double Tree::lnPriorRatio(double nh, double oh) {
nh = nh * treeScale;
oh = oh * treeScale;
if (treeTimePrior == 1) {
}
else if (treeTimePrior == 2) {
double diff = modelPtr->getActiveSpeciation()->getNetDiversification();
double nator = (-(diff) * nh);
double dator = (-(diff) * oh);
return nator - dator;
} else {
Speciation *s = modelPtr->getActiveSpeciation();
double diff = s->getNetDiversification(); // br-dr
double rel = s->getRelativeDeath(); // dr / br
double zn = log(1 - (rel) * exp(-(diff) * nh));
double nator = -2 * zn + (-(diff) * nh);
double zd = log(1 - (rel) * exp(-(diff) * oh));
double dator = -2 * zd + (-(diff) * oh);
return nator - dator;
}
return 0.0;
}
double Tree::getTreeSpeciationProbability() {
if (treeTimePrior == 1)
return 0.0;
else if (treeTimePrior == 2) {
Speciation *s = modelPtr->getActiveSpeciation();
double diff = s->getNetDiversification();
double c1 = (numTaxa - 1) * log(diff);
double nps = getTreeCBDNodePriorProb(diff, 0.0);
return c1 + nps;
} else {
Speciation *s = modelPtr->getActiveSpeciation();
double diff = s->getNetDiversification(); // br-dr
double rel = s->getRelativeDeath();
double lnC = 0.0;
double c1 = ((numTaxa - 1) * log(diff)) + (numTaxa * log(1 - rel));
double nps = getTreeCBDNodePriorProb(diff, rel);
return lnC + c1 + nps;
}
return 0.0;
}
double Tree::getTreeCBDNodePriorProb() {
double nprb = 0.0;
if (treeTimePrior == 1)
return 0.0;
else if (treeTimePrior == 2) {
Speciation *s = modelPtr->getActiveSpeciation();
double diff = s->getNetDiversification(); // br-dr
for (int i = 0; i < numNodes; i++) {
Node *p = &nodes[i];
if (p->getIsLeaf() == false) {
double nh = p->getNodeDepth() * treeScale;
double l = (-(diff) * nh);
if (p == root) {
l += (-(diff) * nh);
}
nprb += l;
}
}
return nprb;
} else {
Speciation *s = modelPtr->getActiveSpeciation();
double diff = s->getNetDiversification(); // br-dr
double rel = s->getRelativeDeath(); // dr / br
for (int i = 0; i < numNodes; i++) {
Node *p = &nodes[i];
if (p->getIsLeaf() == false) {
double nh = p->getNodeDepth() * treeScale;
double zn = log(1 - (rel) * exp(-(diff) * nh));
double l = -2 * zn + (-(diff) * nh);
if (p == root) {
l += (-(diff) * nh) - zn;
}
nprb += l;
}
}
return nprb;
}
return 0.0;
}
Parameter& Parameter::operator=(Parameter &p) {
if (this != &p){
ranPtr = p.ranPtr;
name = p.name;
{
Basefreq *thatDerivedPtr = dynamic_cast<Basefreq *>(&p);
Basefreq *thisDerivedPtr = dynamic_cast<Basefreq *>(this);
if ( thatDerivedPtr != 0 && thisDerivedPtr != 0 ){
thisDerivedPtr->clone( *thatDerivedPtr );
goto exitOperator;
}
}
{
Exchangeability *thatDerivedPtr = dynamic_cast<Exchangeability *>(&p);
Exchangeability *thisDerivedPtr = dynamic_cast<Exchangeability *>(this);
if ( thatDerivedPtr != 0 && thisDerivedPtr != 0 ){
thisDerivedPtr->clone( *thatDerivedPtr );
goto exitOperator;
}
}
{
Shape *thatDerivedPtr = dynamic_cast<Shape *>(&p);
Shape *thisDerivedPtr = dynamic_cast<Shape *>(this);
if ( thatDerivedPtr != 0 && thisDerivedPtr != 0 ){
thisDerivedPtr->clone( *thatDerivedPtr );
goto exitOperator;
}
}
{
Tree *thatDerivedPtr = dynamic_cast<Tree *>(&p);
Tree *thisDerivedPtr = dynamic_cast<Tree *>(this);
if ( thatDerivedPtr != 0 && thisDerivedPtr != 0 ){
thisDerivedPtr->clone( *thatDerivedPtr );
goto exitOperator;
}
}
{
NodeRate *thatDerivedPtr = dynamic_cast<NodeRate *>(&p);
NodeRate *thisDerivedPtr = dynamic_cast<NodeRate *>(this);
if ( thatDerivedPtr != 0 && thisDerivedPtr != 0 ){
thisDerivedPtr->clone( *thatDerivedPtr );
goto exitOperator;
}
}
{
Cphyperp *thatDerivedPtr = dynamic_cast<Cphyperp *>(&p);
Cphyperp *thisDerivedPtr = dynamic_cast<Cphyperp *>(this);
if ( thatDerivedPtr != 0 && thisDerivedPtr != 0 ){
thisDerivedPtr->clone( *thatDerivedPtr );
goto exitOperator;
}
}
{
Treescale *thatDerivedPtr = dynamic_cast<Treescale *>(&p);
Treescale *thisDerivedPtr = dynamic_cast<Treescale *>(this);
if ( thatDerivedPtr != 0 && thisDerivedPtr != 0 ){
thisDerivedPtr->clone( *thatDerivedPtr );
goto exitOperator;
}
}
{
Speciation *thatDerivedPtr = dynamic_cast<Speciation *>(&p);
Speciation *thisDerivedPtr = dynamic_cast<Speciation *>(this);
if ( thatDerivedPtr != 0 && thisDerivedPtr != 0 ){
thisDerivedPtr->clone( *thatDerivedPtr );
goto exitOperator;
}
}
{
ExpCalib *thatDerivedPtr = dynamic_cast<ExpCalib *>(&p);
ExpCalib *thisDerivedPtr = dynamic_cast<ExpCalib *>(this);
if ( thatDerivedPtr != 0 && thisDerivedPtr != 0 ){
thisDerivedPtr->clone( *thatDerivedPtr );
goto exitOperator;
}
}
exitOperator:
;
}
return *this;
}
double Treescale::getLnTreeProb(Tree *t) {
if(treeTimePrior == 1)
return 0.0;
else if(treeTimePrior == 2 || treeTimePrior == 3){
return t->getTreeCBDNodePriorProb();
}
else if(treeTimePrior == 4 || treeTimePrior == 5){
Speciation *s = modelPtr->getActiveSpeciation();
double nps = t->getTreeBDSSTreeNodePriorProb(s->getNetDiversification(),
s->getRelativeDeath(), s->getBDSSFossilSampRatePsi(),
s->getBDSSSppSampRateRho(), treeOriginTime);
return nps;
}
else if(treeTimePrior == 6){
Speciation *s = modelPtr->getActiveSpeciation();
s->setAllBDFossParams();
double nps = t->getTreeCalBDSSTreeNodePriorProb(s->getBDSSSpeciationRateLambda(),
s->getBDSSExtinctionRateMu(),
s->getBDSSFossilSampRatePsi(),
s->getBDSSSppSampRateRho());
return nps;
}
else if(treeTimePrior == 7){
Speciation *s = modelPtr->getActiveSpeciation();
s->setAllBDFossParams();
double nps = t->getTreeAncCalBDSSTreeNodePriorProb(s->getBDSSSpeciationRateLambda(),
s->getBDSSExtinctionRateMu(),
s->getBDSSFossilSampRatePsi(),
s->getBDSSSppSampRateRho());
return nps;
}
return 0.0;
}
