kruskalwalliscommand.cpp

   1 /*
   2  * File:   kruskalwalliscommand.cpp
   3  * Author: kiverson
   4  *
   5  * Created on June 26, 2012, 11:06 AM
   6  */
   7 #include "kruskalwalliscommand.h"
   8
   9 //**********************************************************************************************************************
  10 class groupRank {
  11 public:
  12     string group;
  13     double value;
  14     double rank;
  15 };
  16 //**********************************************************************************************************************
  17 vector<string> KruskalWallisCommand::setParameters(){
  18         try {
  19                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  20                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  21
  22                 vector<string> myArray;
  23                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  24                 return myArray;
  25         }
  26         catch(exception& e) {
  27                 m->errorOut(e, "KruskalWallisCommand", "setParameters");
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32 string KruskalWallisCommand::getHelpString(){
  33         try {
  34                 string helpString = "";
  35                 helpString += "The kruskalwallis command parameter options are \n";
  36         helpString += "Kruskal–Wallis one-way analysis of variance is a non-parametric method for testing whether samples originate from the same distribution.";
  37                 return helpString;
  38         }
  39         catch(exception& e) {
  40                 m->errorOut(e, "KruskalWallisCommand", "getHelpString");
  41                 exit(1);
  42         }
  43 }
  44 //**********************************************************************************************************************
  45 string KruskalWallisCommand::getOutputFileNameTag(string type, string inputName=""){
  46         try {
  47         string outputFileName = "";
  48                 map<string, vector<string> >::iterator it;
  49
  50         //is this a type this command creates
  51         it = outputTypes.find(type);
  52         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  53         else {
  54             if (type == "summary") {  outputFileName =  "cooccurence.summary"; }
  55             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  56         }
  57         return outputFileName;
  58         }
  59         catch(exception& e) {
  60                 m->errorOut(e, "KruskalWallisCommand", "getOutputFileNameTag");
  61                 exit(1);
  62         }
  63 }
  64 //**********************************************************************************************************************
  65 KruskalWallisCommand::KruskalWallisCommand(){
  66         try {
  67                 abort = true; calledHelp = true;
  68                 setParameters();
  69         vector<string> tempOutNames;
  70                 outputTypes["summary"] = tempOutNames;
  71
  72         }
  73         catch(exception& e) {
  74                 m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
  75                 exit(1);
  76         }
  77 }
  78 //**********************************************************************************************************************
  79 KruskalWallisCommand::KruskalWallisCommand(string option) {
  80         try {
  81                 abort = false; calledHelp = false;
  82
  83                 //allow user to run help
  84                 if(option == "help") { help(); abort = true; calledHelp = true; }
  85                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  86
  87                 else {
  88                         vector<string> myArray = setParameters();
  89
  90                         OptionParser parser(option);
  91                         map<string,string> parameters = parser.getParameters();
  92                         map<string,string>::iterator it;
  93
  94                         ValidParameters validParameter;
  95
  96                         //check to make sure all parameters are valid for command
  97                         for (it = parameters.begin(); it != parameters.end(); it++) {
  98                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  99                         }
 100
 101
 102                         //if the user changes the input directory command factory will send this info to us in the output parameter
 103                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 104                         if (inputDir == "not found"){   inputDir = "";          }
 105                         else {
 106                                 string path;
 107                                 it = parameters.find("shared");
 108                                 //user has given a template file
 109                                 if(it != parameters.end()){
 110                                         path = m->hasPath(it->second);
 111                                         //if the user has not given a path then, add inputdir. else leave path alone.
 112                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 113                                 }
 114                         }
 115
 116             vector<string> tempOutNames;
 117             outputTypes["summary"] = tempOutNames;
 118
 119
 120                 }
 121
 122         }
 123         catch(exception& e) {
 124                 m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
 125                 exit(1);
 126         }
 127 }
 128 //**********************************************************************************************************************
 129 int KruskalWallisCommand::execute(){
 130         try {
 131                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 132
 133         //math goes here
 134
 135         int N;
 136         double ss, H;
 137         double tmp = 0.0;
 138
 139         //merge all groups into a vector
 140         //rank function here
 141
 142         //test statistic
 143         for (int i=0;i<N;i++) { tmp = tmp + (pow(rankSums[i],2) / counts[i]); }
 144
 145         H = (12 / (N*(N+1))) * tmp - (3*(N+1));
 146
 147         //ss = tmp - pow(accumulate(rankSums.begin(), rankSums.end(), 0), 2);
 148
 149         //H = ss / ( (N * (N + 1))/12 );
 150
 151         //correction for ties?
 152
 153         //p-value calculation
 154
 155
 156
 157                 return 0;
 158         }
 159         catch(exception& e) {
 160                 m->errorOut(e, "KruskalWallisCommand", "execute");
 161                 exit(1);
 162         }
 163 }
 164 //**********************************************************************************************************************
 165 multimap<double,double> KruskalWallisCommand::getRank(vector<groupRank> vec) {
 166     try {
 167         multimap<double,double> rankMap;
 168         double rank = 1;
 169         double previous;
 170         double tie = 0.0;
 171         int tiecount = 0;
 172
 173         sort (vec.begin(), vec.end());
 174
 175         for (int i=0;i<vec.size();i++) {
 176             if (vec[i] != previous) { rankMap[rank] = vec[i]; }
 177             else {tie = tie + rank; tiecount++;}
 178             rank++;
 179             previous = vec[i];
 180         }
 181     }
 182     catch(exception& e) {
 183                 m->errorOut(e, "KruskalWallisCommand", "getRank");
 184                 exit(1);
 185         }
 186
 187 }
 188 //**********************************************************************************************************************
 189
 190 //**********************************************************************************************************************
 191 //**********************************************************************************************************************
 192 //**********************************************************************************************************************