X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=corraxescommand.cpp;h=26cdcda0178bcfdbfc8c89fbbbced8866edb796c;hb=5bb0453ee6ab8f7e700b5d0c61a84fdc73db4976;hp=64ac9b931545f853ae2b960259d60edce06564eb;hpb=0983603e15dcb69eb01934685d55408156d3b85f;p=mothur.git diff --git a/corraxescommand.cpp b/corraxescommand.cpp index 64ac9b9..26cdcda 100644 --- a/corraxescommand.cpp +++ b/corraxescommand.cpp @@ -387,23 +387,6 @@ int CorrAxesCommand::calcPearson(map >& axes, ofstream& ou int CorrAxesCommand::calcSpearman(map >& axes, ofstream& out) { try { - /*axes.clear(); - axes["1a"].push_back(1); - axes["1b"].push_back(1); - axes["1c"].push_back(1); - axes["2a"].push_back(2); - axes["2b"].push_back(2); - axes["2c"].push_back(2); - axes["3a"].push_back(3); - axes["3b"].push_back(3); - axes["3c"].push_back(3); - axes["4a"].push_back(4); - axes["4b"].push_back(4); - axes["4c"].push_back(4); - axes["5a"].push_back(5); - axes["5b"].push_back(5); - axes["5c"].push_back(5);*/ - //format data vector< map > tableX; tableX.resize(numaxes); map::iterator itTable; @@ -571,25 +554,6 @@ int CorrAxesCommand::calcSpearman(map >& axes, ofstream& o int CorrAxesCommand::calcKendall(map >& axes, ofstream& out) { try { - numaxes = 1; - axes.clear(); - axes["1a"].push_back(1); - axes["1b"].push_back(1); - axes["1c"].push_back(1); - axes["2a"].push_back(2); - axes["2b"].push_back(2); - axes["2c"].push_back(2); - axes["3a"].push_back(3); - axes["3b"].push_back(3); - axes["3c"].push_back(3); - axes["4a"].push_back(4); - axes["4b"].push_back(4); - axes["4c"].push_back(4); - axes["5a"].push_back(5); - axes["5b"].push_back(5); - axes["5c"].push_back(5); - - //format data vector< vector > scores; scores.resize(numaxes); for (map >::iterator it = axes.begin(); it != axes.end(); it++) { @@ -629,32 +593,6 @@ int CorrAxesCommand::calcKendall(map >& axes, ofstream& ou } } } - cout << "axes ranks = "; - for(int i = 0; i < scores[0].size(); i++) { cout << scores[0][i].score << '\t'; } - cout << endl; - lookupFloat.clear(); - lookupFloat.resize(15); - for (int i = 0; i < lookupFloat.size(); i++) { - lookupFloat[i] = new SharedRAbundFloatVector(); - } - lookupFloat[0]->push_back(0.2288227, "1a"); lookupFloat[0]->setGroup("1a"); - lookupFloat[1]->push_back(0.7394062, "1b"); lookupFloat[1]->setGroup("1b"); - lookupFloat[2]->push_back(0.4521187, "1c"); lookupFloat[2]->setGroup("1c"); - lookupFloat[3]->push_back(0.1598630, "2a"); lookupFloat[3]->setGroup("2a"); - lookupFloat[4]->push_back(0.09588156, "2b"); lookupFloat[4]->setGroup("2b"); - - lookupFloat[5]->push_back(0.933174, "2c"); lookupFloat[5]->setGroup("2c"); - lookupFloat[6]->push_back(0.3958304, "3a"); lookupFloat[6]->setGroup("3a");; - lookupFloat[7]->push_back(0.2364419, "3b"); lookupFloat[7]->setGroup("3b"); - lookupFloat[8]->push_back(0.1697712, "3c"); lookupFloat[8]->setGroup("3c"); - lookupFloat[9]->push_back(0.4077173, "4a"); lookupFloat[9]->setGroup("4a"); - - lookupFloat[10]->push_back(0.6116547, "4b"); lookupFloat[10]->setGroup("4b"); - lookupFloat[11]->push_back(0.9374322, "4c"); lookupFloat[11]->setGroup("4c"); - lookupFloat[12]->push_back(0.852184, "5a"); lookupFloat[12]->setGroup("5a"); - lookupFloat[13]->push_back(0.845094, "5b"); lookupFloat[13]->setGroup("5b"); - lookupFloat[14]->push_back(0.5795778, "5c"); lookupFloat[14]->setGroup("5c"); - //for each otu for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) { @@ -704,38 +642,13 @@ int CorrAxesCommand::calcKendall(map >& axes, ofstream& ou int numCoor = 0; int numDisCoor = 0; - //assemble otus ranks in same order as axis ranks, if ties, put in the best order possible - //NOTE: after this ordering the scores[j] indexes may not match the otus indexes within tied sections - //since we do not use the axes ranks except to order the otu ranks, I did not take the time to reorder the axes ranks vector otus; vector otusTemp; for (int l = 0; l < scores[j].size(); l++) { spearmanRank member(scores[j][l].name, rankOtus[scores[j][l].name]); - otusTemp.push_back(member); - - if (l != (scores[j].size()-1)) { // you are not the last so you can look ahead - if (scores[j][l].score != scores[j][l+1].score) { // you are done with ties, order them and continue - //order otus within tied section in the best way possible to make coor pairs - sort(otusTemp.begin(), otusTemp.end(), compareSpearmanReverse); - - //save order in otus - for (int h = 0; h < otusTemp.size(); h++) { ; otus.push_back(otusTemp[h]); } - - otusTemp.clear(); - } - }else { // you are the last one - //order otus within tied section in the best way possible to make coor pairs - sort(otusTemp.begin(), otusTemp.end(), compareSpearmanReverse); - - //save order in otus - for (int h = 0; h < otusTemp.size(); h++) { otus.push_back(otusTemp[h]); } - } + otus.push_back(member); } - cout << "otu ranks = "; - for (int h = 0; h < otus.size(); h++ ) { cout << otus[h].score << '\t'; } - cout << endl; - int count = 0; for (int l = 0; l < scores[j].size(); l++) { @@ -753,14 +666,11 @@ int CorrAxesCommand::calcKendall(map >& axes, ofstream& ou numDisCoor += numWithLowerRank; } - //sample size - //int n = lookupFloat.size(); //comparing to yourself count -= lookupFloat.size(); - //double p = ( (4 * P) / (float) ((n * (n - 1)) - numTies) ) - 1.0; double p = (numCoor - numDisCoor) / (float) count; - cout << "numCoor = " << numCoor << " numDisCoor = " << numDisCoor << " p = " << p << " count = " << count << endl; + out << '\t' << p; pValues[j] = p;