
for (size_t i = 0; i < numTaxa; i++)
{
for (size_t j = 0; j < numTaxa; j++)
{
double r = storedResiduals[i * numTaxa + j];
r = exp(lambda*r);
if (r > 0.0 && i != j)
//if (i != j)
{
residualWeights_a[i] += r;
sumResidualWeights_a += r;
}
}
}
size_t k_a = admixtureParent->getIndex();
bwdProposal *= (residualWeights_a[k_a] / sumResidualWeights_a);
// get sum of positive residuals for each taxon wrt taxon A
std::vector<double> residualWeights_b(numTaxa,0.0);
double sumResidualWeights_b = 0.0;
for (size_t i = 0; i < numTaxa; i++)
{
double r = storedResiduals[k_a * numTaxa + i];
r = exp(lambda*r);
if (r > 0.0 && k_a != i)
//if (k_a != i)
{
residualWeights_b[i] += r;
sumResidualWeights_b += r;
}
}
size_t k_b = admixtureChild->getIndex();
bwdProposal *= (residualWeights_b[k_b] / sumResidualWeights_b);
// prior & propsal admixture weights cancel...
//double lnW = 0.0;
// prior * proposal ratio
numEvents = (int)tau.getNumberOfAdmixtureChildren();
admixtureCount->setValue(new int(numEvents));
return 0.0;
//double lnFwdProposal = -log(numEvents+1);
//return lnW + log(bwdProposal) - lnFwdProposal;
}
}
/** Perform the move */
double AdmixtureNearestNeighborInterchangeAndRateShift::performSimpleMove( void ) {
//std::cout << "\nDiv Node NNI & Rate Rescale\n";
failed = false;
// Get random number generator
RandomNumberGenerator* rng = GLOBAL_RNG;
AdmixtureTree& tau = variable->getValue();
// pick a random node which is not the root and neithor the direct descendant of the root
AdmixtureNode* node;
do {
double u = rng->uniform01();
size_t index = std::floor(tau.getNumberOfNodes() * u);
node = &tau.getNode(index);
} while ( node->isRoot() || node->getTopologyParent().isRoot() || node->getNumberOfChildren() != 2);
int nodeChildMoveIdx = (int)std::floor(rng->uniform01() * 2.0);
int nodeBrotherIdx = 0;
//std::cout << "nodeChildeMoveIdx " << nodeChildMoveIdx << "\n";
// divergence location
AdmixtureNode* childMove = &node->getChild(nodeChildMoveIdx);
AdmixtureNode* parent = &node->getTopologyParent();
AdmixtureNode* brother = &parent->getTopologyChild( nodeBrotherIdx );
// check if we got the correct child lineage
if ( brother == node )
{
if (nodeBrotherIdx == 0)
nodeBrotherIdx = 1;
else
nodeBrotherIdx = 0;
}
// get brother of node (not divergence child node)
brother = &parent->getChild(nodeBrotherIdx);
if (brother->getAge() > node->getAge())
{
//std::cout << "failed, bro > node\n";
failed = true;
return RbConstants::Double::neginf;
}
else if (childMove->getAge() > parent->getAge())
{
//std::cout << "failed, child > parent\n";
failed = true;
return RbConstants::Double::neginf;
}
else if (childMove->isOutgroup() != brother->isOutgroup())
{
//std::cout << "failed, outgroup mismatch\n";
failed = true;
return RbConstants::Double::neginf;
}
// update parent clade
storedNodeParent = parent;
storedNodeChildMove = childMove;
storedBrother = brother;
storedNode = node;
// swap
storedNode->removeChild(storedNodeChildMove);
storedNodeParent->removeChild(storedBrother);
storedNode->addChild(storedBrother);
storedNodeParent->addChild(storedNodeChildMove);
storedBrother->setParent(storedNode);
storedNodeChildMove->setParent(storedNodeParent);
// get branch rate index
storedChildRateIndex = (int)node->getTopologyChild(nodeChildMoveIdx).getIndex();
storedBrotherRateIndex = (int)parent->getTopologyChild(nodeBrotherIdx).getIndex();
// storedNodeRateIndex = node->getIndex();
// store branch rate values
storedChildRate = branchRates[storedChildRateIndex]->getValue();
// storedNodeRate = branchRates[storedNodeRateIndex]->getValue();
storedBrotherRate = branchRates[storedBrotherRateIndex]->getValue();
// update
//double cnr = 0.0;
//double snr = 0.0;
//double sbr = 0.0;
double scaleChildRate = exp(delta*(rng->uniform01() - 0.5));
// double scaleNodeRate = exp(delta*(rng->uniform01() - 0.5));
double scaleBrotherRate = exp(delta*(rng->uniform01() - 0.5));
branchRates[storedChildRateIndex]->setValue(new double(storedChildRate*scaleChildRate));
// branchRates[storedNodeRateIndex]->setValue(new double(storedNodeRate * scaleNodeRate));
branchRates[storedBrotherRateIndex]->setValue(new double(storedBrotherRate * scaleBrotherRate));
//branchRates[storedChildRateIndex]->touch();
//std::cout << "chld rate " << storedChildRate << " -> " << storedChildRate*scaleChildRate << "\n";
// std::cout << "node rate " << storedNodeRate << " -> " << storedNodeRate*scaleNodeRate << "\n";
//std::cout << "bro rate " << storedBrotherRate << " -> " << storedBrotherRate*scaleBrotherRate << "\n";
if (storedChildRate * scaleChildRate == 0.0)
{
;//std::cout << "new scaledChildRate == 0.0\n";
}
//if (storedNodeRate * scaleNodeRate == 0.0)
//{
// std::cout << "new scaledNodeRate == 0.0\n";
//}
if (storedBrotherRate * scaleBrotherRate == 0.0)
{
;//std::cout << "new scaledBrotherRate == 0.0\n";
}
//std::cout << scaleChildRate*scaleBrotherRate << " " << log(scaleChildRate*scaleBrotherRate) << "\n";
// MH
// return 0.0;
return log(scaleChildRate*scaleBrotherRate);
}
