*
* Created on June 26, 2012, 11:06 AM
*/
+
#include "kruskalwalliscommand.h"
-//**********************************************************************************************************************
-class groupRank {
-public:
- string group;
- double value;
- double rank;
-};
//**********************************************************************************************************************
vector<string> KruskalWallisCommand::setParameters(){
try {
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pgroups);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string KruskalWallisCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
-
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "summary") { outputFileName = "cooccurence.summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "KruskalWallisCommand", "getOutputFileNameTag");
- exit(1);
- }
+string KruskalWallisCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "summary") { pattern = "[filename],cooccurence.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "KruskalWallisCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
KruskalWallisCommand::KruskalWallisCommand(){
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
-
-
+
+ //get shared file
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") {
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setSharedFile(sharedfile); }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(sharedfile); }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ }
+ m->setGroups(Groups);
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ InputData* input = new InputData(sharedfile, "sharedfile");
+ vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
+
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ ofstream out;
+ map<string,string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ string outputFileName = getOutputFileName("summary",variables);
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ out << "H\tpvalue\n";
+
//math goes here
- int N;
- double ss, H;
+ int N = m->getNumGroups();
+ double H;
double tmp = 0.0;
+ vector<groupRank> vec;
+ vector<string> groups = m->getGroups();
+ 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 = groups[i];
+ 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]); }
//p-value calculation
-
-
return 0;
}
catch(exception& e) {
}
}
//**********************************************************************************************************************
-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, j;
+ vector<groupRank>::iterator it, oldit;
- sort (vec.begin(), vec.end());
+ sort (vec.begin(), vec.end(), comparevalue);
+
+ it = vec.begin();
+
+ while ( it != vec.end() ) {
+ j = rank;
+ oldit = it;
+ if (!equalvalue(*it, *(it+1))) {
+ (*it).rank = rank;
+ rank = rank+1;
+ it++; }
+ else {
+ while(equalrank(*it, *(it+1))) {
+ j = j + (j+1);
+ 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");
}
//**********************************************************************************************************************
-
+void KruskalWallisCommand::assignValue(vector<groupRank> &vec) {
+
+}
//**********************************************************************************************************************
//**********************************************************************************************************************
-//**********************************************************************************************************************
\ No newline at end of file
+//**********************************************************************************************************************
+
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