/* ML estimation of parameters in mixture model via EM; maximum-likelihood
* estimation of parameters in the mixture model via the EM algorithm, using
* multilocus information, but assuming known recombination frequencies
*/
double QTLmixture(MQMMarkerMatrix loci, cvector cofactor, vector r, cvector position,
vector y, ivector ind, int Nind, int Naug,
int Nloci,
double *variance, int em, vector *weight, const bool useREML,const bool fitQTL,const bool dominance, MQMCrossType crosstype, int verbose) {
//debug_trace("QTLmixture called Nloci=%d Nind=%d Naug=%d, REML=%d em=%d fit=%d domi=%d cross=%c\n",Nloci,Nind,Naug,useREML,em,fitQTL,dominance,crosstype);
//for (int i=0; i<Nloci; i++){ debug_trace("loci %d : recombfreq=%f\n",i,r[i]); }
int iem= 0, i, j;
bool warnZeroDist=false;
bool biasadj=false;
double oldlogL=-10000, delta=1.0, calc_i, Pscale=1.75;
vector indweight = newvector(Nind);
int newNaug = ((!fitQTL) ? Naug : 3*Naug);
vector Fy = newvector(newNaug);
double logP = Nloci*log(Pscale); // only for computational accuracy
bool varknown = (((*variance)==-1.0) ? false : true );
vector Ploci = newvector(newNaug);
#ifndef STANDALONE
R_CheckUserInterrupt(); /* check for ^C */
R_FlushConsole();
#endif
if (!useREML) {
varknown=false;
biasadj=false;
}
for (i=0; i<newNaug; i++) { Ploci[i]= 1.0; }
if (!fitQTL) {
for (j=0; j<Nloci; j++) {
for (i=0; i<Naug; i++)
Ploci[i]*= Pscale;
if ((position[j]==MLEFT)||(position[j]==MUNLINKED)) {
for (i=0; i<Naug; i++) {
calc_i = start_prob(crosstype, loci[j][i]); // calc_i= prob(loci, r, i, j, MH, crosstype, 0, 1);
Ploci[i]*= calc_i;
//Als Ploci > 0 en calc_i > 0 then we want to assert Ploci[] != 0
}
}
if ((position[j]==MLEFT)||(position[j]==MMIDDLE)) {
for (i=0; i<Naug; i++) {
calc_i =left_prob(r[j],loci[j][i],loci[j+1][i],crosstype); //calc_i = prob(loci, r, i, j, loci[j+1][i], crosstype, 0);
if(calc_i == 0.0){calc_i=1.0;warnZeroDist=true;}
Ploci[i]*= calc_i;
}
}
}
} else {
for (j=0; j<Nloci; j++) {
for (i=0; i<Naug; i++) {
Ploci[i]*= Pscale; // only for computational accuracy; see use of logP
Ploci[i+Naug]*= Pscale; // only for computational accuracy; see use of logP
Ploci[i+2*Naug]*= Pscale; // only for computational accuracy; see use of logP
}
if ((position[j]==MLEFT)||(position[j]==MUNLINKED)) {
if (cofactor[j]<=MCOF){
for (i=0; i<Naug; i++) {
calc_i = start_prob(crosstype, loci[j][i]); // calc_i= prob(loci, r, i, j, MH, crosstype, 0, 1);
Ploci[i] *= calc_i;
Ploci[i+Naug] *= calc_i;
Ploci[i+2*Naug] *= calc_i;
}
}else{
for (i=0; i<Naug; i++) {
Ploci[i]*= start_prob(crosstype, MAA); //startvalue for MAA for new chromosome
Ploci[i+Naug]*= start_prob(crosstype, MH); //startvalue for MH for new chromosome
Ploci[i+2*Naug] *= start_prob(crosstype, MBB); //startvalue for MBB for new chromosome
}
}
}
if ((position[j]==MLEFT)||(position[j]==MMIDDLE)) {
if ((cofactor[j]<=MCOF)&&(cofactor[j+1]<=MCOF))
for (i=0; i<Naug; i++) {
calc_i =left_prob(r[j],loci[j][i],loci[j+1][i],crosstype); //calc_i = prob(loci, r, i, j, loci[j+1][i], crosstype, 0);
if(calc_i == 0.0){calc_i=1.0;warnZeroDist=true;}
Ploci[i]*= calc_i;
Ploci[i+Naug]*= calc_i;
Ploci[i+2*Naug]*= calc_i;
}
else if (cofactor[j]<=MCOF) // locus j+1 == QTL
for (i=0; i<Naug; i++) { // QTL==MAA || MH || MBB means: What is the prob of finding an MAA at J=1
calc_i =left_prob(r[j],loci[j][i],MAA,crosstype); //calc_i = prob(loci, r, i, j, MAA, crosstype, 0);
Ploci[i]*= calc_i;
calc_i = left_prob(r[j],loci[j][i],MH,crosstype); //calc_i = prob(loci, r, i, j, MH, crosstype, 0);
Ploci[i+Naug]*= calc_i;
calc_i = left_prob(r[j],loci[j][i],MBB,crosstype); //calc_i = prob(loci, r, i, j, MBB, crosstype, 0);
Ploci[i+2*Naug]*= calc_i;
}
else // locus j == QTL
for (i=0; i<Naug; i++) { // QTL==MQTL
calc_i = left_prob(r[j],MAA,loci[j+1][i],crosstype); //calc_i = prob(loci, r, i, j+1, MAA, crosstype, -1);
Ploci[i]*= calc_i;
calc_i = left_prob(r[j],MH,loci[j+1][i],crosstype); //calc_i = prob(loci, r, i, j+1, MH, crosstype, -1);
Ploci[i+Naug]*= calc_i;
calc_i = left_prob(r[j],MBB,loci[j+1][i],crosstype); //calc_i = prob(loci, r, i, j+1, MBB, crosstype, -1);
Ploci[i+2*Naug]*= calc_i;
}
}
}
}
if(warnZeroDist)info("!!! 0.0 from Prob !!! Markers at same Cm but different genotype !!!");
// Rprintf("INFO: Done fitting QTL's\n");
if ((*weight)[0]== -1.0) {
for (i=0; i<Nind; i++) indweight[i]= 0.0;
if (!fitQTL) {
for (i=0; i<Naug; i++) indweight[ind[i]]+=Ploci[i];
for (i=0; i<Naug; i++) (*weight)[i]= Ploci[i]/indweight[ind[i]];
} else {
for (i=0; i<Naug; i++) indweight[ind[i]]+=Ploci[i]+Ploci[i+Naug]+Ploci[i+2*Naug];
for (i=0; i<Naug; i++) {
(*weight)[i] = Ploci[i]/indweight[ind[i]];
(*weight)[i+Naug] = Ploci[i+Naug]/indweight[ind[i]];
(*weight)[i+2*Naug]= Ploci[i+2*Naug]/indweight[ind[i]];
}
}
}
debug_trace("Weights done\n");
debug_trace("Individual->trait,indweight weight Ploci\n");
//for (int j=0; j<Nind; j++){
// debug_trace("%d->%f,%f %f %f\n", j, y[j],indweight[i], (*weight)[j], Ploci[j]);
//}
double logL = 0;
vector indL = newvector(Nind);
while ((iem<em)&&(delta>1.0e-5)) {
iem+=1;
if (!varknown) *variance=-1.0;
logL = regression(Nind, Nloci, cofactor, loci, y, weight, ind, Naug, variance, Fy, biasadj, fitQTL, dominance);
logL = 0.0;
for (i=0; i<Nind; i++) indL[i]= 0.0;
if (!fitQTL) // no QTL fitted
for (i=0; i<Naug; i++) {
(*weight)[i]= Ploci[i]*Fy[i];
indL[ind[i]]= indL[ind[i]] + (*weight)[i];
}
else // QTL moved along the chromosomes
for (i=0; i<Naug; i++) {
(*weight)[i]= Ploci[i]*Fy[i];
(*weight)[i+Naug] = Ploci[i+Naug]* Fy[i+Naug];
(*weight)[i+2*Naug]= Ploci[i+2*Naug]*Fy[i+2*Naug];
indL[ind[i]]+=(*weight)[i]+(*weight)[i+Naug]+(*weight)[i+2*Naug];
}
for (i=0; i<Nind; i++) logL+=log(indL[i])-logP;
for (i=0; i<Nind; i++) indweight[i]= 0.0;
if (!fitQTL) {
for (i=0; i<Naug; i++) indweight[ind[i]]+=(*weight)[i];
for (i=0; i<Naug; i++) (*weight)[i]/=indweight[ind[i]];
} else {
for (i=0; i<Naug; i++)
indweight[ind[i]]+=(*weight)[i]+(*weight)[i+Naug]+(*weight)[i+2*Naug];
for (i=0; i<Naug; i++) {
(*weight)[i] /=indweight[ind[i]];
(*weight)[i+Naug] /=indweight[ind[i]];
(*weight)[i+2*Naug]/=indweight[ind[i]];
}
}
delta= fabs(logL-oldlogL);
oldlogL= logL;
}
if ((useREML)&&(!varknown)) { // Bias adjustment after finished ML estimation via EM
*variance=-1.0;
biasadj=true;
logL = regression(Nind, Nloci, cofactor, loci, y, weight, ind, Naug, variance, Fy, biasadj, fitQTL, dominance);
logL = 0.0;
for (int _i=0; _i<Nind; _i++) indL[_i]= 0.0;
if (!fitQTL)
for (i=0; i<Naug; i++) {
(*weight)[i]= Ploci[i]*Fy[i];
indL[ind[i]]+=(*weight)[i];
}
else
for (i=0; i<Naug; i++) {
(*weight)[i]= Ploci[i]*Fy[i];
(*weight)[i+Naug]= Ploci[i+Naug]*Fy[i+Naug];
(*weight)[i+2*Naug]= Ploci[i+2*Naug]*Fy[i+2*Naug];
indL[ind[i]]+=(*weight)[i];
indL[ind[i]]+=(*weight)[i+Naug];
indL[ind[i]]+=(*weight)[i+2*Naug];
}
for (i=0; i<Nind; i++) logL+=log(indL[i])-logP;
for (i=0; i<Nind; i++) indweight[i]= 0.0;
if (!fitQTL) {
for (i=0; i<Naug; i++) indweight[ind[i]]+=(*weight)[i];
for (i=0; i<Naug; i++) (*weight)[i]/=indweight[ind[i]];
} else {
for (i=0; i<Naug; i++) {
indweight[ind[i]]+=(*weight)[i];
indweight[ind[i]]+=(*weight)[i+Naug];
indweight[ind[i]]+=(*weight)[i+2*Naug];
}
for (i=0; i<Naug; i++) {
(*weight)[i] /=indweight[ind[i]];
(*weight)[i+Naug] /=indweight[ind[i]];
(*weight)[i+2*Naug]/=indweight[ind[i]];
}
}
}
//for (i=0; i<Nind; i++){ debug_trace("IND %d Ploci: %f Fy: %f UNLOG:%f LogL:%f LogL-LogP: %f\n", i, Ploci[i], Fy[i], indL[i], log(indL[i]), log(indL[i])-logP); }
Free(Fy);
Free(Ploci);
Free(indweight);
Free(indL);
return logL;
}
/*
* ML estimation of recombination frequencies via EM; calculation of multilocus
* genotype probabilities; ignorance of unlikely genotypes. Called by the
* mqmscan. maximum-likelihood estimation of recombination frequencies via the
* EM algorithm, using multilocus information (default: the recombination
* frequencies are not estimated but taken from mqm.in)
*
* When reestimate is 'n' the method is skipped
*/
double rmixture(MQMMarkerMatrix marker, vector weight, vector r,
cvector position, ivector ind, int Nind, int Naug, int Nmark,
vector *mapdistance, char reestimate, MQMCrossType crosstype,
int verbose) {
int i, j;
int iem= 0;
double Nrecom, oldr=0.0, newr, rdelta=1.0;
double maximum = 0.0;
float last_step = 0.0;
vector indweight;
indweight = newvector(Nind);
vector distance;
distance = newvector(Nmark+1);
if (reestimate=='n') {
if (verbose==1) {
Rprintf("INFO: recombination parameters are not re-estimated\n");
}
for (j=0; j<Nmark; j++) {
if (maximum < (*mapdistance)[j]) {
maximum = (*mapdistance)[j];
}
}
} else {
if (verbose==1) {
Rprintf("INFO: recombination parameters are re-estimated\n");
}
//Reestimation of map now works
while ((iem<1000)&&(rdelta>0.0001)) {
iem+=1;
rdelta= 0.0;
/* calculate weights = conditional genotype probabilities */
for (i=0; i<Naug; i++) weight[i]=1.0;
for (j=0; j<Nmark; j++) {
if ((position[j]==MLEFT)||(position[j]==MUNLINKED))
for (i=0; i<Naug; i++)
if (marker[j][i]==MH) weight[i]*= 0.5;
else weight[i]*= 0.25;
if ((position[j]==MLEFT)||(position[j]==MMIDDLE))
for (i=0; i<Naug; i++) {
double calc_i = left_prob(r[j],marker[j][i],marker[j+1][i],crosstype); //double calc_i = prob(marker, r, i, j, marker[j+1][i], crosstype, 0);
weight[i]*=calc_i;
}
}
for (i=0; i<Nind; i++) {
indweight[i]= 0.0;
}
for (i=0; i<Naug; i++) {
indweight[ind[i]]+=weight[i];
}
for (i=0; i<Naug; i++) {
weight[i]/=indweight[ind[i]];
}
for (j=0; j<Nmark; j++) {
if ((position[j]==MLEFT)||(position[j]==MMIDDLE)) {
newr= 0.0;
for (i=0; i<Naug; i++) {
Nrecom= fabs((double)(marker[j][i]-marker[j+1][i]));
if ((marker[j][i]==MH)&&(marker[j+1][i]==MH))
Nrecom= 2.0*r[j]*r[j]/(r[j]*r[j]+(1-r[j])*(1-r[j]));
newr+= Nrecom*weight[i];
}
if (reestimate=='y' && position[j]!=MRIGHT) { //only update if it isn't the last marker of a chromosome ;)
oldr=r[j];
r[j]= newr/(2.0*Nind);
rdelta+=pow(r[j]-oldr, 2.0);
} else rdelta+=0.0;
}
}
}
/* print new estimates of recombination frequencies */
//Rprintf("INFO: Reestimate? %c\n", reestimate);
//Rprintf("INFO: looping over all markers %d\n", Nmark);
for (j=0; j<Nmark; j++) {
if (position[j+1]==MRIGHT) {
last_step = (*mapdistance)[j+1]-(*mapdistance)[j];
}
if (position[j]!=MLEFT) {
if (position[j]!=MRIGHT) {
(*mapdistance)[j]= -50*log(1-2.0*r[j])+(*mapdistance)[j-1];
} else {
(*mapdistance)[j]= (*mapdistance)[j-1]+last_step;
}
} else {
(*mapdistance)[j]= -50*log(1-2.0*r[j]);
}
if (maximum < (*mapdistance)[j]) {
maximum = (*mapdistance)[j];
}
//Rprintf("r(%d)= %f -> %f\n", j, r[j], (*mapdistance)[j]);
}
}
if (verbose==1) {
Rprintf("INFO: Re-estimation of the genetic map took %d iterations, to reach a rdelta of %f\n", iem, rdelta);
}
Free(indweight);
freevector(distance);
return maximum;
}
int mqmaugment(const MQMMarkerMatrix marker, const vector y,
MQMMarkerMatrix* augmarker, vector *augy,
ivector* augind, ivector* sucind, int *Nind, int *Naug, const int Nmark,
const cvector position, vector r, const int maxNaug,
const int imaxNaug, const double minprob,
const MQMCrossType crosstype, const int verbose)
{
int retvalue = 1; //[Danny] Assume everything will go right, (it never returned a 1 OK, initialization to 0 and return
int jj;
const int nind0 = *Nind; //Original number of individuals
(*Naug) = maxNaug; // sets and returns the maximum size of augmented dataset
// new variables sized to maxNaug:
MQMMarkerMatrix newmarker;
vector newy;
MQMMarkerVector imarker;
ivector newind;
ivector succesind;
double minprobratio = (1.0f/minprob);
if(minprob!=1){
minprobratio += 0.00001;
}
newmarker = newMQMMarkerMatrix(Nmark+1, maxNaug); // augmented marker matrix
newy = newvector(maxNaug); // phenotypes
newind = newivector(maxNaug); // individuals index
succesind = newivector(nind0); // Tracks if the augmentation is a succes
imarker = newMQMMarkerVector(Nmark);
int iaug = 0; // iaug keeps track of current augmented individual
double prob0, prob1, prob2, sumprob,
prob0left, prob1left, prob2left,
prob0right=0.0, prob1right=0.0, prob2right = 0.0f;
vector newprob = newvector(maxNaug);
vector newprobmax = newvector(maxNaug);
if (verbose) Rprintf("INFO: Crosstype determined by the algorithm: %c\n", crosstype);
if (verbose) Rprintf("INFO: Augmentation parameters: Maximum augmentation=%d, Maximum augmentation per individual=%d, Minprob=%f\n", maxNaug, imaxNaug, minprob);
// ---- foreach individual create one in the newmarker matrix
int newNind = nind0; //Number of unique individuals
int previaug = 0; // previous index in newmarkers
for (int i=0; i<nind0; i++) {
//Loop through individuals
succesind[i] = 1; //Assume we succeed in augmentation
#ifndef STANDALONE
//R_ProcessEvents(); /* Try not to crash windows */
R_FlushConsole();
#endif
const int dropped = nind0-newNind; //How many are dropped
const int iidx = i - dropped; //Individuals I's new individual number based on dropped individuals
newind[iaug] = iidx; // iidx corrects for dropped individuals
newy[iaug] = y[i]; // cvariance (phenotype)
newprob[iaug] = 1.0; //prop
double probmax = 1.0; //current maximum probability
for (int j=0; j<Nmark; j++){
newmarker[j][iaug]=marker[j][i]; // copy markers into newmarkers for the new indidivudal under investigation
}
for (int j=0; j<Nmark; j++) {
//Loop through markers:
const int maxiaug = iaug; // fixate maxiaug
if ((maxiaug-previaug)<=imaxNaug) // within bounds for individual?
for (int ii=previaug; ii<=maxiaug; ii++) {
#ifndef STANDALONE
R_CheckUserInterrupt(); /* check for ^C */
#endif
debug_trace("i=%d ii=%d iidx=%d maxiaug=%d previaug=%d,imaxNaug=%d\n",i,ii,iidx,maxiaug,previaug,imaxNaug);
// ---- walk from previous augmented to current augmented genotype
//WE HAVE 3 SPECIAL CASES: (1) NOTAA, (2) NOTBB and (3)UNKNOWN, and the std case of a next known marker
if (newmarker[j][ii]==MNOTAA) {
//NOTAA augment data to contain AB and BB
for (jj=0; jj<Nmark; jj++) imarker[jj] = newmarker[jj][ii];
if ((position[j]==MLEFT||position[j]==MUNLINKED)) {
prob1left= start_prob(crosstype, MH);
prob2left= start_prob(crosstype, MBB);
} else {
prob1left= left_prob(r[j-1],newmarker[j-1][ii],MH,crosstype); //prob1left= prob(newmarker, r, ii, j-1, MH, crosstype, 0);
prob2left= left_prob(r[j-1],newmarker[j-1][ii],MBB,crosstype); //prob2left= prob(newmarker, r, ii, j-1, MBB, crosstype, 0);
}
switch (crosstype) {
case CF2:
prob1right= right_prob_F2(MH, j, imarker, r, position); //prob1right= probright(MH, j, imarker, r, position, crosstype);
prob2right= right_prob_F2(MBB, j, imarker, r, position); //prob2right= probright(MBB, j, imarker, r, position, crosstype);
break;
case CBC:
prob1right= right_prob_BC(MH, j, imarker, r, position);
prob2right= right_prob_BC(MBB, j, imarker, r, position);
break;
case CRIL:
prob1right= right_prob_RIL(MH, j, imarker, r, position);
prob2right= right_prob_RIL(MBB, j, imarker, r, position);
break;
case CUNKNOWN:
fatal("Strange: unknown crosstype in mqm augment()", "");
break;
}
prob1= prob1left*prob1right;
prob2= prob2left*prob2right;
if (ii==previaug) probmax = (prob2>prob1 ? newprob[ii]*prob2 : newprob[ii]*prob1);
if (prob1>prob2) {
if (probmax/(newprob[ii]*prob2)<minprobratio) {
if (++iaug >= maxNaug) goto bailout;
newmarker[j][iaug]= MBB;
newprob[iaug]= newprob[ii]*prob2left;
newprobmax[iaug]= newprob[iaug]*prob2right;
for (jj=0; jj<Nmark; jj++) {
if (jj!=j) newmarker[jj][iaug]=newmarker[jj][ii];
}
newind[iaug]=iidx;
newy[iaug]=y[i];
}
newmarker[j][ii]= MH;
newprobmax[ii]= newprob[ii]*prob1;
newprob[ii]= newprob[ii]*prob1left;
} else {
if (probmax/(newprob[ii]*prob1)<minprobratio) {
if (++iaug >= maxNaug) goto bailout;
newmarker[j][iaug]= MH;
newprob[iaug]= newprob[ii]*prob1left;
newprobmax[iaug]= newprob[iaug]*prob1right;
for (jj=0; jj<Nmark; jj++) {
if (jj!=j) newmarker[jj][iaug]=newmarker[jj][ii];
}
newind[iaug]=iidx;
newy[iaug]=y[i];
}
newmarker[j][ii]= MBB;
newprobmax[ii]= newprob[ii]*prob2;
newprob[ii]*= prob2left;
}
probmax = (probmax>newprobmax[ii] ? probmax : newprobmax[ii]);
} else if (newmarker[j][ii]==MNOTBB) {
//NOTBB: augment data can contain MH and MAA
for (jj=0; jj<Nmark; jj++) imarker[jj]= newmarker[jj][ii];
if ((position[j]==MLEFT||position[j]==MUNLINKED)) {
prob0left= start_prob(crosstype, MAA);
prob1left= start_prob(crosstype, MH);
} else {
prob0left= left_prob(r[j-1],newmarker[j-1][ii],MAA,crosstype); //prob0left= prob(newmarker, r, ii, j-1, MAA, crosstype, 0);
prob1left= left_prob(r[j-1],newmarker[j-1][ii],MH,crosstype); //prob1left= prob(newmarker, r, ii, j-1, MH, crosstype, 0);
}
switch (crosstype) {
case CF2:
prob0right= right_prob_F2(MAA, j, imarker, r, position); //prob0right= probright(MAA, j, imarker, r, position, crosstype);
prob1right= right_prob_F2(MH, j, imarker, r, position); //prob1right= probright(MH, j, imarker, r, position, crosstype);
break;
case CBC:
prob0right= right_prob_BC(MAA, j, imarker, r, position);
prob1right= right_prob_BC(MH, j, imarker, r, position);
break;
case CRIL:
prob0right= right_prob_RIL(MAA, j, imarker, r, position);
prob1right= right_prob_RIL(MH, j, imarker, r, position);
break;
case CUNKNOWN:
fatal("Strange: unknown crosstype in mqm augment()", "");
break;
}
prob0= prob0left*prob0right;
prob1= prob1left*prob1right;
if (ii==previaug) probmax= (prob0>prob1 ? newprob[ii]*prob0 : newprob[ii]*prob1);
if (prob1>prob0) {
if (probmax/(newprob[ii]*prob0)<minprobratio) {
if (++iaug >= maxNaug) goto bailout;
newmarker[j][iaug]= MAA;
newprob[iaug]= newprob[ii]*prob0left;
newprobmax[iaug]= newprob[iaug]*prob0right;
for (jj=0; jj<Nmark; jj++) {
if (jj!=j) newmarker[jj][iaug]=newmarker[jj][ii];
}
newind[iaug]=iidx;
newy[iaug]=y[i];
}
newmarker[j][ii]= MH;
newprobmax[ii]= newprob[ii]*prob1;
newprob[ii]*= prob1left;
} else {
if (probmax/(newprob[ii]*prob1)<minprobratio) {
if (++iaug >= maxNaug) goto bailout;
newmarker[j][iaug]= MH;
newprob[iaug]= newprob[ii]*prob1left;
newprobmax[iaug]= newprob[iaug]*prob1right;
for (jj=0; jj<Nmark; jj++) {
if (jj!=j) newmarker[jj][iaug]=newmarker[jj][ii];
}
newind[iaug]=iidx;
newy[iaug]=y[i];
}
newmarker[j][ii]= MAA;
newprobmax[ii]= newprob[ii]*prob0;
newprob[ii]*= prob0left;
}
probmax= (probmax>newprobmax[ii] ? probmax : newprobmax[ii]);
} else if (newmarker[j][ii]==MMISSING) {
//UNKNOWN: augment data to contain AB, AA and BB
for (jj=0; jj<Nmark; jj++) imarker[jj]= newmarker[jj][ii];
if ((position[j]==MLEFT||position[j]==MUNLINKED)) {
prob0left= start_prob(crosstype, MAA);
prob1left= start_prob(crosstype, MH);
prob2left= start_prob(crosstype, MBB);
} else {
prob0left= left_prob(r[j-1],newmarker[j-1][ii],MAA,crosstype); //prob0left= prob(newmarker, r, ii, j-1, MAA, crosstype, 0);
prob1left= left_prob(r[j-1],newmarker[j-1][ii],MH,crosstype); //prob1left= prob(newmarker, r, ii, j-1, MH, crosstype, 0);
prob2left= left_prob(r[j-1],newmarker[j-1][ii],MBB,crosstype); //prob2left= prob(newmarker, r, ii, j-1, MBB, crosstype, 0);
}
switch (crosstype) {
case CF2:
prob0right= right_prob_F2(MAA, j, imarker, r, position); //prob0right= probright(MAA, j, imarker, r, position, crosstype);
prob1right= right_prob_F2(MH, j, imarker, r, position); //prob1right= probright(MH, j, imarker, r, position, crosstype);
prob2right= right_prob_F2(MBB, j, imarker, r, position); //prob2right= probright(MBB, j, imarker, r, position, crosstype);
break;
case CBC:
prob0right= right_prob_BC(MAA, j, imarker, r, position);
prob1right= right_prob_BC(MH, j, imarker, r, position);
prob2right= 0.0;
break;
case CRIL:
prob0right= right_prob_RIL(MAA, j, imarker, r, position);
prob1right= 0.0;
prob2right= right_prob_RIL(MBB, j, imarker, r, position);
break;
case CUNKNOWN:
fatal("Strange: unknown crosstype in mqm augment()", "");
break;
}
prob0= prob0left*prob0right;
prob1= prob1left*prob1right;
prob2= prob2left*prob2right;
if (ii==previaug) {
if ((prob2>prob1)&&(prob2>prob0)) probmax= newprob[ii]*prob2;
else if ((prob1>prob0)&&(prob1>prob2)) probmax= newprob[ii]*prob1;
else probmax= newprob[ii]*prob0;
}
if ((prob2>prob1)&&(prob2>prob0)) {
if (probmax/(newprob[ii]*prob1)<minprobratio) {
if (++iaug >= maxNaug) goto bailout;
newmarker[j][iaug]= MH;
newprob[iaug]= newprob[ii]*prob1left;
newprobmax[iaug]= newprob[iaug]*prob1right;
for (jj=0; jj<Nmark; jj++) {
if (jj!=j) newmarker[jj][iaug]=newmarker[jj][ii];
}
newind[iaug]=iidx;
newy[iaug]=y[i];
}
if (probmax/(newprob[ii]*prob0)<minprobratio) {
if (++iaug >= maxNaug) goto bailout;
newmarker[j][iaug]= MAA;
newprob[iaug]= newprob[ii]*prob0left;
newprobmax[iaug]= newprob[iaug]*prob0right;
for (jj=0; jj<Nmark; jj++) {
if (jj!=j) newmarker[jj][iaug]=newmarker[jj][ii];
}
newind[iaug]=iidx;
newy[iaug]=y[i];
}
newmarker[j][ii]= MBB;
newprobmax[ii]= newprob[ii]*prob2;
newprob[ii]*= prob2left;
} else if ((prob1>prob2)&&(prob1>prob0)) {
if (probmax/(newprob[ii]*prob2)<minprobratio) {
if (++iaug >= maxNaug) goto bailout;
newmarker[j][iaug]= MBB;
newprob[iaug]= newprob[ii]*prob2left;
newprobmax[iaug]= newprob[iaug]*prob2right;
for (jj=0; jj<Nmark; jj++) {
if (jj!=j) newmarker[jj][iaug]=newmarker[jj][ii];
}
newind[iaug]=iidx;
newy[iaug]=y[i];
}
if (probmax/(newprob[ii]*prob0)<minprobratio) {
if (++iaug >= maxNaug) goto bailout;
newmarker[j][iaug]= MAA;
newprob[iaug]= newprob[ii]*prob0left;
newprobmax[iaug]= newprob[iaug]*prob0right;
for (jj=0; jj<Nmark; jj++) {
if (jj!=j) newmarker[jj][iaug]=newmarker[jj][ii];
}
newind[iaug]=iidx;
newy[iaug]=y[i];
}
newmarker[j][ii]= MH;
newprobmax[ii]= newprob[ii]*prob1;
newprob[ii]*= prob1left;
} else {
if (probmax/(newprob[ii]*prob1)<minprobratio) {
if (++iaug >= maxNaug) goto bailout;
newmarker[j][iaug]= MH;
newprob[iaug]= newprob[ii]*prob1left;
newprobmax[iaug]= newprob[iaug]*prob1right;
for (jj=0; jj<Nmark; jj++) {
if (jj!=j) newmarker[jj][iaug]=newmarker[jj][ii];
}
newind[iaug]=iidx;
newy[iaug]=y[i];
}
if (probmax/(newprob[ii]*prob2)<minprobratio) {
if (++iaug >= maxNaug) goto bailout;
newmarker[j][iaug]= MBB;
newprob[iaug]= newprob[ii]*prob2left;
newprobmax[iaug]= newprob[iaug]*prob2right;
for (jj=0; jj<Nmark; jj++) {
if (jj!=j) newmarker[jj][iaug]=newmarker[jj][ii];
}
newind[iaug]=iidx;
newy[iaug]=y[i];
}
newmarker[j][ii]= MAA;
newprobmax[ii]= newprob[ii]*prob0;
newprob[ii]*= prob0left;
}
probmax= (probmax>newprobmax[ii] ? probmax : newprobmax[ii]);
} else {
//STD case we know what the next marker is nou use probleft to estimate the likelihood of the current location
if ((position[j]==MLEFT||position[j]==MUNLINKED)) {
prob0left= start_prob(crosstype, newmarker[j][ii]);
} else {
prob0left= left_prob(r[j-1],newmarker[j-1][ii],newmarker[j][ii],crosstype); //prob0left= prob(newmarker, r, ii, j-1, newmarker[j][ii], crosstype, 0);
}
newprob[ii]*= prob0left;
}
if (iaug+3>maxNaug) {
Rprintf("ERROR: augmentation (this code should not be reached)\n");
goto bailout;
}
}
if ((iaug-previaug+1)>imaxNaug) {
newNind-= 1;
iaug= previaug-1;
succesind[i]=0;
//for(int x=previaug;x<previaug+imaxNaug;x++){
// Rprintf("INFO: Individual: %d, variant: %d, prob: %f",i,x,newprob[x]);
//}
if (verbose) Rprintf("INFO: Individual %d moved to second augmentation round\n", i);
}
sumprob= 0.0;
for (int ii=previaug; ii<=iaug; ii++) sumprob+= newprob[ii];
for (int ii=previaug; ii<=iaug; ii++) newprob[ii]/= sumprob;
}
if (++iaug >= maxNaug) goto bailout;
previaug=iaug;
}
*Naug = iaug;
*Nind = newNind;
*augmarker = newMQMMarkerMatrix(Nmark, *Naug);
*augy = newvector(*Naug);
*augind = newivector(*Naug);
*sucind = newivector(nind0);
for (int i=0; i<nind0; i++) {
(*sucind)[i] = succesind[i];
}
for (int i=0; i<(*Naug); i++) {
(*augy)[i]= newy[i];
(*augind)[i]= newind[i];
for (int j=0; j<Nmark; j++) (*augmarker)[j][i]= newmarker[j][i];
}
goto cleanup;
bailout:
Rprintf("INFO: Dataset too large after augmentation\n");
if (verbose) fatal("Recall procedure with larger value for augmentation parameters or increase the parameter minprob\n");
retvalue = 0;
cleanup:
Free(newy);
delMQMMarkerMatrix(newmarker, Nmark+1); //Free(newmarker);
Free(newind);
Free(newprob);
Free(newprobmax);
Free(imarker);
return retvalue;
}
