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#include "computePosteriorExpectationOfSubstitutions.h"
#include "definitions.h"
#include "computeDownAlg.h"
#include "computeUpAlg.h"
#include "matrixUtils.h"
#include "treeIt.h"
#include "likelihoodComputation.h"
using namespace std;
/********************************************************************************************
computePosteriorExpectationOfSubstitutions
*********************************************************************************************/
computePosteriorExpectationOfSubstitutions::computePosteriorExpectationOfSubstitutions(const tree &tr, const sequenceContainer &sc, const stochasticProcess *sp):
_tr(tr), _sc(sc){
if(!sp){
errorMsg::reportError("error in the constructor computePosteriorExpectationOfSubstitutions sp argument is NULL");
}
else{
_sp = sp;
}
}
/********************************************************************************************
Expectation of number of substitutions from character u to v --- =
sum over all substitutions x,y:
Posterior(Node=x,Father=y|D)*Exp(substitutions u to v|Node=x,Father=y)
The second term is given to the function as input (can be obtained via simulations)
*********************************************************************************************/
VVdouble computePosteriorExpectationOfSubstitutions::computeExpectationAcrossTree(
simulateJumpsAbstract &sim, //input given from simulation studies
const VVVdouble &posteriorProbs,
VVVdouble &expForBranch)
{
//int numNodes = _tr.getNodesNum();
int alphabetSize = _sp->alphabetSize();
VVdouble res;
resizeMatrix(res,alphabetSize,alphabetSize);
treeIterTopDownConst tIt(_tr);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
for (int fromState=0;fromState<alphabetSize;++fromState)
{
for (int toState=0;toState<alphabetSize;++toState)
{
if (fromState==toState)
continue;
expForBranch[mynode->id()][fromState][toState] = computeExpectationOfChangePerBranch(sim,posteriorProbs,mynode,fromState,toState);
res[fromState][toState] +=expForBranch[mynode->id()][fromState][toState];
}
}
}
return res;
}
/********************************************************************************************
Posterior probabilities computed across entire tree, for all substitutions from character u to v
*********************************************************************************************/
VVdouble computePosteriorExpectationOfSubstitutions::computePosteriorAcrossTree(
simulateJumpsAbstract &sim, //input given from simulation studies
const VVVdouble &posteriorProbsGivenTerminals,VVVdouble &probsForBranch)
{
//int numNodes = _tr.getNodesNum();
int alphabetSize = _sp->alphabetSize();
// N: resized before
//probsForBranch.resize(numNodes);
//for (int n=0;n<numNodes;++n)
// resizeMatrix(probsForBranch[n],alphabetSize,alphabetSize);
VVdouble res;
resizeMatrix(res,alphabetSize,alphabetSize);
treeIterTopDownConst tIt(_tr);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
for (int fromState=0;fromState<alphabetSize;++fromState)
{
for (int toState=0;toState<alphabetSize;++toState)
{
if (fromState==toState)
continue;
probsForBranch[mynode->id()][fromState][toState]= computePosteriorOfChangePerBranch(sim,posteriorProbsGivenTerminals,mynode,fromState,toState);
res[fromState][toState] +=probsForBranch[mynode->id()][fromState][toState];
}
}
}
return res;
}
/********************************************************************************************
*********************************************************************************************/
MDOUBLE computePosteriorExpectationOfSubstitutions::computePosteriorOfChangePerBranch(simulateJumpsAbstract &sim, //input given from simulation studies
const VVVdouble &posteriorProbs,
tree::nodeP node,
int fromState, int toState)
{
int alphabetSize = _sp->alphabetSize();
MDOUBLE res = 0;
for (int x=0;x<alphabetSize;++x)
{
for (int y=0;y<alphabetSize;++y)
{
res+=sim.getProb(node->name(),x,y,fromState,toState)*posteriorProbs[node->id()][x][y];
}
}
return res;
}
/********************************************************************************************
Posterior of observing a certain state substitution along a branch:
P(Node=x,Father=y|D) = P(D,Node=x,Father=y)/P(D)
usage: posteriorPerNodePer2States[mynode->id()][fatherState][sonState]
*********************************************************************************************/
void computePosteriorExpectationOfSubstitutions::computePosteriorOfChangeGivenTerminals(VVVdouble &posteriorPerNodePer2States, int pos){
int numNodes = _tr.getNodesNum();
int alphabetSize = _sp->alphabetSize();
posteriorPerNodePer2States.resize(numNodes);
for (int n=0;n<posteriorPerNodePer2States.size();++n)
resizeMatrix(posteriorPerNodePer2States[n],alphabetSize,alphabetSize);
suffStatGlobalHomPos sscUp;
suffStatGlobalHomPos sscDown; //for a reversible model
sscUp.allocatePlace(numNodes,alphabetSize);
computePijHom pi;
pi.fillPij(_tr,*_sp);
computeUpAlg comp_Up;
computeDownAlg comp_Down;
comp_Up.fillComputeUp(_tr,_sc,pos,pi,sscUp);
comp_Down.fillComputeDown(_tr,_sc,pos,pi,sscDown,sscUp);
treeIterTopDownConst tIt(_tr);
MDOUBLE ll = convert(likelihoodComputation::getLofPos(pos,_tr,_sc,pi,*_sp));
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
for (int sonState = 0; sonState<alphabetSize; ++sonState){
for (int fatherState = 0; fatherState<alphabetSize; ++fatherState){
posteriorPerNodePer2States[mynode->id()][fatherState][sonState]= computePosterioGivenTerminalsPerBranch(mynode->id(),sonState,fatherState,sscUp,sscDown, pi,ll,mynode->name());
}
}
}
}
/********************************************************************************************
Posterior of observing a certain state substitution along a branch:
P(Node=sonState,Father=fatherState|D) = P(D,Node=sonState,Father=fatherState)/P(D)
usage: posteriorPerNodePer2States[mynode->id()][fatherState][sonState]
*********************************************************************************************/
MDOUBLE computePosteriorExpectationOfSubstitutions::computePosterioGivenTerminalsPerBranch
(int nodeId,int sonState, int fatherState,suffStatGlobalHomPos &sscUp,
suffStatGlobalHomPos &sscDown,computePijHom &pi, MDOUBLE &LLData, const string nodeName)
{
MDOUBLE res, Down, Up, pij;
Down = convert(sscDown.get(nodeId,fatherState));
Up = convert(sscUp.get(nodeId,sonState));
pij = pi.getPij(nodeId,fatherState,sonState);
res=_sp->freq(fatherState)*Down*Up*pij;
res/=LLData;
// if(gainLossOptions::_printDEBUGinfo)
// LOG(3,<<nodeName<<" son "<<sonState<<" Down "<<Down<<" father "<<fatherState<<" Up "<<Up<<" pij "<<pij<<" resDXY "<<resDXY<<" LLData "<<LLData<<" prob "<<res<<endl);
if (res > 1 + 1e-4){
LOGnOUT(3,<<nodeId<<" son "<<sonState<<" Down "<<Down<<" father "<<fatherState<<" Up "<<Up<<" pij "<<pij<<" res "<<res<<" LLData "<<LLData<<endl);
res = 1;
}
if (res<-1e-4){
LOGnOUT(3,<<nodeId<<" son "<<sonState<<" Down "<<Down<<" father "<<fatherState<<" Up "<<Up<<" pij "<<pij<<" res "<<res<<" LLData "<<LLData<<endl);
res = 0;
}
if ((res > 1 + 0.000001) || (res<-0.000001)){
string err = "Error in computePosteriorExpectationOfSubstitutions::computePosterioGivenTerminalsPerBranch, non probability value ";
err+=double2string(res);
err+=" at node ";
err+=int2string(nodeId);
err+= " sonState ";
err+= int2string(sonState);
err+= " fatherState ";
err+= int2string(fatherState);
errorMsg::reportError(err);
}
return res;
}
/********************************************************************************************
*********************************************************************************************/
MDOUBLE computePosteriorExpectationOfSubstitutions::computeExpectationOfChangePerBranch(
simulateJumpsAbstract &sim, //input given from simulation studies
const VVVdouble &posteriorProbsGivenTerminals,
tree::nodeP node,int fromState, int toState)
{
int alphabetSize = _sp->alphabetSize();
MDOUBLE nodeExpectation = 0;
for (int x = 0; x<alphabetSize; ++x){
for (int y = 0; y<alphabetSize; ++y){
nodeExpectation+=(posteriorProbsGivenTerminals[node->id()][x][y]*
sim.getExpectation(node->name(),x,y,fromState,toState));
//DEBUG
LOG(6,<<"node "<<node->id()<<endl);
LOG(6,<<"from "<<fromState<<" to "<<toState<<" given "<<x<<" and "<<y
<<" post= "<<posteriorProbsGivenTerminals[node->id()][x][y]<<" sim= "<< sim.getExpectation(node->name(),x,y,fromState,toState)<<endl);
}
}
return nodeExpectation;
}
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