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;
}
/**
* Monitor value at generation gen
*/
void AbstractFileMonitor::monitorVariables(unsigned long gen)
{
for (std::vector<DagNode*>::iterator i = nodes.begin(); i != nodes.end(); ++i)
{
// add a separator before every new element
out_stream << separator;
// get the node
DagNode *node = *i;
// print the value
node->printValueElements(out_stream, separator, -1, true, flatten);
}
}
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 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 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;
}
/**
* Basic destructor doing nothing.
*/
MetropolisHastingsMove::~MetropolisHastingsMove( void )
{
for (std::set<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it)
{
// get the pointer to the current node
DagNode* theNode = *it;
// add myself to the set of moves
theNode->removeMove( this );
// decrease the DAG node reference count because we also have a pointer to it
if ( theNode->decrementReferenceCount() == 0 )
{
delete theNode;
}
}
delete proposal;
}
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;
}
/**
* Constructor
*
* Here we simply allocate and initialize the move object.
*
* \param[in] w The weight how often the proposal will be used (per iteration).
* \param[in] t If auto tuning should be used.
*/
AbstractMove::AbstractMove( const std::vector<DagNode*> &n, double w, bool t ) :
nodes( n ),
affectedNodes( ),
weight( w ),
autoTuning( t )
{
for (std::vector<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it)
{
// get the pointer to the current node
DagNode* theNode = *it;
// add myself to the set of moves
theNode->addMove( this );
// increase the DAG node reference count because we also have a pointer to it
theNode->incrementReferenceCount();
}
// remove all "core" nodes from affectedNodes so their probabilities are not double-counted
for (size_t i = 0; i < affectedNodes.size(); ++i)
{
RbOrderedSet<DagNode*>::iterator it = affectedNodes.begin();
std::advance(it, i);
for (size_t j = 0; j < nodes.size(); ++j)
{
if ( nodes[j] == *it )
{
affectedNodes.erase(*it);
--i;
break;
}
}
}
}
/**
* Copy constructor.
* We need to create a deep copy of the proposal here.
*
* \param[in] m The object to copy.
*
*/
MetropolisHastingsMove::MetropolisHastingsMove(const MetropolisHastingsMove &m) : AbstractMove(m),
affectedNodes( m.affectedNodes ),
nodes( m.nodes ),
numAccepted( m.numAccepted ),
proposal( m.proposal->clone() )
{
for (std::set<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it)
{
// get the pointer to the current node
DagNode* theNode = *it;
// add myself to the set of moves
theNode->addMove( this );
// increase the DAG node reference count because we also have a pointer to it
theNode->incrementReferenceCount();
}
}
/**
* Basic destructor doing nothing.
*/
AbstractMove::~AbstractMove( void )
{
// clean up my pointers to the nodes
for (size_t i = 0; i < nodes.size(); ++i)
{
// get the pointer to the current node
DagNode* theNode = nodes[i];
// add myself to the set of moves
theNode->removeMove( this );
// decrease the DAG node reference count because we also have a pointer to it
if ( theNode->decrementReferenceCount() == 0 )
{
delete theNode;
}
}
}
AbstractMove::AbstractMove( const AbstractMove &m ) : Move( m ),
nodes( m.nodes ),
affectedNodes( m.affectedNodes ),
weight( m.weight ),
autoTuning( m.autoTuning )
{
for (size_t i = 0; i < nodes.size(); ++i)
{
// get the pointer to the current node
DagNode* theNode = nodes[i];
// add myself to the set of moves
theNode->addMove( this );
// increase the DAG node reference count because we also have a pointer to it
theNode->incrementReferenceCount();
}
}
/**
* Constructor
*
* Here we simply allocate and initialize the move object.
*
* \param[in] w The weight how often the proposal will be used (per iteration).
* \param[in] t If auto tuning should be used.
*/
MetropolisHastingsMove::MetropolisHastingsMove( Proposal *p, double w, bool t ) : AbstractMove(w,t),
affectedNodes(),
nodes(),
numAccepted( 0 ),
proposal( p )
{
nodes = proposal->getNodes();
for (std::set<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it)
{
// get the pointer to the current node
DagNode* theNode = *it;
// add myself to the set of moves
theNode->addMove( this );
// increase the DAG node reference count because we also have a pointer to it
theNode->incrementReferenceCount();
// get the affected nodes if we would update this node
// then we don't need to get the affected nodes every time again
theNode->getAffectedNodes( affectedNodes );
}
// remove all "core" nodes from affectedNodes so their probabilities are not double-counted
for (size_t i = 0; i < affectedNodes.size(); ++i)
{
std::set<DagNode*>::iterator it = affectedNodes.begin();
std::advance(it, i);
if ( nodes.find(*it) != nodes.end() )
{
affectedNodes.erase(*it);
--i;
}
}
}
/**
* Overloaded assignment operator.
* We need a deep copy of the operator.
*/
MetropolisHastingsMove& MetropolisHastingsMove::operator=(const RevBayesCore::MetropolisHastingsMove &m)
{
if ( this != &m )
{
// free memory
delete proposal;
for (std::set<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it)
{
// get the pointer to the current node
DagNode* theNode = *it;
// add myself to the set of moves
theNode->removeMove( this );
// decrease the DAG node reference count because we also have a pointer to it
if ( theNode->decrementReferenceCount() == 0 )
{
delete theNode;
}
}
affectedNodes = m.affectedNodes;
nodes = m.nodes;
numAccepted = m.numAccepted;
proposal = m.proposal->clone();
for (std::set<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it)
{
// get the pointer to the current node
DagNode* theNode = *it;
// add myself to the set of moves
theNode->addMove( this );
// increase the DAG node reference count because we also have a pointer to it
theNode->incrementReferenceCount();
}
}
return *this;
}
/**
* Overloaded assignment operator.
* We need a deep copy of the operator.
*/
AbstractMove& AbstractMove::operator=(const RevBayesCore::AbstractMove &m)
{
if ( this != &m )
{
// delegate
Move::operator=(m);
for (size_t i = 0; i < nodes.size(); ++i)
{
// get the pointer to the current node
DagNode* theNode = nodes[i];
// add myself to the set of moves
theNode->removeMove( this );
// decrease the DAG node reference count because we also have a pointer to it
if ( theNode->decrementReferenceCount() == 0 )
{
delete theNode;
}
}
affectedNodes = m.affectedNodes;
nodes = m.nodes;
for (size_t i = 0; i < nodes.size(); ++i)
{
// get the pointer to the current node
DagNode* theNode = nodes[i];
// add myself to the set of moves
theNode->addMove( this );
// increase the DAG node reference count because we also have a pointer to it
theNode->incrementReferenceCount();
}
}
return *this;
}
/**
* Reset the currently monitored DAG nodes by extracting the DAG nodes from the model again
* and store this in the set of DAG nodes.
*/
void ModelMonitor::resetDagNodes( void )
{
// for savety we empty our dag nodes
nodes.clear();
if ( model != NULL )
{
// we only want to have each nodes once
// this should by default happen by here we check again
std::set<std::string> varNames;
const std::vector<DagNode*> &n = model->getDagNodes();
for (std::vector<DagNode*>::const_iterator it = n.begin(); it != n.end(); ++it)
{
DagNode *theNode = *it;
// only simple numeric variable can be monitored (i.e. only integer and real numbers)
if ( theNode->isSimpleNumeric() && !theNode->isClamped())
{
if ( (!stochasticNodesOnly && !theNode->isConstant() && theNode->getName() != "" && !theNode->isHidden() && !theNode->isElementVariable() ) || ( theNode->isStochastic() && !theNode->isClamped() && theNode->isHidden() == false && theNode->isElementVariable() == false ) )
{
const std::string &name = theNode->getName();
if ( varNames.find( name ) == varNames.end() )
{
nodes.push_back( theNode );
varNames.insert( name );
}
else
{
/*
std::cerr << "Trying to add variable with name '" << name << "' twice." << std::endl;
*/
}
}
}
}
}
}
/** Monitor value at generation gen */
void ScreenMonitor::monitor(unsigned long gen) {
// get the printing frequency
unsigned long samplingFrequency = printgen;
if (gen % samplingFrequency == 0) {
// print the iteration number first
std::cout << gen;
if ( posterior ) {
// add a separator before every new element
std::cout << separator;
const std::vector<DagNode*> &n = model->getDagNodes();
double pp = 0.0;
for (std::vector<DagNode*>::const_iterator it = n.begin(); it != n.end(); ++it) {
pp += (*it)->getLnProbability();
}
std::cout << pp;
}
if ( likelihood ) {
// add a separator before every new element
std::cout << separator;
const std::vector<DagNode*> &n = model->getDagNodes();
double pp = 0.0;
for (std::vector<DagNode*>::const_iterator it = n.begin(); it != n.end(); ++it) {
if ( (*it)->isClamped() ) {
pp += (*it)->getLnProbability();
}
}
std::cout << pp;
}
if ( prior ) {
// add a separator before every new element
std::cout << separator;
const std::vector<DagNode*> &n = model->getDagNodes();
double pp = 0.0;
for (std::vector<DagNode*>::const_iterator it = n.begin(); it != n.end(); ++it) {
if ( !(*it)->isClamped() ) {
pp += (*it)->getLnProbability();
}
}
std::cout << pp;
}
for (std::vector<DagNode*>::iterator i = nodes.begin(); i != nodes.end(); ++i) {
// add a separator before every new element
std::cout << separator;
// get the node
DagNode *node = *i;
// print the value
node->printValue(std::cout, separator);
}
std::cout << std::endl;
}
}
/**
* Swap the current variable for a new one.
*
* \param[in] oldN The old variable that needs to be replaced.
* \param[in] newN The new variable.
*/
void AbstractMove::swapNode(DagNode *oldN, DagNode *newN)
{
// find the old node
for (size_t i = 0; i < nodes.size(); ++i)
{
// get the pointer to the current node
DagNode* theNode = nodes[i];
if ( theNode == oldN )
{
nodes[i] = newN;
}
}
// remove myself from the old node and add myself to the new node
oldN->removeMove( this );
newN->addMove( this );
// increment and decrement the reference counts
newN->incrementReferenceCount();
if ( oldN->decrementReferenceCount() == 0 )
{
throw RbException("Memory leak in Metropolis-Hastings move. Please report this bug to Sebastian.");
}
affectedNodes.clear();
for (std::vector<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it)
{
// get the pointer to the current node
DagNode* theNode = *it;
// get the affected nodes if we would update this node
// then we don't need to get the affected nodes every time again
theNode->getAffectedNodes( affectedNodes );
}
// remove all "core" nodes from affectedNodes so their probabilities are not double-counted
for (size_t i = 0; i < affectedNodes.size(); ++i)
{
RbOrderedSet<DagNode*>::iterator it = affectedNodes.begin();
std::advance(it, i);
for (size_t j = 0; j < nodes.size(); ++j)
{
if ( nodes[j] == *it )
{
affectedNodes.erase(*it);
--i;
break;
}
}
}
swapNodeInternal(oldN, newN);
}
void HillClimber::initializeSampler( void )
{
std::vector<DagNode *>& dagNodes = model->getDagNodes();
std::vector<DagNode *> orderedStochNodes = model->getOrderedStochasticNodes( );
// Get rid of previous move schedule, if any
if ( schedule )
{
delete schedule;
}
schedule = NULL;
// Get initial lnProbability of model
// first we touch all nodes so that the likelihood is dirty
for (std::vector<DagNode *>::iterator i=dagNodes.begin(); i!=dagNodes.end(); i++)
{
DagNode *the_node = *i;
the_node->setMcmcMode( true );
the_node->setPriorOnly( false );
the_node->touch();
}
int numTries = 0;
int maxNumTries = 100;
double lnProbability = 0.0;
for ( ; numTries < maxNumTries; numTries ++ )
{
// a flag if we failed to find a valid starting value
bool failed = false;
lnProbability = 0.0;
for (std::vector<DagNode *>::iterator i=dagNodes.begin(); i!=dagNodes.end(); i++)
{
DagNode* node = (*i);
node->touch();
double lnProb = node->getLnProbability();
if ( !RbMath::isAComputableNumber(lnProb) )
{
std::stringstream ss;
ss << "Could not compute lnProb for node " << node->getName() << "." << std::endl;
node->printValue( ss );
ss << std::endl;
RBOUT( ss.str() );
// set the flag
failed = true;
break;
}
lnProbability += lnProb;
}
// now we keep all nodes so that the likelihood is stored
for (std::vector<DagNode *>::iterator i=dagNodes.begin(); i!=dagNodes.end(); i++)
{
(*i)->keep();
}
if ( failed == true )
{
std::cout << "Drawing new initial states ... " << std::endl;
for (std::vector<DagNode *>::iterator i=orderedStochNodes.begin(); i!=orderedStochNodes.end(); i++)
{
if ( !(*i)->isClamped() && (*i)->isStochastic() )
{
(*i)->redraw();
(*i)->reInitialized();
}
else if ( (*i)->isClamped() )
{
// make sure that the clamped node also recompute their probabilities
(*i)->reInitialized();
(*i)->touch();
}
}
}
else
{
break;
}
}
if ( numTries == maxNumTries )
{
std::stringstream msg;
msg << "Unable to find a starting state with computable probability";
if ( numTries > 1 )
{
msg << " after " << numTries << " tries";
}
throw RbException( msg.str() );
}
// Create the move scheduler
if ( scheduleType == "sequential" )
{
schedule = new SequentialMoveSchedule( &moves );
}
else if ( scheduleType == "single" )
{
schedule = new SingleRandomMoveSchedule( &moves );
}
else
{
schedule = new RandomMoveSchedule( &moves );
}
generation = 0;
}