added mantel command

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index 4f8dccb167fc8e8e6d08597f11504d4df2b26f24..f47427d62c2cc7f03615149b11cbfdee5135b083 100644 (file)
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -645,7 +645,7 @@ int CorrAxesCommand::calcKendall(map<string, vector<float> >& axes, ofstream& ou
                                        int numWithLowerRank = 0;
                                        float thisrank = otus[l].score;
                                        
-                                       for (int u = l; u < scores[j].size(); u++) {
+                                       for (int u = l+1; u < scores[j].size(); u++) {
                                                if (otus[u].score > thisrank) { numWithHigherRank++; }
                                                else if (otus[u].score < thisrank) { numWithLowerRank++; }
                                                count++;
@@ -655,9 +655,6 @@ int CorrAxesCommand::calcKendall(map<string, vector<float> >& axes, ofstream& ou
                                        numDisCoor += numWithLowerRank;
                                }
                                
-                               //comparing to yourself
-                               count -= lookupFloat.size();
-                               
                                double p = (numCoor - numDisCoor) / (float) count;
 
                                out << '\t' << p;

diff --git a/linearalgebra.cpp b/linearalgebra.cpp
index 9308627d1335920ea49f9b4c5bbd543de629ae85..33464ca5b3519f615b1029b22793694d595eee2d 100644 (file)
--- a/linearalgebra.cpp
+++ b/linearalgebra.cpp
@@ -637,7 +637,7 @@ double LinearAlgebra::calcKendall(vector< vector<double> >& euclidDists, vector<
                        int numWithLowerRank = 0;
                        float thisrank = user[l].score;
                                        
-                       for (int u = l; u < scores.size(); u++) {
+                       for (int u = l+1; u < scores.size(); u++) {
                                if (user[u].score > thisrank) { numWithHigherRank++; }
                                else if (user[u].score < thisrank) { numWithLowerRank++; }
                                count++;
@@ -647,9 +647,6 @@ double LinearAlgebra::calcKendall(vector< vector<double> >& euclidDists, vector<
                        numDisCoor += numWithLowerRank;
                }
                                
-               //comparing to yourself
-               count -= userDists.size();
-                               
                r = (numCoor - numDisCoor) / (float) count;
                
                //divide by zero error

diff --git a/mantelcommand.cpp b/mantelcommand.cpp
index 0f6d0d7277fbaf7271f2e428b3d11cd0abd303f3..a1f7b3bafc35e3e7009462d3d944005bf055bd94 100644 (file)
--- a/mantelcommand.cpp
+++ b/mantelcommand.cpp
@@ -136,9 +136,11 @@ MantelCommand::MantelCommand(string option)  {
 
 void MantelCommand::help(){
        try {
+               m->mothurOut("Sokal, R. R., & Rohlf, F. J. (1995). Biometry, 3rd edn. New York: Freeman.\n");
                m->mothurOut("The mantel command reads two distance matrices and calculates the mantel correlation coefficient.\n");
-               m->mothurOut("The mantel command parameters are phylip1, phylip2 and method.  The phylip1 and phylip2 parameters are required.  Matrices must be the same size and contain the same names.\n");
+               m->mothurOut("The mantel command parameters are phylip1, phylip2, iters and method.  The phylip1 and phylip2 parameters are required.  Matrices must be the same size and contain the same names.\n");
                m->mothurOut("The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n");
+               m->mothurOut("The iters parameter allows you to set number of randomization for the P value.  The default is 1000. \n");
                m->mothurOut("The mantel command should be in the following format: mantel(phylip1=veg.dist, phylip2=env.dist).\n");
                m->mothurOut("The mantel command outputs a .mantel file.\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n\n");
@@ -173,82 +175,19 @@ int MantelCommand::execute(){
                
                //read phylip2
                ReadPhylipVector readMatrix2(phylipfile2);
-               vector<seqDist> temp; //seqDist - int, int, float
-               vector<string> names2 = readMatrix2.read(temp);
+               vector< vector<double> > matrix2;
+               vector<string> names2 = readMatrix2.read(matrix2);
                
                if (m->control_pressed) { return 0; }
                
-               //fill matrix2 making sure to make sure the distances are in the same order as matrix1
-               vector< vector<double> > matrix2;
+               //make sure matrix2 and matrix1 are in the same order
                if (names1 == names2) { //then everything is in same order and same size
-                       
-                       //initialize space
-                       matrix2.resize(names2.size());
-                       for (int i = 0; i < matrix2.size(); i++) { matrix2[i].resize(names2.size(), 0.0); }
-                       
-                       //fill matrix2
-                       for (int i = 0; i < temp.size(); i++) {
-                               matrix2[temp[i].seq1][temp[i].seq2] = temp[i].dist;
-                               matrix2[temp[i].seq2][temp[i].seq1] = temp[i].dist;
-                       }
-                       
                }else if (names1.size() != names2.size()) { //wrong size no need to order, abort
                        m->mothurOut("[ERROR]: distance matrices are not the same size, aborting."); m->mothurOutEndLine();
                        m->control_pressed = true;
                }else { //sizes are the same, but either the names are different or they are in different order
-                       
-                       //map location of name in names1 to location of name in names2
-                       map<string, int> names1Map;
-                       map<string, int>::iterator it;
-                       for (int i = 0; i < names1.size(); i++) {  names1Map[names1[i]] = i; }
-                       
-                       map<string, int> names2Map;
-                       bool nameError = false;
-                       for (int i = 0; i < names2.size(); i++) {  
-                               
-                               //if you find one name error stop looking
-                               if (!nameError) {
-                                       it = names1Map.find(names2[i]);
-                                       if (it == names1Map.end()) { nameError = true; }
-                               }
-                               
-                               //are names different
-                               names2Map[names2[i]] = i; 
-                       }
-                       
-                       //initialize space
-                       matrix2.resize(names2.size());
-                       for (int i = 0; i < matrix2.size(); i++) { matrix2[i].resize(names2.size(), 0.0); }
-                       
-                       //fill matrix2
-                       //are we comparing apples to apples?
-                       if (nameError) { 
-                               m->mothurOut("[WARNING]: Names do not match between distance files. Comparing based on order in files."); m->mothurOutEndLine();
-                               
-                               for (int i = 0; i < temp.size(); i++) {
-                                       matrix2[temp[i].seq1][temp[i].seq2] = temp[i].dist;
-                                       matrix2[temp[i].seq2][temp[i].seq1] = temp[i].dist;
-                               }
-                               
-                       }else { //no name error just different orders, so reorder
-                               
-                               for (int i = 0; i < temp.size(); i++) {
-                                       
-                                       //what's the location of this distance comparison in matrix1
-                                       string matrix2NameI = names2[temp[i].seq1];
-                                       string matrix2NameJ = names2[temp[i].seq2];
-                                       int locationI = names1Map[matrix2NameI];
-                                       int locationJ = names1Map[matrix2NameJ];
-                                       
-                                       matrix2[locationI][locationJ] = temp[i].dist;
-                                       matrix2[locationJ][locationI] = temp[i].dist;
-                               }
-                       }
-                       
-               }
-               
-               //frees up space
-               temp.clear();
+                       m->mothurOut("[WARNING]: Names do not match between distance files. Comparing based on order in files."); m->mothurOutEndLine();
+               }       
                
                if (m->control_pressed) { return 0; }