#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 {
int CorrAxesCommand::calcSpearman(map<string, vector<float> >& 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<float, int> > tableX; tableX.resize(numaxes);
map<float, int>::iterator itTable;
}
}
- /*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<spearmanRank*> ties;
int rankTotal = 0;
for (int j = 0; j < scores[i].size(); j++) {
- rankTotal += j;
+ rankTotal += (j+1);
ties.push_back(&(scores[i][j]));
- if (j != scores.size()-1) { // you are not the last so you can look ahead
+ if (j != scores[i].size()-1) { // you are not the last so you can look ahead
if (scores[i][j].score != scores[i][j+1].score) { // you are done with ties, rank them and continue
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
vector<spearmanRank> ties;
int rankTotal = 0;
for (int j = 0; j < otuScores.size(); j++) {
- rankTotal += j;
+ rankTotal += (j+1);
ties.push_back(otuScores[j]);
- if (j != scores.size()-1) { // you are not the last so you can look ahead
+ if (j != otuScores.size()-1) { // you are not the last so you can look ahead
if (otuScores[j].score != otuScores[j+1].score) { // you are done with ties, rank them and continue
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
}
}
}
+
+
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;
+
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);
}
+ 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;
+ //comparing to yourself
+ count -= lookupFloat.size();
+ double p = (numCoor - numDisCoor) / (float) count;
+
out << '\t' << p;
pValues[j] = p;
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