void AdmixtureEdgeReplaceResidualsFNPR::findNewBrothers(std::vector<AdmixtureNode *> &b, AdmixtureNode &p, AdmixtureNode *n) {
if (&p != n) {
size_t numChildren = n->getNumberOfChildren();
AdmixtureNode* child;
for (size_t i = 0; i < numChildren; i++)
{
child = &n->getChild( i );
if ( child->getAge() < p.getAge() && child->getNumberOfChildren() != 1) { // && child != &q ) {
b.push_back( child );
} else {
findNewBrothers(b, p, child);
}
}
}
}
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 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;
}
/* Build newick string */
std::string ExtendedNewickAdmixtureTreeMonitor::buildExtendedNewick( AdmixtureNode* n ) {
// create the newick string
std::stringstream o;
// extended data is only found on admixture nodes
std::string additionalInfo = "";
// loop over admixture nodes per branch
std::stringstream admixturestream;
double br = 1.0;
if (!n->isRoot())
{
if (showRates)
br = branchRates->getValue()[n->getIndex()];
//std::cout << "hmm\n";
// [{s=&srcPtr,d=&dstPtr,t=double,w=double},{...},...,{...}]
if (showMetadata)
{
admixturestream << "[";
AdmixtureNode* p = &n->getParent();
while (p->getNumberOfChildren() == 1)
{
// std::cout << "ok\n";
admixturestream << "{s=";
if (&p->getAdmixtureParent() == NULL)
admixturestream << p;
else
admixturestream << &p->getAdmixtureParent();
admixturestream << ",d=";
if (&p->getAdmixtureChild() == NULL)
admixturestream << p;
else
admixturestream << &p->getAdmixtureChild();
admixturestream << ",t=" << p->getAge();
admixturestream << ",w=" << p->getWeight();
admixturestream << "}";
p = &p->getParent();
if (p->getNumberOfChildren() == 1)
admixturestream << ",";
}
admixturestream << "]";
additionalInfo = admixturestream.str();
}
}
// std::cout << br << "\n";
//std::cout << additionalInfo << "\n";
// test whether this is a internal or external node
if (n->isTip()) {
//std::cout << "tipnode\t" << additionalInfo << "\n";
// this is a tip so we just return the name of the node
o << n->getName() << additionalInfo << ":" << n->getTopologyBranchLength() * br;
}
else {
//std::cout << "intnode\t" << additionalInfo << "\n";
o << "(";
for (size_t i=0; i<(n->getNumberOfChildren()-1); i++) {
o << buildExtendedNewick( &n->getTopologyChild(i) ) << ",";
}
o << buildExtendedNewick( &n->getTopologyChild(n->getNumberOfChildren()-1) ) << ")" << additionalInfo << ":" << n->getTopologyBranchLength() * br;
}
return o.str();
}
/** 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);
}