/** Execute function */
RevPtr<RevVariable> Func_mapTree::execute( void )
{
// get the x% hpd
double x = 0.95;
const TraceTree& tt = static_cast<const TraceTree&>( args[0].getVariable()->getRevObject() );
const std::string& filename = static_cast<const RlString&>( args[1].getVariable()->getRevObject() ).getValue();
int burnin = static_cast<const Integer &>(args[2].getVariable()->getRevObject()).getValue();
RevBayesCore::TreeSummary summary = RevBayesCore::TreeSummary( tt.getValue() );
// set the burnin
summary.setBurnin( burnin );
RevBayesCore::Tree* tree = summary.map( tt.getValue().isClock() );
// get the tree with x% HPD node ages
summary.annotateHPDAges(*tree, x );
// get the tree with x% HPD node ages
summary.annotate(*tree);
if ( filename != "" )
{
RevBayesCore::NexusWriter writer(filename);
writer.openStream();
std::vector<RevBayesCore::Taxon> taxa;
tree->getRoot().getTaxa(taxa);
RevBayesCore::Clade c( taxa );
writer.writeNexusBlock(c);
writer.writeNexusBlock(*tree);
writer.closeStream();
}
return new RevVariable( new Tree( tree ) );
}
/** Execute function */
RevPtr<RevVariable> Func_annotateTree::execute( void )
{
size_t arg_index = 0;
// get the input tree
RevBayesCore::Tree* tree = static_cast<const Tree&>( this->args[arg_index++].getVariable()->getRevObject() ).getValue().clone();
// get the tree trace
TraceTree& tt = static_cast<TraceTree&>( args[arg_index++].getVariable()->getRevObject() );
// get the filename
const std::string& filename = static_cast<const RlString&>( args[arg_index++].getVariable()->getRevObject() ).getValue();
RevBayesCore::AnnotationReport report;
report.ages = static_cast<const RlBoolean &>( this->args[arg_index++].getVariable()->getRevObject() ).getValue();
report.cc_ages = static_cast<const RlBoolean &>( this->args[arg_index++].getVariable()->getRevObject() ).getValue();
report.ccp = static_cast<const RlBoolean &>( this->args[arg_index++].getVariable()->getRevObject() ).getValue();
report.tree_ages = static_cast<const RlBoolean &>( this->args[arg_index++].getVariable()->getRevObject() ).getValue();
report.hpd = static_cast<const Probability &>(args[arg_index++].getVariable()->getRevObject()).getValue();
report.mean = static_cast<const RlBoolean &>( this->args[arg_index++].getVariable()->getRevObject() ).getValue();
report.sa = static_cast<const RlBoolean &>( this->args[arg_index++].getVariable()->getRevObject() ).getValue();
//
// // get burnin
// int burnin = static_cast<const Integer &>(args[arg_index++].getVariable()->getRevObject()).getValue();
// do not make a new tree summary object
// this way we don't need to resummarize every time we annotate a tree
// RevBayesCore::TreeSummary summary = RevBayesCore::TreeSummary( tt.getValue() );
bool verbose = true;
tt.getValue().annotateTree( *tree, report, verbose );
// return the tree
if ( filename != "" )
{
RevBayesCore::NexusWriter writer(filename);
writer.openStream(false);
std::vector<RevBayesCore::Taxon> taxa;
tree->getRoot().getTaxa(taxa);
RevBayesCore::Clade c( taxa );
writer.writeNexusBlock(c);
writer.writeNexusBlock(*tree);
writer.closeStream();
}
Tree* t;
if( tt.getValue().getTreeTrace().isClock() )
{
t = new TimeTree( tree );
}
else
{
t = new BranchLengthTree( tree );
}
return new RevVariable( t );
}