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/*
* sharedace.cpp
* Dotur
*
* Created by Sarah Westcott on 1/8/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "sharedace.h"
/***********************************************************************/
EstOutput SharedAce::getValues(vector<SharedRAbundVector*> shared) {
try {
data.resize(1,0);
string label;
label = shared[0]->getLabel();
double fARare, fBRare, S12Rare, S12Abund, S12, f11, tempA, tempB, t10, t01, t11, t21, t12, t22, C12Numerator;
fARare = 0; fBRare = 0; S12Rare = 0; S12Abund = 0; S12 = 0; f11 = 0; t10 = 0; t01 = 0; t11= 0; t21= 0; t12= 0; t22= 0; C12Numerator = 0;
double Sharedace, C12, part1, part2, part3, part4, part5, Gamma1, Gamma2, Gamma3;
/*fARare = number of OTUs with one individual found in A and less than or equal to 10 in B.
fBRare = number of OTUs with one individual found in B and less than or equal to 10 in A.
arare = number of sequences from A that contain less than 10 sequences.
brare = number of sequences from B that contain less than 10 sequences.
S12Rare = number of shared OTUs where both of the communities are represented by less than or equal to 10 sequences
S12Abund = number of shared OTUs where at least one of the communities is represented by more than 10 sequences
S12 = number of shared OTUs in A and B
This estimator was changed to reflect Caldwell's changes, eliminating the nrare / nrare - 1 */
for (int i = 0; i < shared[0]->getNumBins(); i++) {
//store in temps to avoid multiple repetitive function calls
tempA = shared[0]->getAbundance(i);
tempB = shared[1]->getAbundance(i);
if ((tempA != 0) && (tempB != 0)) {//they are shared
S12++;
//do both A and B have one
if ((tempA == 1) && (tempB == 1)) { f11++; }
//is A one and B rare
if ((tempA == 1) && (tempB <= abund)) { fARare++; }
//is B one and A rare
if ((tempB == 1) && (tempA <= abund)) { fBRare++; }
if ((tempA <= abund) && (tempB <= abund)) { //shared and both rare
S12Rare++;
t10 += tempA; //Sum Xi
t01 += tempB; //Sum Yi
//calculate top of C12
// YiI(Xi = 1)
if (tempA == 1) { C12Numerator += tempB; }
//XiI(Yi = 1)
if (tempB == 1) { C12Numerator += tempA; }
//-I(Xi=Yi=1)
if ((tempA == 1) && (tempB == 1)) { C12Numerator--; }
//calculate t11 - Sum of XiYi
t11 += tempA * tempB;
//calculate t21 - Sum of Xi(Xi - 1)Yi
t21 += tempA * (tempA - 1) * tempB;
//calculate t12 - Sum of Xi(Yi - 1)Yi
t12 += tempA * (tempB - 1) * tempB;
//calculate t22 - Sum of Xi(Xi - 1)Yi(Yi - 1)
t22 += tempA * (tempA - 1) * tempB * (tempB - 1);
}
if ((tempA > 10) || (tempB > 10)) {
S12Abund++;
}
}
}
C12 = 1 - (C12Numerator /(float) t11);
part1 = S12Rare / (float)C12;
part2 = 1 / (float)C12;
//calculate gammas
Gamma1 = ((S12Rare * t21) / (float)((C12 * t10 * t11)) - 1);
Gamma2 = ((S12Rare * t12) / (float)((C12 * t01 * t11)) - 1);
Gamma3 = ((S12Rare / C12) * (S12Rare / C12)) * ( t22 / (float)(t10 * t01 * t11));
Gamma3 = Gamma3 - ((S12Rare * t11) / (float)(C12 * t01 * t10)) - Gamma1 - Gamma2;
if (isnan(Gamma1) || isinf(Gamma1)) { Gamma1 = 0; }
if (isnan(Gamma2) || isinf(Gamma2)) { Gamma2 = 0; }
if (isnan(Gamma3) || isinf(Gamma3)) { Gamma3 = 0; }
if (isnan(part1) || isinf(part1)) { part1 = 0; }
if (isnan(part2) || isinf(part2)) { part2 = 0; }
part3 = fARare * Gamma1;
part4 = fBRare * Gamma2;
part5 = f11 * Gamma3;
Sharedace = S12Abund + part1 + (part2 * (part3 + part4 + part5));
data[0] = Sharedace;
return data;
}
catch(exception& e) {
m->errorOut(e, "SharedAce", "getValues");
exit(1);
}
}
/***********************************************************************/
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