From: Kathryn Iverson <kd.iverson@gmail.com>
Date: Thu, 28 Jun 2012 13:31:03 +0000 (-0400)
Subject: updated kruskalwallis command
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=f954b4d65ce86218f9f7262737f36d1e7faf58d6

updated kruskalwallis command
---

diff --git a/kruskalwalliscommand.cpp b/kruskalwalliscommand.cpp
index 263b1c5..f67fef8 100644
--- a/kruskalwalliscommand.cpp
+++ b/kruskalwalliscommand.cpp
@@ -6,13 +6,6 @@
  */
 #include "kruskalwalliscommand.h"
 
-//**********************************************************************************************************************
-class groupRank {
-public:
-    string group;
-    double value;
-    double rank;
-};
 //**********************************************************************************************************************
 vector<string> KruskalWallisCommand::setParameters(){	
 	try {
@@ -132,12 +125,32 @@ int KruskalWallisCommand::execute(){
         
         //math goes here
         
-        int N;
-        double ss, H;
+        int N; //= thisLookUp.size();
+        double H;
         double tmp = 0.0;
+        vector<groupRank> vec;
+        string group;
+        int count;
+        double sum;
                 
         //merge all groups into a vector
         //rank function here
+        assignRank(vec);
+        
+        //populate counts and ranSums vectors
+        for (int i=0;i<N;i++) {
+            count = 0;
+            sum = 0;
+            //group = next group
+            for(int j;j<vec.size();j++) {
+                if (vec[j].group == group) {
+                    count++;
+                    sum = sum + vec[j].rank;
+                }
+            }
+            counts[i] = count;
+            rankSums[i] = sum;
+        }
         
         //test statistic
         for (int i=0;i<N;i++) { tmp = tmp + (pow(rankSums[i],2) / counts[i]); }
@@ -152,8 +165,6 @@ int KruskalWallisCommand::execute(){
         
         //p-value calculation
         
-        
-        
 		return 0;
 	}
 	catch(exception& e) {
@@ -162,22 +173,36 @@ int KruskalWallisCommand::execute(){
 	}
 }
 //**********************************************************************************************************************
-multimap<double,double> KruskalWallisCommand::getRank(vector<groupRank> vec) {
+void KruskalWallisCommand::assignRank(vector<groupRank> &vec) {
     try {
-        multimap<double,double> rankMap;
         double rank = 1;
-        double previous;
-        double tie = 0.0;
-        int tiecount = 0;
+        double numRanks, avgRank;
+        vector<groupRank>::iterator it, oldit;
+
+        sort (vec.begin(), vec.end(), comparevalue);
 
-        sort (vec.begin(), vec.end());
+        it = vec.begin();
+
+        while ( it != vec.end() ) {
+            j = rank;
+            oldit = it;
+            if (!equalvalue(*it, *it+1)) { *it->rank = rank; rank++; it++; }
+            else {
+                while(equalrank(*it, *it+1)) {
+                    j = j + (j+1.0);
+                    rank++;
+                    it++;
+                }
+                numRanks = double (distance(oldit, it));
+                avgRank = j / numRanks;
+                while(oldit != it) {
+                    *oldit->rank = avgRank;
+                    oldit++;
+                }
+            }
 
-        for (int i=0;i<vec.size();i++) {
-            if (vec[i] != previous) { rankMap[rank] = vec[i]; }
-            else {tie = tie + rank; tiecount++;}
-            rank++;
-            previous = vec[i];
         }
+
     }
     catch(exception& e) {
 		m->errorOut(e, "KruskalWallisCommand", "getRank");
diff --git a/kruskalwalliscommand.h b/kruskalwalliscommand.h
index 7e52613..003ea91 100644
--- a/kruskalwalliscommand.h
+++ b/kruskalwalliscommand.h
@@ -10,10 +10,16 @@
 
 #include "command.hpp"
 
-class KruskalWallisCommand : public Command {
+    struct groupRank {
+        sstring group;
+        double value;
+        double rank;        
+    };
 
+class KruskalWallisCommand : public Command {
+   
 public:
-	
+	    
 	KruskalWallisCommand(string);	
 	KruskalWallisCommand();
 	~KruskalWallisCommand(){}
@@ -28,7 +34,7 @@ public:
     
     int execute(); 
 	void help() { m->mothurOut(getHelpString()); }
-    multimap<double,double> getRank(vector<KruskalWallisCommand::groupRank>);
+    void assignRank(vector<groupRank>);
     
 private:
     string outputDir;
@@ -36,6 +42,14 @@ private:
     vector<double> rankSums;
     vector<double> rankMeans;
     
+  
+        
+    bool comparevalue(const groupRank &a, const groupRank &b) { return a.value < b.value; }
+    bool equalvalue(const groupRank &a, const groupRank &b) { return a.value == b.value; }
+    bool comparerank(const groupRank &a, const groupRank &b) { return a.rank < b.rank; }
+    bool equalrank(const groupRank &a, const groupRank &b) { return a.rank == b.rank; }
+    bool equalgroup(const groupRank &a, const groupRank &b) { return a.group == b.group; }
+    
 };
 
 #endif	/* KRUSKALWALLISCOMMAND_H */