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Parameter_tree.cpp
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Parameter_tree.cpp
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/*
* DPPDiv version 1.0b source code (git: 9c0ac3d2258f89827cfe9ba2b5038f0f656b82c1)
* Copyright 2009-2011
* Tracy Heath(1,2,3) (NSF postdoctoral fellowship in biological informatics DBI-0805631)
* Mark Holder(1)
* John Huelsenbeck(2)
*
* (1) Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045
* (2) Integrative Biology, University of California, Berkeley, CA 94720-3140
* (3) email: tracyh@berkeley.edu
*
* DPPDiv is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* General Public License (the file gpl.txt included with this
* distribution or http://www.gnu.org/licenses/gpl.txt for more
* details.
*
* Some of this code is from publicly available source by John Huelsenbeck
*/
#include "Alignment.h"
#include "Calibration.h"
#include "MbMath.h"
#include "MbRandom.h"
#include "Model.h"
#include "Parameter.h"
#include "Parameter_expcalib.h"
#include "Parameter_rate.h"
#include "Parameter_speciaton.h"
#include "Parameter_tree.h"
#include <iostream>
#include <sstream>
#include <iomanip>
#include <vector>
#include <algorithm>
#include <fstream>
using namespace std;
Node::Node(void) {
lft = NULL;
rht = NULL;
anc = NULL;
idx = 0;
name = "";
activeCl = 0;
activeTi = 0;
isClDirty = true;
isTiDirty = true;
nodeDepth = 0.0;
isLeaf = false;
isCalib = false;
youngt = -1.0;
oldt = -1.0;
branchTime = 0.0;
rateGVal = 0.0;
rateGrpIdx = -1;
userBL = 0.0;
nodeCalibPrD = 1;
nodeExpCalRate = -1.0;
taintFossil = false;
redFlag = 0;
}
Tree::Tree(MbRandom *rp, Model *mp, Alignment *ap, string ts, bool ubl, bool allnm,
bool rndNods, vector<Calibration *> clb, double rth, bool sb, bool exhpc,
ExpCalib *ec) : Parameter(rp, mp) {
alignmentPtr = ap;
numTaxa = 0;
numNodes = 0;
nodes = NULL;
root = NULL;
downPassSequence = NULL;
useInputBLs = ubl;
moveAllNodes = allnm;
calibNds = clb;
treeScale = rth;
treeTimePrior = modelPtr->getTreeTimePriorNum();
name = "TR";
randShufNdMv = rndNods;
softBounds = sb;
isCalibTree = false;
expHyperPrCal = exhpc;
buildTreeFromNewickDescription(ts);
if(calibNds.size() > 0){
isCalibTree = true;
setNodeCalibrationPriors(ec);
initializeCalibratedNodeDepths();
while(checkTreeForCalibrationCompatibility() > 0){
zeroNodeRedFlags();
initializeCalibratedNodeDepths();
}
}
else{
isCalibTree = false;
if(useInputBLs)
initializeNodeDepthsFromUserBL();
else
initializeNodeDepths();
}
setAllNodeBranchTimes();
}
Tree::~Tree(void) {
delete [] nodes;
delete [] downPassSequence;
}
void Tree::buildTreeFromNewickDescription(string ts) {
numTaxa = alignmentPtr->getNumTaxa();
numNodes = 2 * numTaxa - 1;
nodes = new Node[numNodes];
downPassSequence = new Node*[numNodes];
for (int i=0; i<numNodes; i++)
nodes[i].setIdx(i);
bool readingBrlen = false;
Node *p = NULL, *q = NULL;
int nextInteriorNode = numTaxa;
for (unsigned i=0; i<ts.size(); i++)
{
// cout << "Building Node " << i << "of " << ts.size() << endl;
char c = ts[i];
if ( c == '(' )
{
q = &nodes[nextInteriorNode++];
if (p == NULL)
{
p = q;
root = p;
}
else
{
q->setAnc(p);
if (p->getLft() == NULL)
p->setLft(q);
else if (p->getRht() == NULL)
p->setRht(q);
else
{
cerr << "ERROR1: Problem adding interior node to tree" << endl;
exit(1);
}
}
p = q;
readingBrlen = false;
}
else if ( c == ')' )
{
if (p->getAnc() == NULL)
{
cerr << "ERROR: Problem moving down the tree" << endl;
exit(1);
}
else
p = p->getAnc();
readingBrlen = false;
}
else if ( c == ',' )
{
if (p->getAnc() == NULL)
{
cerr << "ERROR: Problem moving down the tree" << endl;
exit(1);
}
else
p = p->getAnc();
readingBrlen = false;
}
else if ( c == ':' )
{
readingBrlen = true;
}
else if ( c == ';' )
{
// we are finished with the tree...check
}
else
{
string s = "";
while ( isValidChar(ts[i]) )
s += ts[i++];
i--;
if (readingBrlen == false)
{
if ( alignmentPtr->isTaxonPresent(s) == false )
{
cerr << "ERROR: Cannot find taxon in alignment" << endl;
exit(1);
}
int indexForTaxon = alignmentPtr->getIndexForTaxonNamed(s);
q = &nodes[indexForTaxon];
if (p == NULL)
{
cerr << "ERROR: Problem adding a tip to the tree" << endl;
exit(1);
}
else
{
q->setAnc(p);
if (p->getLft() == NULL)
p->setLft(q);
else if (p->getRht() == NULL)
p->setRht(q);
else
{
cerr << "ERROR2: Problem adding interior node to tree" << endl;
exit(1);
}
}
p = q;
p->setName(s);
p->setIsLeaf(true);
}
else
{
double x;
istringstream buf(s);
buf >> x;
p->setUerBL(x);
}
}
}
getDownPassSequence();
root->setRtGrpVal(0.5);
}
Tree& Tree::operator=(const Tree &t) {
if (this != &t)
clone(t);
return *this;
}
void Tree::clone(const Tree &t) {
if (numNodes != t.numNodes || numTaxa != t.numTaxa)
{
cerr << "ERROR: Attempting to clone trees of unequal size" << endl;
exit(1);
}
for (int i=0; i<numNodes; i++){
Node *pTo = &nodes[i];
Node *pFrom = &t.nodes[i];
pTo->setName( pFrom->getName() );
pTo->setActiveCl( pFrom->getActiveCl() );
pTo->setActiveTi( pFrom->getActiveTi() );
pTo->setIsClDirty( pFrom->getIsClDirty() );
pTo->setIsTiDirty( pFrom->getIsTiDirty() );
pTo->setNodeDepth( pFrom->getNodeDepth() );
pTo->setIsLeaf( pFrom->getIsLeaf() );
pTo->setRtGrpVal( pFrom->getRateGVal() );
pTo->setBranchTime( pFrom->getBranchTime() );
pTo->setIsCalibratedDepth( pFrom->getIsCalibratedDepth() );
pTo->setNodeYngTime( pFrom->getNodeYngTime() );
pTo->setNodeOldTime( pFrom->getNodeOldTime() );
pTo->setRtGrpIdx( pFrom->getRateGrpIdx() );
pTo->setNodeCalibPrDist( pFrom->getNodeCalibPrDist() );
pTo->setNumDecendantTax( pFrom->getNumDecendantTax() );
pTo->setNodeExpCalRate( pFrom->getNodeExpCalRate() );
if (pFrom->getLft() == NULL)
pTo->setLft(NULL);
else
pTo->setLft( &nodes[pFrom->getLft()->getIdx()] );
if (pFrom->getRht() == NULL)
pTo->setRht(NULL);
else
pTo->setRht( &nodes[pFrom->getRht()->getIdx()] );
if (pFrom->getAnc() == NULL)
pTo->setAnc(NULL);
else
pTo->setAnc( &nodes[pFrom->getAnc()->getIdx()] );
}
root = &nodes[t.root->getIdx()];
treeScale = t.treeScale;
treeTimePrior = t.treeTimePrior;
for (int i=0; i<numNodes; i++)
downPassSequence[i] = &nodes[ t.downPassSequence[i]->getIdx() ];
}
int Tree::dex(const Node *p) {
return (p == NULL ? -1 : p->getIdx());
}
void Tree::getDownPassSequence(void) {
int x = 0;
passDown(root, &x);
}
void Tree::initializeNodeDepthsFromUserBL(void) {
double inDepth = 0.0;
int k = 0;
Node *p = &nodes[k];
while(!p->getIsLeaf())
p = &nodes[k++];
while(p != root){
inDepth += p->getUerBL();
p = p->getAnc();
}
double scaler = 1.0 / inDepth;
Node *q = NULL;
double nodeDepth = 0.0;
for(int i=0; i<numNodes; i++){
p = &nodes[i];
if(p->getIsLeaf())
p->setNodeDepth(0.0);
else if(p == root)
p->setNodeDepth(1.0);
else {
nodeDepth = p->getUerBL();
q = p->getAnc();
while(q != root){
nodeDepth += q->getUerBL();
q = q->getAnc();
}
p->setNodeDepth(1.0 - (nodeDepth * scaler));
}
}
}
void Tree::initializeNodeDepths(void) {
vector<Node*> potentialSplits;
vector<double> nodeTimes;
for (int i=0; i<numTaxa-2; i++)
nodeTimes.push_back( ranPtr->uniformRv() );
sort( nodeTimes.begin(), nodeTimes.end(), greater<double>() );
for (unsigned i=0; i<nodeTimes.size(); i++)
cout << nodeTimes[i] << " ";
cout << endl;
root->setNodeDepth(1.0);
if (root->getLft()->getIsLeaf() == false)
potentialSplits.push_back(root->getLft());
if (root->getRht()->getIsLeaf() == false)
potentialSplits.push_back(root->getRht());
int nextTime = 0;
while (potentialSplits.size() > 0)
{
Node *p = potentialSplits[(int)(ranPtr->uniformRv()*potentialSplits.size())];
p->setNodeDepth(nodeTimes[nextTime++]);
for (vector<Node *>::iterator n=potentialSplits.begin(); n != potentialSplits.end(); n++)
{
if ( (*n) == p )
{
potentialSplits.erase( n );
break;
}
}
if (p->getLft()->getIsLeaf() == false)
potentialSplits.push_back(p->getLft());
if (p->getRht()->getIsLeaf() == false)
potentialSplits.push_back(p->getRht());
}
}
void Tree::initializeCalibratedNodeDepths(void) {
root->setNodeDepth(1.0);
bool goodinit = false;
while(!goodinit){
for(vector<Calibration *>::iterator v = calibNds.begin(); v != calibNds.end(); v++){
Node *p = &nodes[(*v)->getNodeIndex()];
if(p != root){
Node *anc, *ldes, *rdes;
anc = p->getAnc();
ldes = p->getLft();
rdes = p->getRht();
double ltime = ldes->getNodeDepth();
double rtime = rdes->getNodeDepth();
double atime = anc->getNodeDepth();
double oldbound = 0.0;
double yngbound = p->getNodeYngTime() / treeScale;
if(p->getNodeCalibPrDist() == 1)
oldbound = p->getNodeOldTime() / treeScale;
else
oldbound = getTemporaryNodeMaxBound(p) / treeScale;
if(p->getNodeOldTime() == p->getNodeYngTime()){
double newNodeDepth = yngbound;
p->setNodeDepth(newNodeDepth);
goodinit = true;
}
else{
if(ltime > 0.0 || rtime > 0.0){
if(rtime > ltime){
if(rtime > yngbound)
yngbound = rtime;
}
else{
if(ltime > yngbound)
yngbound = ltime;
}
}
if(atime > 0.0){
if(atime < oldbound)
oldbound = atime;
}
if(oldbound > root->getNodeDepth())
oldbound = root->getNodeDepth();
if(yngbound > oldbound){
goodinit = false;
break;
}
else{
double newNodeDepth = yngbound + ranPtr->uniformRv()*(oldbound-yngbound);
p->setNodeDepth(newNodeDepth);
goodinit = true;
}
}
}
else
goodinit = true;
}
}
setNodesNumberDecendantTaxa(root);
int nnc = 0;
recursiveNodeDepthInitialization(root, nnc, 1.0);
}
double Tree::getTemporaryNodeMaxBound(Node *p){
double tempmax = treeScale;
Node *q = p->getAnc();
while(q != root && tempmax == treeScale){
if(q->getIsCalibratedDepth())
tempmax = q->getNodeYngTime();
else
q = q->getAnc();
}
return tempmax;
}
vector<double> Tree::recursiveNodeDepthInitialization(Node *p, int &nCont, double maxD) {
vector<double> ndTimesC;
if(p->getIsLeaf()){
for(int i=0; i< nCont; i++)
ndTimesC.push_back( ranPtr->uniformRv()*(maxD) );
if(ndTimesC.size() > 1)
sort( ndTimesC.begin(), ndTimesC.end() );
return ndTimesC;
}
else{
bool getDFrmVec = false;
int nAncN = nCont;
double myDepth = maxD;
if(p->getIsCalibratedDepth()){
myDepth = p->getNodeDepth();
nCont = 0;
getDFrmVec = false;
}
else{
nCont += 1;
getDFrmVec = true;
}
Node *d1 = p->getLft();
Node *d2 = p->getRht();
if(p->getLft()->getNumDecendantTax() < p->getRht()->getNumDecendantTax()){
if(p->getRht()->getIsCalibratedDepth() == false && p->getLft()->getIsCalibratedDepth() == true){
d1 = p->getLft();
d2 = p->getRht();
}
else{
d2 = p->getLft();
d1 = p->getRht();
}
}
else{
if(p->getRht()->getIsCalibratedDepth() == true && p->getLft()->getIsCalibratedDepth() == false){
d2 = p->getLft();
d1 = p->getRht();
}
else{
d1 = p->getLft();
d2 = p->getRht();
}
}
ndTimesC = recursiveNodeDepthInitialization(d1, nCont, myDepth);
if(getDFrmVec){
if(p->getNodeDepth() > 0.0){
myDepth = p->getNodeDepth();
if(ndTimesC.size() > 0)
ndTimesC.erase(ndTimesC.begin()+0);
}
else{
if(ndTimesC.size() == 0){
int myID = p->getIdx();
cerr << "ERROR: node vector is empty at Node " << myID << endl;
exit(1);
}
myDepth = ndTimesC[0];
p->setNodeDepth(myDepth);
ndTimesC.erase(ndTimesC.begin()+0);
}
}
nCont = 0;
recursiveNodeDepthInitialization(d2, nCont, myDepth);
if(getDFrmVec)
return ndTimesC;
else{
if(ndTimesC.size() > 0){
int myID = p->getIdx();
cout << "Calibrated " << myID << " (MAX = " << maxD*treeScale;
cout << ") (MIN = " << myDepth*treeScale << ") ";
for(vector<double>::iterator v = ndTimesC.begin(); v != ndTimesC.end(); v++){
cout << " " << (*v)*treeScale << " ";
}
cout << endl;
cerr << "ERROR: node vector has stuff in it" << endl;
exit(1);
}
if(myDepth > maxD){
double badDep = maxD;
vector<int> idNFix;
Node *ancs = p->getAnc();
while(badDep < myDepth){
badDep = ancs->getNodeDepth();
if(badDep < myDepth)
idNFix.push_back(ancs->getIdx());
ancs = ancs->getAnc();
}
for(int i=0; i<idNFix.size(); i++)
ndTimesC.push_back( myDepth + ranPtr->uniformRv()*(badDep - myDepth) );
sort( ndTimesC.begin(), ndTimesC.end() );
for(int i=0; i<idNFix.size(); i++){
nodes[idNFix[i]].setNodeDepth(ndTimesC[i]);
}
ndTimesC.clear();
return ndTimesC;
}
for(int i=0; i< nAncN; i++)
ndTimesC.push_back( myDepth + ranPtr->uniformRv()*(maxD - myDepth) );
sort( ndTimesC.begin(), ndTimesC.end() );
return ndTimesC;
}
}
return ndTimesC;
}
void Tree::adjustNodesCompatibleWCalabrations(void) {
}
int Tree::setNodesNumberDecendantTaxa(Node *p) {
if(p->getIsLeaf()){
p->setNumDecendantTax(0);
return 1;
}
else{
int nds = setNodesNumberDecendantTaxa(p->getLft());
nds += setNodesNumberDecendantTaxa(p->getRht());
p->setNumDecendantTax(nds);
return nds;
}
return 0;
}
bool Tree::isValidChar(char c) {
if ( c == '(' || c == ')' || c == ',' || c == ':' || c == ';' )
return false;
return true;
}
void Tree::passDown(Node *p, int *x) {
if ( p != NULL )
{
passDown(p->getLft(), x);
passDown(p->getRht(), x);
downPassSequence[(*x)++] = p;
}
}
void Tree::print(std::ostream & o) const {
o << "Tree:\n";
showNodes(root, 3, o);
}
double Tree::update(double &oldLnL) {
double lppr = 0.0;
if(moveAllNodes){
if(randShufNdMv)
lppr = updateAllNodesRnd(oldLnL);
else lppr = updateAllNodes(oldLnL);
}
else lppr = updateOneNode();
setAllNodeBranchTimes();
return lppr;
}
double Tree::updateOneNode() {
Node *p = NULL;
do {
p = downPassSequence[(int)(ranPtr->uniformRv()*numNodes)];
} while (p->getLft() == NULL || p->getRht() == NULL || p->getAnc() == NULL);
double largestTime = p->getAnc()->getNodeDepth();
double smallestTime = p->getLft()->getNodeDepth();
if (p->getRht()->getNodeDepth() > smallestTime)
smallestTime = p->getRht()->getNodeDepth();
if(p->getIsCalibratedDepth() && softBounds == false){
double ycal = p->getNodeYngTime() / treeScale;
double ocal = largestTime;
if(p->getNodeCalibPrDist() == 1)
ocal = p->getNodeOldTime() / treeScale;
if(ycal > smallestTime)
smallestTime = ycal;
if(ocal < largestTime)
largestTime = ocal;
}
double currDepth = p->getNodeDepth();
double newNodeDepth = currDepth;
double lnPrRatio = 0.0;
if(largestTime > smallestTime){
newNodeDepth = smallestTime + ranPtr->uniformRv()*(largestTime-smallestTime);
p->setNodeDepth(newNodeDepth);
flipToRootClsTis(p);
updateToRootClsTis(p);
modelPtr->setTiProb();
if(p->getIsCalibratedDepth()){
if(softBounds && p->getNodeCalibPrDist() == 1){
double ycal = p->getNodeYngTime();
double ocal = p->getNodeOldTime();
lnPrRatio += lnCalibPriorRatio(newNodeDepth*treeScale, currDepth*treeScale, ycal, ocal);
}
if(p->getNodeCalibPrDist() == 2){
double offst = p->getNodeYngTime();
double nodeExCR = p->getNodeExpCalRate();
lnPrRatio += lnExpCalibPriorRatio(newNodeDepth*treeScale, currDepth*treeScale, offst, nodeExCR);
}
}
}
lnPrRatio += lnPriorRatio(newNodeDepth, currDepth);
return lnPrRatio;
}
double Tree::updateAllNodes(double &oldLnL) {
upDateAllCls();
upDateAllTis();
double oldLike = oldLnL;
Node *p = NULL;
for(int i = 0; i<numNodes; i++){
p = downPassSequence[i];
if(p != root && !p->getIsLeaf()){
double currDepth = p->getNodeDepth();
double largestTime = p->getAnc()->getNodeDepth();
double smallestTime = p->getLft()->getNodeDepth();
if (p->getRht()->getNodeDepth() > smallestTime)
smallestTime = p->getRht()->getNodeDepth();
if(p->getIsCalibratedDepth() && softBounds == false){
double ycal = p->getNodeYngTime() / treeScale;
double ocal = largestTime;
if(p->getNodeCalibPrDist() == 1)
ocal = p->getNodeOldTime() / treeScale;
if(ycal > smallestTime)
smallestTime = ycal;
if(ocal < largestTime)
largestTime = ocal;
}
if (largestTime > smallestTime){
double newNodeDepth = smallestTime + ranPtr->uniformRv()*(largestTime-smallestTime);
p->setNodeDepth(newNodeDepth);
flipToRootClsTis(p);
updateToRootClsTis(p);
modelPtr->setTiProb();
double newLnl = modelPtr->lnLikelihood();
double lnLRatio = newLnl - oldLike;
double lnPrRatio = lnPriorRatio(newNodeDepth, currDepth);
if(p->getIsCalibratedDepth()){
if(softBounds && p->getNodeCalibPrDist() == 1){
double ycal = p->getNodeYngTime();
double ocal = p->getNodeOldTime();
lnPrRatio += lnCalibPriorRatio(newNodeDepth*treeScale, currDepth*treeScale, ycal, ocal);
}
if(p->getNodeCalibPrDist() == 2){
double offst = p->getNodeYngTime();
double nodeExCR = p->getNodeExpCalRate();
lnPrRatio += lnExpCalibPriorRatio(newNodeDepth*treeScale, currDepth*treeScale, offst, nodeExCR);
}
}
double lnR = lnPrRatio + lnLRatio + 0.0;
double r = modelPtr->safeExponentiation(lnR);
if(ranPtr->uniformRv() < r)
oldLike = newLnl;
else{
p->setNodeDepth(currDepth);
flipToRootClsTis(p);
updateToRootClsTis(p);
}
}
}
}
oldLnL = oldLike;
return 0.0;
}
double Tree::updateAllNodesRnd(double &oldLnL) {
upDateAllCls();
upDateAllTis();
double oldLike = oldLnL;
Node *p = NULL;
vector<int> rndNodeIDs;
for(int i=0; i<numNodes; i++)
rndNodeIDs.push_back(i);
random_shuffle(rndNodeIDs.begin(), rndNodeIDs.end());
for(vector<int>::iterator it=rndNodeIDs.begin(); it!=rndNodeIDs.end(); it++){
p = downPassSequence[(*it)];
if(p != root && !p->getIsLeaf()){
double currDepth = p->getNodeDepth();
double largestTime = p->getAnc()->getNodeDepth();
double smallestTime = p->getLft()->getNodeDepth();
if (p->getRht()->getNodeDepth() > smallestTime)
smallestTime = p->getRht()->getNodeDepth();
if(p->getIsCalibratedDepth() && softBounds == false){
double ycal = p->getNodeYngTime() / treeScale;
double ocal = largestTime;
if(p->getNodeCalibPrDist() == 1)
ocal = p->getNodeOldTime() / treeScale;
if(ycal > smallestTime)
smallestTime = ycal;
if(ocal < largestTime)
largestTime = ocal;
}
if (largestTime > smallestTime){
double newNodeDepth = smallestTime + ranPtr->uniformRv()*(largestTime-smallestTime);
p->setNodeDepth(newNodeDepth);
flipToRootClsTis(p);
updateToRootClsTis(p);
modelPtr->setTiProb();
double newLnl = modelPtr->lnLikelihood();
double lnLRatio = newLnl - oldLike;
double lnPrRatio = lnPriorRatio(newNodeDepth, currDepth);
if(p->getIsCalibratedDepth()){
if(softBounds && p->getNodeCalibPrDist() == 1){
double ycal = p->getNodeYngTime();
double ocal = p->getNodeOldTime();
lnPrRatio += lnCalibPriorRatio(newNodeDepth*treeScale, currDepth*treeScale, ycal, ocal);
}
if(p->getNodeCalibPrDist() == 2){
double offst = p->getNodeYngTime();
double nodeExCR = p->getNodeExpCalRate();
lnPrRatio += lnExpCalibPriorRatio(newNodeDepth*treeScale, currDepth*treeScale, offst, nodeExCR);
}
}
double lnR = lnPrRatio + lnLRatio + 0.0;
double r = modelPtr->safeExponentiation(lnR);
if(ranPtr->uniformRv() < r){
oldLike = newLnl;
}
else{
p->setNodeDepth(currDepth);
flipToRootClsTis(p);
updateToRootClsTis(p);
}
}
}
}
oldLnL = oldLike;
return 0.0;
}
void Tree::setAllNodeBranchTimes(void) {
for (int n=0; n<numNodes; n++){
Node *p = &nodes[n];
if(p != root){
double branchtime = (p->getAnc()->getNodeDepth() - p->getNodeDepth()) * treeScale;
if(branchtime < 0){
int myID = p->getIdx();
cerr << "ERROR: The tree has a negative branch length! " << branchtime << " At Node " << myID << endl;
exit(1);
}
else
p->setBranchTime(branchtime);
}
}
}
double Tree::lnPrior() {
return 0.0;
}
double Tree::lnPriorRatio(double nh, double oh) {
nh = nh*treeScale;
oh = oh*treeScale;
if(treeTimePrior == 1)
return 0.0;
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::lnCalibPriorRatio(double nh, double oh, double lb, double ub) {
/*
Prior ratio for a uniform dist on calibrated nodes with soft bounds
From Yang and Rannala, MBE (2006)
*/
double numr = 0.0;
double dnom = 0.0;
double th1 = (0.95 * lb) / (0.025 * (ub - lb));
double th2 = 0.95 / (0.025 * (ub - lb));
if(nh <= lb)
numr += log(0.025) + log(th1 / lb) + ((th1 - 1) * log(nh / lb));
else if(nh > ub)
numr += log(0.025) + log(th2) + (-th2 * (nh - ub));
else
numr += log(0.95) - log(ub - lb);
if(oh <= lb)
dnom += log(0.025) + log(th1 / lb) + ((th1 - 1) * log(oh / lb));
else if(oh > ub)
dnom += log(0.025) + log(th2) + (-th2 * (oh - ub));
else
dnom += log(0.95) - log(ub - lb);
return numr - dnom;
}
double Tree::lnExpCalibPriorRatio(double nh, double oh, double offSt, double expRate) {
double numr = 0.0;
double dnom = 0.0;
numr = ranPtr->lnExponentialPdf(expRate, nh - offSt);
dnom = ranPtr->lnExponentialPdf(expRate, oh - offSt);
return numr - dnom;
}
void Tree::flipAllCls(void) {
for (int n=0; n<numNodes; n++)
nodes[n].flipCl();
}
void Tree::flipAllTis(void) {
for (int n=0; n<numNodes; n++)
nodes[n].flipTi();
}
void Tree::upDateAllCls(void) {
for (int n=0; n<numNodes; n++)
nodes[n].setIsClDirty(true);
}
void Tree::upDateAllTis(void) {
for (int n=0; n<numNodes; n++)
nodes[n].setIsTiDirty(true);
}
void Tree::flipToRootClsTis(Node *p){
Node *q = p;
if(!q->getIsLeaf()){
q->getLft()->flipCl();
q->getRht()->flipCl();
q->getLft()->flipTi();
q->getRht()->flipTi();
}
while(q != NULL){
q->flipCl();
q->flipTi();
q = q->getAnc();
}
}
void Tree::updateToRootClsTis(Node *p){
Node *q = p;
if(!q->getIsLeaf()){
q->getLft()->setIsClDirty(true);
q->getRht()->setIsClDirty(true);
q->getLft()->setIsTiDirty(true);
q->getRht()->setIsTiDirty(true);
}
while(q != NULL){
q->setIsClDirty(true);
q->setIsTiDirty(true);
q = q->getAnc();
}
}
void Tree::flipToRootClsTis(int ndID){
Node *q = &nodes[ndID];
while(q != NULL){
q->flipCl();
q->flipTi();
q = q->getAnc();
}
}
void Tree::updateToRootClsTis(int ndID){
Node *q = &nodes[ndID];
while(q != NULL){
q->setIsClDirty(true);
q->setIsTiDirty(true);
q = q->getAnc();
}
}
string Tree::getTreeDescription(void){
stringstream ss;
writeTree(root, ss);
ss << ";";
string treDesc = ss.str();
return treDesc;
}
void Tree::writeTree(Node *p, stringstream &ss){
if (p != NULL){
if(p->getLft() == NULL){
ss << p->getName();
}
else{
ss << "(";
writeTree(p->getLft(), ss);
ss << ":" << p->getLft()->getBranchTime();
ss << ",";
writeTree(p->getRht(), ss);
ss << ":" << p->getRht()->getBranchTime();
ss << ")";