double right_prob_BC(const char markerL, const int j, const MQMMarkerVector imarker, const vector rs, const cvector position){
R_CheckUserInterrupt(); /* check for ^C */
if(position[j] == MRIGHT||position[j] == MUNLINKED){
return 1.0;
}
if (markerL == MBB) {
return 0.0; //info("Strange: encountered BB genotype in BC");
}
const char markerR = imarker[j+1]; //Next marker at the right side
const double r = rs[j]; //Recombination freq beween markerL and markerR
double prob0 = 0.0; //Internal variable holding the probability AA if the next rightmarker is (Semi) Unknown
double prob1 = 0.0; //Internal variable holding the probability H if the next rightmarker is (Semi) Unknown
const double rr = 1.0-r; //Breeding Logic (see prob_new)
const int recombinations = abs(markerL-markerR); //Number of recombinations between markerL and markerR
if (is_knownMarker(markerR, CBC)) {
return ((recombinations==0)? rr : r );
} else {
if (markerL==MAA) {
prob0= rr;
prob1= r;
} else {
prob0= r;
prob1= rr;
}
return prob0*right_prob_BC(MAA, j+1, imarker, rs, position) + prob1*right_prob_BC(MH, j+1, imarker, rs, position);
}
}
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;
}
