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;
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++) {
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]);
- 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++) {
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;
void MergeGroupsCommand::help(){
try {
m->mothurOut("The merge.groups command reads a shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file.\n");
- m->mothurOut("The metastats command outputs a .shared file. \n");
- m->mothurOut("The metastats command parameters are shared, groups, label and design. The design and shared parameter are required.\n");
+ m->mothurOut("The merge.groups command outputs a .shared file. \n");
+ m->mothurOut("The merge.groups command parameters are shared, groups, label and design. The design and shared parameter are required.\n");
m->mothurOut("The design parameter allows you to assign your groups to sets when you are running metastat. mothur will run all pairwise comparisons of the sets. It is required. \n");
m->mothurOut("The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.\n");
m->mothurOut("The groups parameter allows you to specify which of the groups in your shared you would like included. The group names are separated by dashes.\n");
m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
- m->mothurOut("The merge.groups command should be in the following format: metastats(design=yourDesignFile, shared=yourSharedFile).\n");
- m->mothurOut("Example metastats(design=temp.design, groups=A-B-C, shared=temp.shared).\n");
+ m->mothurOut("The merge.groups command should be in the following format: merge.groups(design=yourDesignFile, shared=yourSharedFile).\n");
+ m->mothurOut("Example merge.groups(design=temp.design, groups=A-B-C, shared=temp.shared).\n");
m->mothurOut("The default value for groups is all the groups in your sharedfile, and all labels in your inputfile will be used.\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
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