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 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 AdmixtureEdgeReplaceResidualWeights::performSimpleMove( void ) {
// std::cout << "Admix Node Repl RW\n";
failed = false;
failedAdd = false;
// Get random number generator
RandomNumberGenerator* rng = GLOBAL_RNG;
AdmixtureTree& tau = variable->getValue();
AdmixtureNode* root = &tau.getRoot();
size_t numTaxa = tau.getNumberOfTips();
std::vector<AdmixtureNode*> admixtureParents = tau.getAdmixtureParents();
// if no admixtureParent exists, the proposal fails
if (admixtureParents.size() == 0)
{
failed = true;
// std::cout << "no admixture evts\n";
return RbConstants::Double::neginf;
}
// otherwise, proceed
else
{
storedResiduals = residuals->getValue();
// std::cout << "\nBEFORE\n";
// for (size_t i = 0; i < numTaxa; i++)
// {
// for (size_t j = 0; j < numTaxa; j++)
// {
// double r = storedResiduals[i * numTaxa + j];
// std::cout << r << " ";
// }
// std::cout << "\n";
// }
// proposal densities
// double fwdProposal = 1.0;
// double bwdProposal = 1.0;
failed = false;
failedAdd = false;
// sample a random admixture parent node
double u = rng->uniform01();
size_t index = std::floor(admixtureParents.size() * u);
// size_t numAdmixtureEdges = admixtureParents.size();
// store admixture edge position
storedAdmixtureParent = admixtureParents[index];
storedAdmixtureChild = &storedAdmixtureParent->getAdmixtureChild();
storedAdmixtureChildParent = &storedAdmixtureChild->getParent();
storedAdmixtureChildChild = &storedAdmixtureChild->getChild(0);
storedAdmixtureParentParent = &storedAdmixtureParent->getParent();
storedAdmixtureParentChild = &storedAdmixtureParent->getChild(0);
// std::cout << "rem " << tau.getAdmixtureEdgeStr(storedAdmixtureParent, storedAdmixtureChild) << "\n";
// int oldChildBranchIdx = (int)storedAdmixtureChild->getTopologyChild(0).getIndex();
// int oldParentBranchIdx = (int)storedAdmixtureParent->getTopologyChild(0).getIndex();
// remove admixture edge from graph
storedAdmixtureChild->removeChild(storedAdmixtureChildChild);
storedAdmixtureChildChild->setParent(storedAdmixtureChildParent);
storedAdmixtureChildParent->removeChild(storedAdmixtureChild);
storedAdmixtureChildParent->addChild(storedAdmixtureChildChild);
storedAdmixtureParent->removeChild(storedAdmixtureParentChild);
storedAdmixtureParentChild->setParent(storedAdmixtureParentParent);
storedAdmixtureParentParent->removeChild(storedAdmixtureParent);
storedAdmixtureParentParent->addChild(storedAdmixtureParentChild);
// get age for admixture event
storedAdmixtureAge = storedAdmixtureChild->getAge();
storedAdmixtureWeight = storedAdmixtureChild->getWeight();
// initialize NA__
newAdmixtureChildChild = storedAdmixtureChildChild;
newAdmixtureChildParent = storedAdmixtureChildParent;
newAdmixtureParentChild = storedAdmixtureParentChild;
newAdmixtureParentParent = storedAdmixtureParentParent;
variable->touch();
// std::cout << "\nSAMPLE\n";
// storedResiduals = residuals->getValue();
// for (size_t i = 0; i < numTaxa; i++)
// {
// for (size_t j = 0; j < numTaxa; j++)
// {
// double r = storedResiduals[i * numTaxa + j];
// std::cout << r << " ";
// }
// std::cout << "\n";
// }
//tau.checkAllEdgesRecursively(root);
//////////////////////////////////////////////////
// add event ...
//std::cout << "\n\treplace, add\n";
double maxStoredResidual = 0.0;
for (size_t i = 0; i < storedResiduals.size(); i++)
if (storedResiduals[i] > maxStoredResidual)
maxStoredResidual = storedResiduals[i];
double lambda = delta / maxStoredResidual;
//double lambda = 10.0;
AdmixtureNode* nodeSrc = NULL;
AdmixtureNode* nodeDst = NULL;
size_t k_a = 0;
size_t k_b = 0;
// std::cout << "numTaxa\t" << numTaxa << "\n";
//double v = rng->uniform01();
// if (v < 0.5)
// if (true)
// {
// 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;
}
}
}
// if there are no positive residuals, abort move
if (sumResidualWeights_a == 0.0)
{
// std::cout << "no pos residuals\n";
failedAdd = true;
return RbConstants::Double::neginf;
}
// sample taxon A from weights
double u_a = rng->uniform01() * sumResidualWeights_a;
double m_a = 0.0;
//size_t k_a = 0;
for (size_t i = 0; i < numTaxa; i++)
{
m_a += residualWeights_a[i];
if (m_a > u_a)
{
k_a = i;
nodeDst = &tau.getNode(k_a);
break;
}
}
//fwdProposal *= (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;
}
}
// sample taxon B from weights
double u_b = rng->uniform01() * sumResidualWeights_b;
double m_b = 0.0;
//size_t k_b = 0;
for (size_t i = 0; i < numTaxa; i++)
{
m_b += residualWeights_b[i];
if (m_b > u_b)
{
k_b = i;
nodeSrc = &tau.getNode(k_b);
break;
}
}
//
// std::cout << "rw_a\t";
// for (size_t i = 0; i < numTaxa; i++)
// std::cout << residualWeights_a[i] / sumResidualWeights_a << "\t";
// std::cout << "\n";
// std::cout << "pick " << k_a << " " << (residualWeights_a[k_a] / sumResidualWeights_a) << "\n";
//
//
//
// std::cout << "rw_b\t";
// for (size_t i = 0; i < numTaxa; i++)
// std::cout << residualWeights_b[i] / sumResidualWeights_b << "\t";
// std::cout << "\n";
// std::cout << "pick " << k_b << " " << (residualWeights_b[k_b] / sumResidualWeights_b) << "\n";
//
//fwdProposal *= (residualWeights_b[k_b] / sumResidualWeights_b);
// }
// else
// {
// //std::cout << "random\n";
// k_a = rng->uniform01() * numTaxa;
// do
// {
// k_b = rng->uniform01() * numTaxa;
// } while(k_a == k_b);
// nodeDst = &tau.getNode(k_a);
// nodeSrc = &tau.getNode(k_b);
// }
//
// std::cout << "taxa pair\t" << k_a << "\t" << k_b << "\n";
//std::cout << "fwdProposal\t" << fwdProposal << "\tlnFwdProposal\t" << log(fwdProposal) << "\n";
// get path from tip to root for both nodes
AdmixtureNode* nd_a = nodeDst;
std::list<AdmixtureNode*> path_a;
// std::cout << "path_a : tip -> root\t" << nd_a << "\n";
while (nd_a != NULL)
{
// std::cout << "\t" << nd_a << "\t" << nd_a->getAge() << "\n";
path_a.push_back(nd_a);
nd_a = &nd_a->getParent();
}
nd_a = path_a.back();
AdmixtureNode* nd_b = nodeSrc;
std::list<AdmixtureNode*> path_b;
// std::cout << "path_b : tip -> root\t" << nd_b << "\n";
while (nd_b != NULL)
{
// std::cout << "\t" << nd_b << "\t" << nd_b->getAge() << "\n";
path_b.push_back(nd_b);
nd_b = &nd_b->getParent();
}
nd_b = path_b.back();
// find the node where the paths diverge by traversing both paths from root to tip
AdmixtureNode* mrca = nd_a;
// std::cout << "mrca : root -> tip\n";
while (nd_a == nd_b && !path_a.empty() && !path_b.empty())
{
mrca = nd_a;
// std::cout << "\t" << mrca << "\t" << mrca->getAge() << "\n";
nd_a = path_a.back();
nd_b = path_b.back();
path_a.pop_back();
path_b.pop_back();
}
// sample u.a.r. between nd_b and present
double minAge = nodeSrc->getAge();
if (minAge < nodeDst->getAge())
minAge = nodeDst->getAge();
double maxAge = mrca->getAge();
int mrcaChIdx = 0;
// if (allowSisterAdmixture == false)
// if (allowSisterAdmixture == false && mrca->getTopologyChild(0).isTip() == false && mrca->getTopologyChild(1).isTip() == false)
if (allowSisterAdmixture == false)// && mrca->getTopologyChild(0).isTip() == false && mrca->getTopologyChild(1).isTip() == false)
{
maxAge = mrca->getTopologyChild(0).getAge();
if (maxAge < mrca->getTopologyChild(1).getAge())
{
maxAge = mrca->getTopologyChild(1).getAge();
mrcaChIdx = 1;
}
}
if (maxAge <= minAge)
{
// std::cout << "maxAge <= minAge\t" << maxAge << " < " << minAge << "\n";
failedAdd = true;
return RbConstants::Double::neginf;
}
//maxAge = mrca->getAge();
//double admixtureAge = rng->uniform01() * (maxAge - minAge) + minAge;
double exp_lambda = 2.0;
double admixtureAge = RbStatistics::Beta::rv(1.0,exp_lambda, *rng) * (maxAge - minAge) + minAge;
double a = 1.0;
double b = 2.0;
double admixtureWeight = RbStatistics::Beta::rv(a, b, *rng);
//admixtureWeight /= 2;
// attach edge as appropriate from aPath to bPath
// front=0, back=1
// std::cout << "a_path : find admixtureAge\n";
while (nd_a->getAge() > admixtureAge && !path_a.empty())
{
nd_a = path_a.back();
// std::cout << "\t" << nd_a << "\t" << nd_a->getAge() << "\n";
path_a.pop_back();
if (nd_a->getParent().getAge() > admixtureAge && nd_a->getAge() < admixtureAge)
break;
}
// ... prob of selecting a certain source branch
// double t_a = nd_a->getParent().getAge();
// fwdProposal *= t_a / (t_a - nodeSrc->getAge());
// std::cout << "b_path : find admixtureAge\n";
while (nd_b->getAge() > admixtureAge && !path_b.empty())
{
nd_b = path_b.back();
// std::cout << "\t" << nd_b << "\t" << nd_b->getAge() << "\n";
path_b.pop_back();
if (nd_b->getParent().getAge() > admixtureAge && nd_b->getAge() < admixtureAge)
break;
}
//////////////////////////////////////////////////
// placeholder for add
// nd_a = storedAdmixtureParentChild;
// nd_b = storedAdmixtureChildChild;
double newAge = admixtureAge;
double newWeight = admixtureWeight;
//newWeight = storedAdmixtureWeight;
// if (storedAdmixtureAge < maxAge && storedAdmixtureAge > minAge)
// newAge = storedAdmixtureAge;
// double newWeight = storedAdmixtureWeight;
// std::cout << "age\t" << newAge << "\n";
// std::cout << "wt \t" << newWeight << "\n";
// add into graph
if (rng->uniform01() < 0.5)
{
AdmixtureNode* tmp = nd_a;
nd_a = nd_b;
nd_b = tmp;
}
// store adjacent nodes to new parent node
newAdmixtureParentChild = nd_a;
newAdmixtureParentParent = &nd_a->getParent();
// insert admixtureParent into graph
storedAdmixtureParent->setAge(newAge);
storedAdmixtureParent->setParent(root);
newAdmixtureParentChild->setParent(storedAdmixtureParent);
newAdmixtureParentParent->addChild(storedAdmixtureParent);
newAdmixtureParentParent->removeChild(newAdmixtureParentChild); //
storedAdmixtureParent->addChild(newAdmixtureParentChild);
storedAdmixtureParent->setParent(newAdmixtureParentParent);
// store adjacent nodes to new child node
newAdmixtureChildChild = nd_b;
newAdmixtureChildParent = &nd_b->getParent();
// insert admixtureChild into graph
storedAdmixtureChild->setAge(newAge);
storedAdmixtureChild->setWeight(newWeight);
storedAdmixtureChild->setParent(root);
newAdmixtureChildChild->setParent(storedAdmixtureChild);
newAdmixtureChildParent->addChild(storedAdmixtureChild);
newAdmixtureChildParent->removeChild(newAdmixtureChildChild);
storedAdmixtureChild->addChild(newAdmixtureChildChild);
storedAdmixtureChild->setParent(newAdmixtureChildParent);
// update with outgroup settings
storedAdmixtureChild->setOutgroup(newAdmixtureChildChild->isOutgroup());
storedAdmixtureParent->setOutgroup(newAdmixtureParentChild->isOutgroup());
// std::cout << "add " << tau.getAdmixtureEdgeStr(storedAdmixtureParent, storedAdmixtureChild) << "\n";
// variable->touch();
// std::cout << "\nAFTER\n";
// storedResiduals = residuals->getValue();
// for (size_t i = 0; i < numTaxa; i++)
// {
// for (size_t j = 0; j < numTaxa; j++)
// {
// double r = storedResiduals[i * numTaxa + j];
// std::cout << r << " ";
// }
// std::cout << "\n";
// }
// update branch rates
//double lnBwdPropRates = 0.0;
/*
storedBranchRates.clear();
double delta = 0.0;
// ... have oldBranchIdx already
int newChildBranchIdx = (int)storedAdmixtureChild->getTopologyChild(0).getIndex();
int newParentBranchIdx = (int)storedAdmixtureParent->getTopologyChild(0).getIndex();
std::set<int> idxSet;
idxSet.insert(oldChildBranchIdx);
idxSet.insert(oldParentBranchIdx);
idxSet.insert(newChildBranchIdx);
idxSet.insert(newParentBranchIdx);
//for (size_t i = 0; i < idxSet.size(); i++)
for (std::set<int>::iterator it = idxSet.begin(); it != idxSet.end(); it++)
{
int idx = *it;
double v = branchRates[idx]->getValue();
storedBranchRates[idx] = v;
double u = exp(delta*(GLOBAL_RNG->uniform01() - 0.5));
branchRates[idx]->setValue(new double(u * v));
// std::cout << "br " << idx << " " << v << " -> " << u*v << "\n";
lnBwdPropRates += log(u);
}
// tau.checkAllEdgesRecursively(root);
// ln hastings ratio
//bwdProposal = 1.0 / numAdmixtureEdges;
//fwdProposal = (residualWeights_a[k_a] / sumResidualWeights_a) * (residualWeights_b[k_b] / sumResidualWeights_b);
double lnFwdProposal = log(fwdProposal);
double lnBwdProposal = log(bwdProposal);
*/
return 0.0;
}
}
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;
}
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();
}
/** Perform the move */
double AdmixtureEdgeReplaceResidualsFNPR::performSimpleMove( void ) {
storedAdmixtureEdges.clear();
newAdmixtureEdges.clear();
failed = false;
numEvents = 0;
AdmixtureTree& tau = variable->getValue();
// Get random number generator
RandomNumberGenerator* rng = GLOBAL_RNG;
// stage FNPR pointers
size_t numIntNodes = tau.getNumberOfInteriorNodes();
size_t numTaxa = tau.getNumberOfTips();
pruneNode = NULL;
while (pruneNode == NULL || pruneNode == &tau.getRoot() || pruneNode->getNumberOfChildren() != 2)
{
pruneNode = &tau.getNode(rng->uniform01() * numIntNodes + numTaxa - 1);
}
pruneParent = &pruneNode->getParent();
// for (size_t i = 0; i < pruneParent->getNumberOfChildren(); i++)
// std::cout << "\t" << &pruneParent->getChild(i) << "\n";
pruneChild = &pruneNode->getTopologyChild(rng->uniform01() * 2);
// pruneNephew = &pruneNode->getChild(nphIdx);
//std::cout << chIdx << " " << nphIdx << "\n";
// get regraft point
std::vector<AdmixtureNode*> new_brothers;
findNewBrothers(new_brothers, *pruneNode, &tau.getRoot());
int index = int(rng->uniform01() * new_brothers.size());
regraftChild = new_brothers[index];
if (pruneChild->isOutgroup() != regraftChild->isOutgroup())
{
failed = true;
return RbConstants::Double::neginf;
}
regraftParent = ®raftChild->getTopologyParent();
// std::cout << "\n";
// std::cout << "pch " << pruneChild << " <- " << &pruneChild->getTopologyParent() << "\n";
// //std::cout << "pnpw " << pruneNephew << " <- " << &pruneNephew->getTopologyParent() << "\n";
// // std::cout << "pnd " << pruneNode << " -> " << &pruneNode->getTopologyChild(chIdx) << " " << &pruneNode->getChild(nphIdx) << "\n";
// std::cout << "ppa " << pruneParent << " -> " << pruneNode << "\n";
// std::cout << "rch " << regraftChild << " <- " << ®raftChild->getTopologyParent() << "\n";
// std::cout << "rpa " << regraftParent << " -> " << ®raftParent->getTopologyChild(0) << " " << ®raftParent->getTopologyChild(1) << "\n";
//
// std::cout << "\n";
// clear and store adm events on prune child lineage
//std::cout << &pruneChild->getParent() << " " << ®raftChild->getParent() << " " << &pruneNephew->getParent() << "\n";
// for (size_t i = 0; i < pruneParent->getNumberOfChildren(); i++)
// std::cout << "0\t" << &pruneParent->getChild(i) << "\n";
storeAdmixtureEventsForLineage(pruneChild);
//std::cout << &pruneChild->getParent() << " " << ®raftChild->getParent() << " " << &pruneNephew->getParent() << "\n";
// for (size_t i = 0; i < pruneParent->getNumberOfChildren(); i++)
// std::cout << "1\t" << &pruneParent->getChild(i) << "\n";
// clear and store adm events on regraft child lineage
storeAdmixtureEventsForLineage(regraftChild);
//std::cout << &pruneChild->getParent() << " " << ®raftChild->getParent() << " " << &pruneNephew->getParent() << "\n";
// for (size_t i = 0; i < pruneParent->getNumberOfChildren(); i++)
// std::cout << "2\t" << &pruneParent->getChild(i) << "\n";
// perform FNPR
//std::cout << "ppa " << pruneParent << " -> " << &pruneParent->getChild(0) << " " << &pruneParent->getChild(1) << " " << &pruneNode->getParent() << "\n";
int nphIdx = 0;
if (pruneChild == &pruneNode->getTopologyChild(nphIdx))
nphIdx = 1;
pruneNephew = &pruneNode->getChild(nphIdx);
pruneParent = &pruneNode->getParent();
// std::cout << &pruneChild->getParent() << " " << ®raftChild->getParent() << " " << &pruneNephew->getParent() << "\n";
// std::cout << "ppa " << pruneParent << " -> " << pruneNode << "\n";
// for (size_t i = 0; i < pruneParent->getNumberOfChildren(); i++)
// std::cout << "\t" << &pruneParent->getChild(i) << "\n";
pruneParent->removeChild(pruneNode,false);
pruneNode->removeChild(pruneNephew,false);
pruneParent->addChild(pruneNephew,false);
pruneNephew->setParent(pruneParent,false);
regraftParent->removeChild(regraftChild,false);
regraftParent->addChild(pruneNode,false);
pruneNode->addChild(regraftChild,false);
pruneNode->setParent(regraftParent,false);
pruneNode->setOutgroup(regraftChild->isOutgroup());
regraftChild->setParent(pruneNode,false);
// get new age
double maxRegraftAge = regraftParent->getAge();
double minRegraftAge = regraftChild->getAge();
if (minRegraftAge < pruneChild->getAge())
minRegraftAge = pruneChild->getAge();
storedPruneAge = pruneNode->getAge();
double newPruneAge = rng->uniform01() * (maxRegraftAge - minRegraftAge) + minRegraftAge;
pruneNode->setAge(newPruneAge);
// draw new admixture edges
//double fwdProposal = 1.0;
//int numEvents = storedAdmixtureEdges.size();
for (unsigned i = 0; i < storedAdmixtureEdges.size(); i++)
{
residuals->touch();
storedResiduals = residuals->getValue();
size_t numTaxa = tau.getNumberOfTips();
AdmixtureNode* nodeSrc = NULL;
AdmixtureNode* nodeDst = NULL;
size_t k_a = 0;
size_t k_b = 0;
/*
if (tau.getNumberOfAdmixtureParents() >= maxEvents)
{
failed = true;
return RbConstants::Double::neginf;
}
*/
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;
}
}
}
// if there are no positive residuals, abort move
if (sumResidualWeights_a == 0.0)
{
//std::cout << "no pos residuals\n";
failed = true;
return RbConstants::Double::neginf;
}
// std::cout << "rw_a\t";
// for (size_t i = 0; i < numTaxa; i++)
// std::cout << residualWeights_a[i] / sumResidualWeights_a << "\t";
// std::cout << "\n";
// sample taxon A from weights
double u_a = rng->uniform01() * sumResidualWeights_a;
double m_a = 0.0;
//size_t k_a = 0;
for (size_t i = 0; i < numTaxa; i++)
{
m_a += residualWeights_a[i];
if (m_a > u_a)
{
k_a = i;
nodeDst = &tau.getNode(k_a);
break;
}
}
//std::cout << "pick " << k_a << "\n";
//fwdProposal *= (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;
}
}
// std::cout << "rw_b\t";
// for (size_t i = 0; i < numTaxa; i++)
// std::cout << residualWeights_b[i] / sumResidualWeights_b << "\t";
// std::cout << "\n";
// sample taxon B from weights
double u_b = rng->uniform01() * sumResidualWeights_b;
double m_b = 0.0;
//size_t k_b = 0;
for (size_t i = 0; i < numTaxa; i++)
{
m_b += residualWeights_b[i];
if (m_b > u_b)
{
k_b = i;
nodeSrc = &tau.getNode(k_b);
break;
}
}
// std::cout << "pick " << k_b << "\n\n";
//fwdProposal *= (residualWeights_b[k_b] / sumResidualWeights_b);
// get path from tip to root for both nodes
AdmixtureNode* nd_a = nodeSrc;
std::list<AdmixtureNode*> path_a;
//std::cout << "path_a : tip -> root\n";
while (nd_a != NULL)
{
//std::cout << "\tnd_a\t" << nd_a->getIndex() << "\t" << nd_a << "\t" << nd_a->getAge() << "\t" << &nd_a->getParent() << "\n";
path_a.push_back(nd_a);
nd_a = &nd_a->getParent();
}
nd_a = path_a.back();
AdmixtureNode* nd_b = nodeDst;
std::list<AdmixtureNode*> path_b;
//std::cout << "path_b : tip -> root\n";
while (nd_b != NULL)
{
//std::cout << "\tnd_b\t" << nd_b->getIndex() << "\t" << nd_b << "\t" << nd_b->getAge() << "\n";
path_b.push_back(nd_b);
nd_b = &nd_b->getParent();
}
nd_b = path_b.back();
// find the node where the paths diverge by traversing both paths from root to tip
AdmixtureNode* mrca = nd_a;
//std::cout << "mrca : root -> tip\n";
while (nd_a == nd_b && !path_a.empty() && !path_b.empty())
{
mrca = nd_a;
// std::cout << "\t" << mrca << "\t" << mrca->getAge() << "\n";
nd_a = path_a.back();
nd_b = path_b.back();
path_a.pop_back();
path_b.pop_back();
}
// sample u.a.r. between nd_b and present (we disallow sister branches to admix...)
double minAge = nodeSrc->getAge();
if (minAge < nodeDst->getAge())
minAge = nodeDst->getAge();
double maxAge = mrca->getAge();
int mrcaChIdx = 0;
if (allowSisterAdmixture == false)// && mrca->getTopologyChild(0).isTip() == false && mrca->getTopologyChild(1).isTip() == false)
{
maxAge = mrca->getTopologyChild(0).getAge();
if (maxAge < mrca->getTopologyChild(1).getAge())
{
maxAge = mrca->getTopologyChild(1).getAge();
mrcaChIdx = 1;
}
}
if (maxAge <= minAge)
{
failed = true;
return RbConstants::Double::neginf;
}
//maxAge = mrca->getAge();
//double admixtureAge = rng->uniform01() * (maxAge - minAge) + minAge;
double exp_lambda = 2.0;
double admixtureAge = RbStatistics::Beta::rv(1.0,exp_lambda, *rng) * (maxAge - minAge) + minAge;
while (nd_a->getAge() > admixtureAge && !path_a.empty())
{
nd_a = path_a.back();
path_a.pop_back();
if (nd_a->getParent().getAge() > admixtureAge && nd_a->getAge() < admixtureAge)
break;
}
while (nd_b->getAge() > admixtureAge && !path_b.empty())
{
nd_b = path_b.back();
path_b.pop_back();
if (nd_b->getParent().getAge() > admixtureAge && nd_b->getAge() < admixtureAge)
break;
}
if (GLOBAL_RNG->uniform01() < 0.5)
{
AdmixtureNode* tmp = nd_a;
nd_a = nd_b;
nd_b = tmp;
}
//std::cout << "ok\n";
// get admixture weight
double a = 1.0;
double b = 2.0;
double admixtureWeight = RbStatistics::Beta::rv(a, b, *rng);
//double lnW = 0.0;
admixtureWeight /= 2;
// add nodes to tree
AdmixtureNode* storedAdmixtureParent = new AdmixtureNode((int)tau.getNumberOfNodes());
tau.pushAdmixtureNode(storedAdmixtureParent);
AdmixtureNode* storedAdmixtureChild = new AdmixtureNode((int)tau.getNumberOfNodes());
tau.pushAdmixtureNode(storedAdmixtureChild);
// add edge
tau.addAdmixtureEdge(storedAdmixtureParent, storedAdmixtureChild, nd_a, nd_b, admixtureAge, admixtureWeight, true);
AdmixtureEdgePosition ap(storedAdmixtureParent, storedAdmixtureChild, nd_a, nd_b, admixtureAge, admixtureWeight);
newAdmixtureEdges.push_front(ap);
}
tau.getRoot().flagNewickRecomputation();
return 0.0;
}
/* 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);
}