double CompoundMove::performMove( double &probRatio ) {
if (changed)
{
throw RbException("Trying to execute a Compound moves twice without accept/reject in the meantime.");
}
changed = true;
double hr = performCompoundMove();
if ( hr != hr || hr == RbConstants::Double::inf )
{
return RbConstants::Double::neginf;
}
std::set<DagNode* > affectedNodes;
for (std::set<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); it++)
{
// touch each node
(*it)->touch();
// calculate the probability ratio for the node we just changed
//std::cout << (*it)->getName() << " " << (*it)->getLnProbabilityRatio() << " " << (*it)->getLnProbability() << "\n";
probRatio += (*it)->getLnProbabilityRatio();
if ( probRatio != RbConstants::Double::inf && probRatio != RbConstants::Double::neginf )
{
// should contain unique nodes, since it is a set
(*it)->getAffectedNodes(affectedNodes);
}
}
for (std::set<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); it++)
{
// if ( nodes.find(oldN) == nodes.end() ) {
// throw RbException("Cannot replace DAG node in this move because the move doesn't hold this DAG node.");
// }
affectedNodes.erase( *it );
}
if ( probRatio != RbConstants::Double::inf && probRatio != RbConstants::Double::neginf )
{
for (std::set<DagNode* >::iterator i=affectedNodes.begin(); i!=affectedNodes.end(); ++i)
{
DagNode* theAffectedNode = *i;
// do not double-count the prob ratio for any elt in both theNodes and affectedNodes
//if ( find(theNodes.begin(), theNodes.end(), *i) == theNodes.end() )
{
//std::cout << " " << theAffectedNode->getName() << " " << theAffectedNode->getLnProbabilityRatio() << " " << theAffectedNode->getLnProbability() << "\n";
probRatio += theAffectedNode->getLnProbabilityRatio();
}
}
}
return hr;
}
double AdmixtureEdgeReplaceResidualsFNPR::performMove( double &probRatio ) {
if (changed) {
throw RbException("Trying to execute a simple moves twice without accept/reject in the meantime.");
}
changed = true;
double hr = performSimpleMove();
if ( hr != hr || hr == RbConstants::Double::inf ) {
return RbConstants::Double::neginf;
}
// touch the node
variable->touch();
probRatio = variable->getLnProbabilityRatio();
if ( probRatio != RbConstants::Double::inf && probRatio != RbConstants::Double::neginf ) {
std::set<DagNode* > affectedNodes;
variable->getAffectedNodes(affectedNodes);
for (std::set<DagNode* >::iterator i=affectedNodes.begin(); i!=affectedNodes.end(); ++i) {
DagNode* theNode = *i;
probRatio += theNode->getLnProbabilityRatio();
//std::cout << theNode->getName() << "\t" << probRatio << "\n";
}
}
return hr;
}
double AdmixtureNearestNeighborInterchangeAndRateShift::performMove( double &probRatio ) {
//std::cout << "NNI::performMove()\n";
if (changed) {
//; throw RbException("Trying to execute a simple moves twice without accept/reject in the meantime.");
}
changed = true;
double hr = performSimpleMove();
if ( hr != hr || hr == RbConstants::Double::inf ) {
return RbConstants::Double::neginf;
}
// touch the node
variable->touch();
// calculate the probability ratio for the node we just changed
probRatio = variable->getLnProbabilityRatio();
//std::cout << "n\t" << variable->getName() << "\t" << probRatio << "\n";
if ( probRatio != RbConstants::Double::inf && probRatio != RbConstants::Double::neginf ) {
if (!failed)
{
// these three rates should be touched due to setValue()
branchRates[storedChildRateIndex]->touch();
probRatio += branchRates[storedChildRateIndex]->getLnProbabilityRatio();
branchRates[storedBrotherRateIndex]->touch();
probRatio += branchRates[storedBrotherRateIndex]->getLnProbabilityRatio();
// probRatio += branchRates[storedNodeRateIndex]->getLnProbabilityRatio();
// std::cout << probRatio << "\n";
}
std::set<DagNode* > affectedNodes;
variable->getAffectedNodes(affectedNodes);
for (std::set<DagNode* >::iterator i=affectedNodes.begin(); i!=affectedNodes.end(); ++i) {
DagNode* theNode = *i;
probRatio += theNode->getLnProbabilityRatio();
//std::cout << "\tch\t" << theNode->getName() << "\t" << theNode->getLnProbabilityRatio() << " " << probRatio << "\n";
}
}
//std::cout << "pr " << probRatio << " hr " << hr << "\n";
return hr;
}
double AdmixtureEdgeReplaceResidualWeights::performMove( double &probRatio ) {
//std::cout << "\nAdmix Edge Replace\n";
if (changed) {
throw RbException("Trying to execute a simple moves twice without accept/reject in the meantime.");
}
changed = true;
double hr = performSimpleMove();
if ( hr != hr || hr == RbConstants::Double::inf || hr == RbConstants::Double::neginf ) {
return RbConstants::Double::neginf;
}
// touch the node
variable->touch(); // if previously touched, this will overwrite lnProb??
probRatio = variable->getLnProbabilityRatio();
//probRatio = 0.0;
for (std::map<int,double>::iterator it = storedBranchRates.begin(); it != storedBranchRates.end(); it++)
{
branchRates[it->first]->touch();
probRatio += branchRates[it->first]->getLnProbabilityRatio();
//std::cout << branchRates[it->first]->getLnProbabilityRatio() << "\n";
}
if ( probRatio != RbConstants::Double::inf && probRatio != RbConstants::Double::neginf ) {
std::set<DagNode* > affectedNodes;
variable->getAffectedNodes(affectedNodes);
for (std::set<DagNode* >::iterator i=affectedNodes.begin(); i!=affectedNodes.end(); ++i) {
DagNode* theNode = *i;
probRatio += theNode->getLnProbabilityRatio();
//std::cout << probRatio << " " << theNode->getName() << "\t" << theNode->getLnProbability() << " " << theNode->getLnProbabilityRatio() << "\n";
}
}
// std::cout << probRatio << "\n";
return hr;
}
double AdmixtureShiftTreeRates::performMove( double &probRatio ) {
if (changed) {
throw RbException("Trying to execute a simple moves twice without accept/reject in the meantime.");
}
changed = true;
double hr = performSimpleMove();
if ( hr != hr || hr == RbConstants::Double::inf ) {
return RbConstants::Double::neginf;
}
// touch the node
treeRate->touch();
// calculate the probability ratio for the node we just changed
probRatio = treeRate->getLnProbabilityRatio();
//std::cout << "n\t" << treeRate->getName() << "\t" << probRatio << "\n";
//for (size_t i = 0; i < branchRates.size(); i++)
for (std::map<int,double>::iterator it = storedRates.begin(); it != storedRates.end(); it++)
{
int idx = it->first;
branchRates[idx]->touch();
probRatio += branchRates[idx]->getLnProbabilityRatio();
//std::cout << "n\t" << branchRates[idx]->getName() << " " << branchRates[idx]->getLnProbability() << " " << exp(branchRates[idx]->getLnProbability()) << " " << probRatio << "\n";
}
if ( probRatio != RbConstants::Double::inf && probRatio != RbConstants::Double::neginf ) {
std::set<DagNode* > affectedNodes;
treeRate->getAffectedNodes(affectedNodes);
for (std::set<DagNode* >::iterator i=affectedNodes.begin(); i!=affectedNodes.end(); ++i) {
DagNode* theNode = *i;
probRatio += theNode->getLnProbabilityRatio();
// std::cout << "\tch\t" << theNode->getName() << "\t" << theNode->getLnProbabilityRatio() << " " << probRatio << "\n";
}
}
return hr;
}
double FossilSafeScaleMove::performMove( double &probRatio ) {
if (changed)
{
throw RbException("Trying to execute a simple move twice without accept/reject in the meantime.");
}
changed = true;
double hr = doMove();
if ( hr != hr || hr == RbConstants::Double::inf )
{
return RbConstants::Double::neginf;
}
// touch the node
scaler->touch();
tree->touch();
// calculate the probability ratio for the node we just changed
probRatio = scaler->getLnProbabilityRatio();
probRatio += tree->getLnProbabilityRatio();
if ( probRatio != RbConstants::Double::inf && probRatio != RbConstants::Double::neginf )
{
std::set<DagNode* > affectedNodes;
scaler->getAffectedNodes(affectedNodes);
tree->getAffectedNodes(affectedNodes);
for (std::set<DagNode* >::iterator i=affectedNodes.begin(); i!=affectedNodes.end(); ++i)
{
DagNode* theAffectedNode = *i;
if (theAffectedNode != tree && theAffectedNode != scaler) {
//std::cout << theAffectedNode->getName() << " " << theAffectedNode->getLnProbabilityRatio() << " " << theAffectedNode->getLnProbability() << "\n";
probRatio += theAffectedNode->getLnProbabilityRatio();
}
}
}
return hr;
}