std::string AdmixtureBipartitionMonitor::buildBipartitionString(void)
{
// return buffer
std::stringstream ss;
// get tree object
AdmixtureTree* tau = &tree->getValue();
std::vector<AdmixtureNode*> nodes;
for (unsigned i = 0; i < tree->getValue().getNumberOfNodes(); i++)
nodes.push_back(&tau->getNode(i));
// bool firstRootHit = false; // necessary?
for (size_t i = 0; i < nodes.size(); i++)
{
AdmixtureNode* p = nodes[i];
/*
if (p->isRoot())
continue;
else if (&p->getParent() == &tau->getRoot() && firstRootHit)
{
firstRootHit = false;
continue;
}
*/
std::vector<bool> pbp = std::vector<bool>(numTaxa,false);
findTaxonBipartition(pbp, p);
// look like s_0,s_1,r_0,r_1,t,w
if (&p->getAdmixtureParent() != NULL)
{
// admixture children are handled by the admixture parent case
continue;
}
else if (p->isRoot())
{
for (size_t i = 0; i < pbp.size(); i++)
{
//std::cout << std::noboolalpha << pbp[i];
ss << std::noboolalpha << pbp[i];
}
//std::cout << "\n";
ss << ",";
ss << "," << p->getAge();
ss << ",";
ss << ",";
ss << ",1";
ss << separator;
}
else if (&p->getAdmixtureChild() == NULL && &p->getAdmixtureParent() == NULL)
{
// skip tips for divergence partitions
// actually, keep 'em for pop-size params...
//if (p->getNumberOfChildren() == 0)
// continue;
//ss << "D";
// print bitstring for divergence partition
for (size_t i = 0; i < pbp.size(); i++)
ss << std::noboolalpha << pbp[i];
ss << ",";
ss << "," << p->getAge();
ss << "," << branchRates->getValue()[p->getIndex()];
ss << ",";
ss << ",1";
ss << separator;
}
else if (&p->getAdmixtureChild() != NULL)
{
AdmixtureNode* c = &p->getAdmixtureChild();
std::vector<bool> cbp = std::vector<bool>(numTaxa,false);
findTaxonBipartition(cbp, c);
for (size_t i = 0; i < pbp.size(); i++)
ss << std::noboolalpha << pbp[i];
ss << ",";
for (size_t i = 0; i < cbp.size(); i++)
ss << std::noboolalpha << cbp[i];
ss << "," << p->getAge();
ss << "," << branchRates->getValue()[p->getTopologyChild(0).getIndex()];
ss << "," << branchRates->getValue()[c->getTopologyChild(0).getIndex()];
ss << "," << c->getWeight();
ss << separator;
}
}
return ss.str();
}
void AdmixtureBipartitionSummaryMonitor::updateBipartitions(void)
{
if (delayTimer->getValue() <= 0)
{
// get tree object
AdmixtureTree* tau = &tree->getValue();
std::vector<AdmixtureNode*> nodes;
for (unsigned i = 0; i < tree->getValue().getNumberOfNodes(); i++)
nodes.push_back(&tau->getNode(i));
// map key iterator used for find()
std::map<std::vector<bool>, std::vector<AdmixtureEdgeRecord> >::iterator it;
// get partitions for all nodes
bool firstRootHit = false;
for (size_t i = 0; i < nodes.size(); i++)
{
AdmixtureNode* p = nodes[i];
if (p->isRoot())
continue;
else if (&p->getParent() == &tau->getRoot() && firstRootHit)
{
firstRootHit = false;
continue;
}
std::vector<bool> p_key = std::vector<bool>(numTaxa,false);
std::vector<bool> c_key;
AdmixtureEdgeRecord er(0,false,0,0,0,0);
findTaxonBipartition(p_key, p);
if (&p->getAdmixtureParent() != NULL)
{
// admixture children are handled by the admixture parent case
continue;
}
else if (&p->getAdmixtureChild() == NULL && &p->getAdmixtureParent() == NULL)
{
// skip tips for tree partitions
if (p->getNumberOfChildren() == 0)
continue;
// topology nodes have complementary disjoint bipartitions
//flipTaxonBipartitionToMinor(p_key);
er = AdmixtureEdgeRecord((int)numSamples,false,p->getWeight(),p->getAge(),p->getBranchLength(),branchRates->getValue()[p->getIndex()]);
// if key exists, push on to existing value as copy of original node
if (treeBipartitions.find(p_key) != treeBipartitions.end())
{
treeBipartitions[p_key].push_back(er);
//std::cout << "\tpush\n";
}
// otherwise, create new vector
else
{
std::vector<AdmixtureEdgeRecord> tmp(1,er);
treeBipartitions[p_key] = tmp;
//std::cout << "\tinsert\n";
}
}
else if (&p->getAdmixtureChild() != NULL)
{
// admixture parent-child pairs have disjoint bipartitions
AdmixtureNode* c = &p->getAdmixtureChild();
c_key = std::vector<bool>(numTaxa,false);
findTaxonBipartition(c_key, c);
er = AdmixtureEdgeRecord((int)numSamples,true,c->getWeight(),c->getAge(),c->getBranchLength(),branchRates->getValue()[c->getTopologyChild(0).getIndex()]);
// if key exists, push on to existing value as copy of original node
if (AdmixtureBipartitionSummarys.find(p_key) != AdmixtureBipartitionSummarys.end() && AdmixtureBipartitionSummarys.at(p_key).find(c_key) != AdmixtureBipartitionSummarys.at(p_key).end())
{
AdmixtureBipartitionSummarys[p_key][c_key].push_back(er);
}
// otherwise, create new vector
else
{
std::vector<AdmixtureEdgeRecord> tmp(1,er);
AdmixtureBipartitionSummarys[p_key][c_key] = tmp;
}
}
}
numSamples++;
}
}
/** 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);
}