kruskalwalliscommand.cpp

   1 /*
   2  * File:   kruskalwalliscommand.cpp
   3  * Author: kiverson
   4  *
   5  * Created on June 26, 2012, 11:06 AM
   6  */
   7
   8 #include "kruskalwalliscommand.h"
   9
  10 //**********************************************************************************************************************
  11 vector<string> KruskalWallisCommand::setParameters(){
  12         try {
  13                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  14                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  15         CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  16         CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
  17
  18                 vector<string> myArray;
  19                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  20                 return myArray;
  21         }
  22         catch(exception& e) {
  23                 m->errorOut(e, "KruskalWallisCommand", "setParameters");
  24                 exit(1);
  25         }
  26 }
  27 //**********************************************************************************************************************
  28 string KruskalWallisCommand::getHelpString(){
  29         try {
  30                 string helpString = "";
  31                 helpString += "The kruskalwallis command parameter options are \n";
  32         helpString += "Kruskal–Wallis one-way analysis of variance is a non-parametric method for testing whether samples originate from the same distribution.";
  33                 return helpString;
  34         }
  35         catch(exception& e) {
  36                 m->errorOut(e, "KruskalWallisCommand", "getHelpString");
  37                 exit(1);
  38         }
  39 }
  40 //**********************************************************************************************************************
  41 string KruskalWallisCommand::getOutputFileNameTag(string type, string inputName=""){
  42         try {
  43         string outputFileName = "";
  44                 map<string, vector<string> >::iterator it;
  45
  46         //is this a type this command creates
  47         it = outputTypes.find(type);
  48         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  49         else {
  50             if (type == "summary") {  outputFileName =  "cooccurence.summary"; }
  51             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  52         }
  53         return outputFileName;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "KruskalWallisCommand", "getOutputFileNameTag");
  57                 exit(1);
  58         }
  59 }
  60 //**********************************************************************************************************************
  61 KruskalWallisCommand::KruskalWallisCommand(){
  62         try {
  63                 abort = true; calledHelp = true;
  64                 setParameters();
  65         vector<string> tempOutNames;
  66                 outputTypes["summary"] = tempOutNames;
  67
  68         }
  69         catch(exception& e) {
  70                 m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
  71                 exit(1);
  72         }
  73 }
  74 //**********************************************************************************************************************
  75 KruskalWallisCommand::KruskalWallisCommand(string option) {
  76         try {
  77                 abort = false; calledHelp = false;
  78
  79                 //allow user to run help
  80                 if(option == "help") { help(); abort = true; calledHelp = true; }
  81                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  82
  83                 else {
  84                         vector<string> myArray = setParameters();
  85
  86                         OptionParser parser(option);
  87                         map<string,string> parameters = parser.getParameters();
  88                         map<string,string>::iterator it;
  89
  90                         ValidParameters validParameter;
  91
  92                         //check to make sure all parameters are valid for command
  93                         for (it = parameters.begin(); it != parameters.end(); it++) {
  94                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  95                         }
  96
  97             //get shared file
  98                         sharedfile = validParameter.validFile(parameters, "shared", true);
  99                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 100                         else if (sharedfile == "not found") {
 101                                 //if there is a current shared file, use it
 102                                 sharedfile = m->getSharedFile();
 103                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 104                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 105                         }else { m->setSharedFile(sharedfile); }
 106
 107             //if the user changes the output directory command factory will send this info to us in the output parameter
 108                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(sharedfile);             }
 109
 110             groups = validParameter.validFile(parameters, "groups", false);
 111             if (groups == "not found") { groups = "";   }
 112             else {
 113             m->splitAtDash(groups, Groups);
 114             }
 115             m->setGroups(Groups);
 116
 117                         //if the user changes the input directory command factory will send this info to us in the output parameter
 118                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 119                         if (inputDir == "not found"){   inputDir = "";          }
 120                         else {
 121                                 string path;
 122                                 it = parameters.find("shared");
 123                                 //user has given a template file
 124                                 if(it != parameters.end()){
 125                                         path = m->hasPath(it->second);
 126                                         //if the user has not given a path then, add inputdir. else leave path alone.
 127                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 128                                 }
 129                         }
 130
 131             vector<string> tempOutNames;
 132             outputTypes["summary"] = tempOutNames;
 133
 134
 135                 }
 136
 137         }
 138         catch(exception& e) {
 139                 m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
 140                 exit(1);
 141         }
 142 }
 143 //**********************************************************************************************************************
 144 int KruskalWallisCommand::execute(){
 145         try {
 146                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 147
 148         InputData* input = new InputData(sharedfile, "sharedfile");
 149         vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 150                 string lastLabel = lookup[0]->getLabel();
 151
 152
 153                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 154                 set<string> processedLabels;
 155                 set<string> userLabels = labels;
 156
 157         ofstream out;
 158                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary");
 159         m->openOutputFile(outputFileName, out);
 160         outputNames.push_back(outputFileName);  outputTypes["summary"].push_back(outputFileName);
 161         out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 162         out << "H\tpvalue\n";
 163
 164         //math goes here
 165
 166         int N = m->getNumGroups();
 167         double H;
 168         double tmp = 0.0;
 169         vector<groupRank> vec;
 170         vector<string> groups = m->getGroups();
 171         string group;
 172         int count;
 173         double sum;
 174
 175         //merge all groups into a vector
 176
 177
 178
 179         //rank function here
 180         assignRank(vec);
 181
 182         //populate counts and ranSums vectors
 183         for (int i=0;i<N;i++) {
 184             count = 0;
 185             sum = 0;
 186             group = groups[i];
 187             for(int j;j<vec.size();j++) {
 188                 if (vec[j].group == group) {
 189                     count++;
 190                     sum = sum + vec[j].rank;
 191                 }
 192             }
 193             counts[i] = count;
 194             rankSums[i] = sum;
 195         }
 196
 197         //test statistic
 198         for (int i=0;i<N;i++) { tmp = tmp + (pow(rankSums[i],2) / counts[i]); }
 199
 200         H = (12 / (N*(N+1))) * tmp - (3*(N+1));
 201
 202         //ss = tmp - pow(accumulate(rankSums.begin(), rankSums.end(), 0), 2);
 203
 204         //H = ss / ( (N * (N + 1))/12 );
 205
 206         //correction for ties?
 207
 208         //p-value calculation
 209
 210                 return 0;
 211         }
 212         catch(exception& e) {
 213                 m->errorOut(e, "KruskalWallisCommand", "execute");
 214                 exit(1);
 215         }
 216 }
 217 //**********************************************************************************************************************
 218 void KruskalWallisCommand::assignRank(vector<groupRank> &vec) {
 219     try {
 220         double rank = 1;
 221         double numRanks, avgRank, j;
 222         vector<groupRank>::iterator it, oldit;
 223
 224         sort (vec.begin(), vec.end(), comparevalue);
 225
 226         it = vec.begin();
 227
 228         while ( it != vec.end() ) {
 229             j = rank;
 230             oldit = it;
 231             if (!equalvalue(*it, *(it+1))) {
 232                 (*it).rank = rank;
 233                 rank = rank+1;
 234                 it++; }
 235             else {
 236                 while(equalrank(*it, *(it+1))) {
 237                     j = j + (j+1);
 238                     rank++;
 239                     it++;
 240                 }
 241                 numRanks = double (distance(oldit, it));
 242                 avgRank = j / numRanks;
 243                 while(oldit != it) {
 244                     (*oldit).rank = avgRank;
 245                     oldit++;
 246                 }
 247             }
 248
 249         }
 250
 251
 252     }
 253     catch(exception& e) {
 254                 m->errorOut(e, "KruskalWallisCommand", "getRank");
 255                 exit(1);
 256         }
 257
 258 }
 259 //**********************************************************************************************************************
 260 void KruskalWallisCommand::assignValue(vector<groupRank> &vec) {
 261
 262 }
 263 //**********************************************************************************************************************
 264 //**********************************************************************************************************************
 265 //**********************************************************************************************************************