#include "sharedutilities.h"
//********************************************************************************************************************
-//sorts highes to lowest
+//sorts highest to lowest
inline bool compareSpearman(spearmanRank left, spearmanRank right){
return (left.score > right.score);
}
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareSpearmanReverse(spearmanRank left, spearmanRank right){
+ return (left.score < right.score);
+}
//**********************************************************************************************************************
vector<string> CorrAxesCommand::getValidParameters(){
try {
}
}
- /*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++) {
int CorrAxesCommand::calcKendall(map<string, vector<float> >& 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<spearmanRank> > scores; scores.resize(numaxes);
for (map<string, vector<float> >::iterator it = axes.begin(); it != axes.end(); it++) {
}
}
}
+ 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++) {
}
}
}
+
+
vector<double> pValues(numaxes);
//calc spearman ranks for each axis for this otu
for (int j = 0; j < numaxes; j++) {
- int P = 0;
- //assemble otus ranks in same order as axis ranks
+ 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<spearmanRank> otus;
+ vector<spearmanRank> otusTemp;
for (int l = 0; l < scores[j].size(); l++) {
spearmanRank member(scores[j][l].name, rankOtus[scores[j][l].name]);
- otus.push_back(member);
+ 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]); }
+ }
}
+ 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++) {
int numWithHigherRank = 0;
+ int numWithLowerRank = 0;
float thisrank = otus[l].score;
for (int u = l; u < scores[j].size(); u++) {
if (otus[u].score > thisrank) { numWithHigherRank++; }
+ else if (otus[u].score < thisrank) { numWithLowerRank++; }
+ count++;
}
- P += numWithHigherRank;
+ numCoor += numWithHigherRank;
+ numDisCoor += numWithLowerRank;
}
- int n = lookupFloat.size();
-
- double p = ( (4 * P) / (float) (n * (n - 1)) ) - 1.0;
+ //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;
projects / mothur.git / commitdiff