--- /dev/null
+/*
+ * calculator.cpp
+ * Dotur
+ *
+ * Created by Sarah Westcott on 11/18/08.
+ * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "calculator.h"
+
+/***********************************************************************/
+void VecCalc::printElements(vector<double> vec){
+ try {
+ for(int i = 0; i < vec.size(); i++)
+ cout << vec.at(i) << " ";
+ cout << "\n\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function printElements. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function printElements. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void VecCalc::printElements(vector<string> vec){
+ try {
+ for(int i = 0; i < vec.size(); i++)
+ cout << vec.at(i) << " ";
+ cout << "\n\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function printElements. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function printElements. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+int VecCalc::findString(vector<string> vec, string str){
+ try {
+ for(int i = 0; i < vec.size(); i++)
+ if(str.compare(vec.at(i)) == 0)
+ return i;
+ return -1;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function findString. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function findString. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double VecCalc::mean(vector<double> vec){
+ return sumElements(vec)/vec.size();
+}
+/***********************************************************************/
+double VecCalc::stError(vector<double> vec){
+ try {
+ double sum = 0;
+ double m = mean(vec);
+ for(int i = 0; i < vec.size(); i++)
+ sum += pow(vec.at(i)-m,2);
+ return pow(sum/(vec.size()*(vec.size()-1)), .5);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function stError. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function stError. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double VecCalc::sumElements(vector<double> vec){
+ try {
+ double sum = 0;
+ for(int i = 0; i < vec.size(); i++)
+ sum += vec.at(i);
+ return sum;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function sumElements. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function sumElements. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double VecCalc::sumElements(vector<double> vec, int index){
+ try {
+ double sum = 0;
+ for(int i = index; i < vec.size(); i++)
+ sum += vec.at(i);
+ return sum;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function sumElements. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function sumElements. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double VecCalc::findMax(vector<double> vec){
+ try {
+ double max = -1000000.0;
+ for(int i = 0; i < vec.size(); i++)
+ if(vec.at(i) > max)
+ max = vec.at(i);
+ return max;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function findMax. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function findMax. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double VecCalc::numNZ(vector<double> vec){
+ try {
+ double numNZ = 0;
+ for(int i = 0; i < vec.size(); i++)
+ if(vec.at(i) != 0)
+ numNZ++;
+ return numNZ;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function numNZ. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function numNZ. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double VecCalc::numPos(vector<double> vec){
+ try {
+ double numPos = 0;
+ for(int i = 0 ; i < vec.size(); i++)
+ if(vec.at(i) > 0)
+ numPos++;
+ return numPos;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function numPos. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function numPos. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double VecCalc::findMaxDiff(vector<double> vec1, vector<double> vec2){
+ try {
+ double maxDiff = -10000000000.0;
+ for(int i = 0; i < vec1.size(); i++)
+ if(fabs(vec1.at(i)-vec2.at(i)) > maxDiff)
+ maxDiff = fabs(vec1.at(i)-vec2.at(i));
+ return maxDiff;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function findMaxDiff. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function findMaxDiff. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double VecCalc::findDStat(vector<double> vec1, vector<double> vec2, double num){
+ try {
+ double mDiff = findMaxDiff(vec1, vec2);
+ return (mDiff+.5)/num;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function findDStat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function findDStat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<int> VecCalc::findQuartiles(vector<double> vec){
+ try {
+ vector<int> quartiles;
+ double max = vec.at(vec.size()-1);
+ double r1 = max/4;
+ double r2 = max*3/4;
+ bool r1found = false;
+ bool r2found = false;
+ for(int i = 0; i < vec.size(); i++)
+ {
+ if(vec.at(i) > r1 && !r1found)
+ {
+ quartiles.push_back(i);
+ r1found = true;
+ }
+ if(vec.at(i) > r2 && !r2found)
+ {
+ quartiles.push_back(i);
+ i = vec.size();
+ }
+ }
+ return quartiles;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function findQuartiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function findQuartiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<double> VecCalc::add(vector<double> vec, double x){
+ try {
+ vector<double> newVec;
+ for(int i = 0; i < vec.size(); i++)
+ newVec.push_back(vec.at(i)+x);
+ return newVec;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function add. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function add. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<double> VecCalc::multiply(vector<double> vec, double x){
+ try {
+ vector<double> newVec;
+ for(int i = 0; i < vec.size(); i++)
+ newVec.push_back(vec.at(i)*x);
+ return newVec;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function multiply. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function multiply. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<double> VecCalc::power(vector<double> vec, double p){
+ try {
+ vector<double> newVec;
+ for(int i = 0; i < vec.size(); i++)
+ newVec.push_back(pow(vec.at(i), p));
+ return newVec;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function power. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function power. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<double> VecCalc::addVecs(vector<double> vec1, vector<double> vec2) //Vectors must be the same size.
+{ try {
+ vector<double> newVec;
+ for(int i = 0; i < vec1.size(); i++)
+ newVec.push_back(vec1.at(i)+vec2.at(i));
+ return newVec;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function addVecs. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function addVecs. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<double> VecCalc::multVecs(vector<double> vec1, vector<double> vec2) //Vectors must be the same size.
+{ try {
+ vector<double> newVec;
+ for(int i = 0; i < vec1.size(); i++)
+ newVec.push_back(vec1.at(i)*vec2.at(i));
+ return newVec;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function multVecs. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function multVecs. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<double> VecCalc::remDup(vector<double> vec){
+ try {
+ vector<double> newVec;
+ newVec.push_back(vec.at(0));
+ for(int i = 1; i < vec.size(); i++)
+ if(vec.at(i) != vec.at(i-1))
+ newVec.push_back(vec.at(i));
+ return newVec;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function remDup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function remDup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<double> VecCalc::genCVec(vector<double> vec1){
+ try {
+ vector<double> vec2;
+ double sum = 0;
+ for(int i = 0; i < vec1.size(); i++)
+ {
+ sum += vec1.at(i);
+ vec2.push_back(sum);
+ }
+ return vec2;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function genCVec. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function genCVec. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<double> VecCalc::genRelVec(vector<double> vec){
+ try {
+ vector<double> newVec;
+ double sum = sumElements(vec);
+ for(int i = 0; i < vec.size(); i++)
+ newVec.push_back(vec.at(i)/sum);
+ return newVec;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function genRelVec. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function genRelVec. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<double> VecCalc::genDiffVec(vector<double> vec1, vector<double> vec2){
+ try {
+ vector<double> newVec;
+ for(int i = 0; i < vec1.size(); i++)
+ newVec.push_back(vec1.at(i)-vec2.at(i));
+ return newVec;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function genDiffVec. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function genDiffVec. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<double> VecCalc::genCSVec(vector<double> vec){
+ try {
+ vector<double> newVec;
+ double curInd = vec.at(vec.size()-1);
+ double sumSpec = 0;
+ double cSumSpec = 0;
+ for(int i = vec.size()-1; i >= 0; i--)
+ {
+ if(vec.at(i) == curInd)
+ sumSpec++;
+ else
+ {
+ cSumSpec += sumSpec;
+ newVec.push_back(cSumSpec);
+ sumSpec = 1;
+ curInd = vec.at(i);
+ }
+ if(i == 0)
+ newVec.push_back(cSumSpec + sumSpec);
+ }
+ return newVec;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function genCSVec. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function genCSVec. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<double> VecCalc::genTotVec(vector<vector<double> > vec){
+ try {
+ vector<double> newVec = vec.at(0);
+ for(int i = 1; i < vec.size(); i++)
+ newVec = addVecs(newVec, vec.at(i));
+ return newVec;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function genTotVec. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function genTotVec. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<double> VecCalc::quicksort(vector<double> vec){
+ try {
+ sort(vec.rbegin(), vec.rend());
+ return vec;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function quicksort. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function quicksort. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<vector<double> > VecCalc::gen2DVec(vector<double> vec, int div, int type){
+ try {
+ vector<vector<double> > vec2D;
+ int gap = vec.size()/div;
+ for(int i = 0; i < div; i++)
+ {
+ vector<double> inVec;
+ for(int j = 0; j < gap; j++)
+ if(type == 0)
+ inVec.push_back(vec.at(j + i*gap)); //Rows
+ else
+ inVec.push_back(vec.at(i + j*div)); //Columns
+ vec2D.push_back(inVec);
+ }
+ return vec2D;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function gen2DVec. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function gen2DVec. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<string> VecCalc::getSData(char name[]){
+ try {
+ vector<string> vec;
+ string data;
+ ifstream file(name);
+ if(file.is_open())
+ {
+ while(file >> data)
+ vec.push_back(data);
+ file.close();
+ }
+ return vec;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function getSData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function getSData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double BDiversity::getWhitt(vector<double> vec1, vector<double> vec2){
+ try {
+ VecCalc vecCalc;
+ double numSpec = vecCalc.numNZ(vecCalc.addVecs(vec1,vec2));
+ return 2*numSpec/(vecCalc.numNZ(vec1)+vecCalc.numNZ(vec2))-1;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BDiversity class Function getWhitt. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BDiversity class function getWhitt. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double BDiversity::getMS(vector<double> vec1, vector<double> vec2){
+ try {
+ VecCalc vecCalc;
+ double a = vecCalc.numNZ(vecCalc.multVecs(vec1, vec2));
+ double b = vecCalc.numPos(vecCalc.addVecs(vecCalc.addVecs(vec1, vecCalc.multiply(vec2, -1)), vecCalc.multiply(vecCalc.multVecs(vec1, vec2), -1)));
+ double c = vecCalc.numPos(vecCalc.addVecs(vecCalc.addVecs(vec2, vecCalc.multiply(vec1, -1)), vecCalc.multiply(vecCalc.multVecs(vec2, vec1), -1)));
+ return a/(a+b+c);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BDiversity class Function getMS. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BDiversity class function getMS. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double BDiversity::getSor(vector<double> vec1, vector<double> vec2){
+ try {
+ double sum = 0;
+ double asum = 0;
+ double bsum = 0;
+ for(int i = 0; i < vec1.size(); i++)
+ {
+ asum += vec1.at(i);
+ bsum += vec2.at(i);
+ if(vec1.at(i) >= vec2.at(i))
+ sum += vec2.at(i);
+ else
+ sum += vec1.at(i);
+ }
+ return 2*sum/(asum+bsum);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BDiversity class Function getSor. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BDiversity class function getSor. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double BDiversity::getMor(vector<double> vec1, vector<double> vec2){
+ try {
+ double sum = 0;
+ double asum = 0;
+ double bsum = 0;
+ double sum1 = 0;
+ double sum2 = 0;
+ for(int i = 0; i < vec1.size(); i++)
+ {
+ sum += vec1.at(i)*vec2.at(i);
+ asum += pow(vec1.at(i),2);
+ bsum += pow(vec2.at(i),2);
+ sum1 += vec1.at(i);
+ sum2 += vec2.at(i);
+ }
+ return 2*sum/((asum/pow(sum1,2)+bsum/pow(sum2,2))*(sum1*sum2));
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BDiversity class Function getMor. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BDiversity class function getMor. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+void BDiversity::printD(vector<vector<double> > columns, int type){
+ try {
+ cout << " ";
+ for(int i = 0; i < columns.size(); i++)
+ cout << "Column:" << i << " ";
+ cout << "\n";
+ for(int i = 0; i < columns.size(); i++)
+ {
+ cout << "Column " << i << ":";
+ for(int j = 0; j < columns.size(); j++)
+ {
+ if(j > i)
+ {
+ double B;
+ if(type == 1)
+ B = getWhitt(columns.at(i), columns.at(j));
+ else if(type == 2)
+ B = 1-getMS(columns.at(i), columns.at(j));
+ else if(type == 3)
+ B = 1-getSor(columns.at(i), columns.at(j));
+ else if(type == 4)
+ B = 1-getMor(columns.at(i), columns.at(j));
+
+ cout << B << " ";
+ }
+ else
+ cout << " ";
+ }
+ cout << "\n";
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BDiversity class Function printD. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BDiversity class function printD. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+void BDiversity::doBD(vector<double> vec, double cols)//vec = The data vector if the data table was read left-to-right, top-to-bottom. cols = the number of columns in the data table.
+{ try {
+ VecCalc vecCalc;
+ vector<vector<double> > columns = vecCalc.gen2DVec(vec,cols,1);
+
+ cout.setf(ios_base::fixed, ios_base::floatfield);
+ cout.precision(6);//This formats the data so the tables look pretty.
+
+ //Whittaker's measure Bw (presence/absence data)
+ cout << "Whittaker's measure Bw (presence/absence data):\n";
+ printD(columns, 1);
+ double sum = 0;
+ for(int i = 0; i < cols; i++)
+ sum += vecCalc.numNZ(columns.at(i));
+ double meanRichness = sum/cols;
+ vector<double> totVec = vecCalc.genTotVec(columns);
+ double totRichness = vecCalc.numNZ(totVec);
+ cout << "\nOverall B Diversity = " << totRichness/meanRichness << "\n\n\n";//The overall B Diversity
+
+ //Marczewski-Steinhaus(MS) distance(Jaccard index) (presence/abscence data)
+ cout << "Marczewski-Steinhaus(MS) distance(Jaccard index) (presence/abscence data):\n";
+ printD(columns, 2);
+ sum = 0;
+ for(int i = 0; i < cols; i++)
+ for(int j = 0; j < cols; j++)
+ if(j > i)
+ sum += vecCalc.numNZ(columns.at(i))+vecCalc.numNZ(columns.at(j)) - 2*vecCalc.numNZ(vecCalc.multVecs(columns.at(i), columns.at(j)));
+ cout << "\nOverall B Diversity = " << sum/cols << "\n\n\n";//The overall B Diversity
+
+ //Sorensen quantitative index (abundance data)
+ cout << "Sorensen quantitative index (abundance data):\n";
+ printD(columns, 3);
+ cout << "\n\n";
+
+ //Sorensen quantitative index (abundance data)
+ cout << "Morisita-Horn index (abundance data):\n";
+ printD(columns,4);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BDiversity class Function doBD. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BDiversity class function doBD. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+void BrokenStick::doBStick(vector<double> vec)//vec = The data vector.
+{ try {
+ VecCalc vecCalc;
+ vec = vecCalc.quicksort(vec);
+ double numInd = vecCalc.sumElements(vec);
+ double numSpec = vecCalc.numNZ(vec);
+ vector<double> cObsVec = vecCalc.genCVec(vec);
+ vector<double> cExpVec;
+ vec = vecCalc.power(vec, -1);
+ double sumExp = 0;
+ for(int i = 0; i < numSpec; i++)
+ {
+ double n = 0;
+ for(int j = i; j < numSpec; j++)
+ n += 1/(double)(j+1);
+
+ sumExp += numInd/numSpec*n;
+ cExpVec.push_back(sumExp);
+ }
+
+ //Statistical analysis
+ double maxDiff = vecCalc.findMaxDiff(cObsVec, cExpVec);
+ double DStatistic = maxDiff/numInd;
+
+ cout << "D-Statistic = " << DStatistic << "\n";
+ if(vec.size() > 30)
+ cout << "Critical value for 95% confidence interval = " << .886/sqrt(vec.size()) << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BrokenStick class Function doBStick. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BrokenStick class function doBStick. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+double kEq(double k, double spec)
+{
+ return k/(1-k)*pow(1-k, spec)/(1-pow(1-k, spec));
+}
+/***********************************************************************/
+void GeometricSeries::doGeomTest(vector<double> vec)//vec = the data vector
+{ try {
+ VecCalc vecCalc;
+ vec = vecCalc.quicksort(vec);//Sorts vec
+ double numInd = vecCalc.sumElements(vec);//numInd = The total number of individuals in the data set.
+ double numSpec = vecCalc.numNZ(vec);//numSpec = the number of nonzero elements in the data set.
+ double min = -1.0*vecCalc.findMax(vecCalc.multiply(vec, -1));
+ double k = .5;
+ double step = .49999;
+ while(fabs(min - numInd*kEq(k, numSpec)) > .0001)//This uses a binary search to find the value of k.
+ {
+ if(numInd*kEq(k, numSpec) > min)
+ k += step;
+ else
+ k -= step;
+ step /= 2;
+ }
+ cout << "k = " << k << "\n";
+ double cK = 1/(1-pow(1-k, numSpec));
+
+ vector<double> cObsVec = vecCalc.genCVec(vec);
+ vector<double> cExpVec;
+ double sumExp = 0;
+ for(int i = 0; i < vec.size(); i++)
+ {
+ sumExp += numInd*cK*k*pow(1-k, i);
+ cExpVec.push_back(sumExp);
+ }
+ double maxDiff = vecCalc.findMaxDiff(cObsVec, cExpVec);
+ double DStatistic = maxDiff/numInd;
+
+ //Statistical Analysis
+ cout << "D-Statistic = " << DStatistic << "\n";
+ if(vec.size() > 30)
+ cout << "Critical value for 95% confidence interval = " << .886/sqrt(vec.size()) << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the GeometricSeries class Function doGeomTest. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the GeometricSeries class function doGeomTest. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+void Jackknifing::doJK(vector<double> vec, double cols)//vec = the data vector if the data table was read left-to-right, top-to-bottom. cols = The number of columns in the data table.
+{ try {
+ VecCalc vecCalc;
+ SSBPDiversityIndices ssbp;
+ double rows = vec.size()/cols;
+ vector<vector<double> > species = vecCalc.gen2DVec(vec, rows, 0);//converts vec into a 2 dimensional vector
+ vector<double> sumRows;
+ vector<double> pVals;
+
+ for(int i = 0; i < rows; i++)
+ sumRows.push_back(vecCalc.sumElements(species.at(i)));
+ double st = 1/ssbp.getSimp(sumRows);//The observed estimate using the Simpson Index. Can be changed to use other indexes of diversity.
+ for(int i = 0; i < cols; i++)
+ {
+ vector<double> newVec;
+ for(int j = 0; j < rows; j++)
+ newVec.push_back(vecCalc.sumElements(species.at(j))-species.at(j).at(i));
+ pVals.push_back(cols*st-((cols-1)/ssbp.getSimp(newVec)));
+ }
+
+ double mean = vecCalc.mean(pVals);
+ double stErr = vecCalc.stError(pVals);//stErr = standard error
+ TDTable table;
+ double confidence = .95;
+ double confLimit;
+ cout << "Confidence Level (.8, .9, .95, .98, .99, .998, .999): ";
+ cin >> confidence;
+ double confLevels[] = {.80,.90,.95,.98,.99,.998,.999};
+ for(int i = 0; i < 7; i++)
+ if(confidence == confLevels[i])
+ {
+ confLimit = table.getConfLimit(cols-2,i);
+ i = 7;
+ }
+
+ //Statistical Analysis
+ cout << "Lower limit = " << mean - confLimit*stErr << "\n";
+ cout << "Upper limit = " << mean + confLimit*stErr << "\n";
+ cout << "Observed estimate = " << st << "\n\n";
+ cout << "Jackknifed estimate = " << mean << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Jackknifing class Function doJK. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Jackknifing class function doJK. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+void KS2SampleTest::doKSTest(vector<double> abun1, vector<double> abun2)//abun1 = 1st vector of abundances, abun2 = 2nd vector of abundances
+{ try {
+ VecCalc vecCalc;
+ double numNZ1 = vecCalc.numNZ(abun1);//Number of nonzero elements in abun1
+ double numNZ2 = vecCalc.numNZ(abun2);//Number of nonzero elements in abun2
+ abun1 = vecCalc.quicksort(abun1);//Sorts abun1
+ abun2 = vecCalc.quicksort(abun2);//Sorts abun2
+ abun1 = vecCalc.genRelVec(abun1);//Generates the relative vector for abun1
+ abun2 = vecCalc.genRelVec(abun2);//Generates the relative vector for abun2
+
+ abun1 = vecCalc.genCVec(abun1);//Generates the cumulative vector for abun1
+ abun2 = vecCalc.genCVec(abun2);//Generates the cumulative vector for abun2
+
+ double maxDiff = vecCalc.findMaxDiff(abun1, abun2);
+ double DStatistic = maxDiff*numNZ1*numNZ2;
+
+ cout << "Null Hypothesis = There is no difference.\n";
+ cout << "D-Statistic = " << DStatistic << "\n";
+
+ double a = pow((numNZ1 + numNZ2)/(numNZ1*numNZ2),.5);
+ double pVal = exp(-2*pow(maxDiff/a,2));
+
+ if(numNZ1 > 25 && numNZ2 > 25) //If the sample sizes are both bigger than 25.
+ cout << "P-Value = " << pVal << "\n\n";
+ else
+ {
+ cout << "D-Statistic must be higher than the critical value to reject the null hypothesis.\n" ;
+ cout << "90% Confidence Critical Value = " << 1.22*a*numNZ1*numNZ2 << "\n";
+ cout << "95% Confidence Critical Value = " << 1.36*a*numNZ1*numNZ2 << "\n";
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the KS2SampleTest class Function doKSTest. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the KS2SampleTest class function doKSTest. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+double logS(double num)
+{
+ return -(1-num)*log(1-num)/num;
+}
+
+/***********************************************************************/
+void LogSD::doLogSD(vector<double> indVec, vector<double> specVec) //indVec = individuals vector, specVec = species vector
+{ try {
+ VecCalc vecCalc;
+ double numSpec = vecCalc.sumElements(specVec);//numSpec = The total number of species
+ cout << "number of species = " << numSpec << "\n";
+ double numInd = vecCalc.sumElements(vecCalc.multVecs(indVec, specVec));
+ double snRatio = numSpec/numInd;
+ double x = .5;
+ double step = .4999999999;
+ while(fabs(snRatio - logS(x)) > .00001) //This uses a binary search to find the value of x.
+ {
+ if(logS(x) > snRatio)
+ x += step;
+ else
+ x -= step;
+ step /= 2;
+ }
+ double alpha = numInd*(1-x)/x;
+
+ int ind;
+ cout << "Number of individuals:"; //Ask the user for the number of individuals.
+ cin >> ind;
+ double spec = alpha*pow(x, ind)/ind;
+ cout << "Number of species expected = " << spec << "\n" << "X value = " << x << "\n" << "Alpha value= " << alpha << "\n";//Outputs the number of species expected with the given number of individuals.
+
+ vector<double> obsSpec;
+ vector<double> cObsSpec;
+ vector<double> expSpec;
+ vector<double> cExpSpec;
+ vector<double> cDiff;
+
+ // Generates the cumulative observed species vector.
+ int oct = 1;
+ double octSumObs = 0;
+ for(int y = 0; y < specVec.size(); y++)
+ {
+ if(indVec.at(y) - .5 < pow(2.0, oct))
+ octSumObs += specVec.at(y);
+ else
+ {
+ obsSpec.push_back(octSumObs);
+ octSumObs = specVec.at(y);
+ oct++;
+ }
+ if(y == specVec.size()-1)
+ obsSpec.push_back(octSumObs);
+ }
+ cObsSpec = vecCalc.genCVec(obsSpec);
+ cObsSpec = vecCalc.add(cObsSpec,-.5);
+
+ // Generates the cumulative expected species vector.
+ oct = 1;
+ double octSumExp = 0;
+ for(int g = 1; g <= indVec.at(indVec.size()-1); g++)
+ {
+ if(g - .5 < pow(2.0, oct))
+ octSumExp += alpha*pow(x,g)/(g);
+ else
+ {
+ expSpec.push_back(octSumExp);
+ octSumExp = alpha*pow(x,g)/(g);
+ oct++;
+ }
+ if(g == indVec.at(indVec.size()-1))
+ expSpec.push_back(octSumExp);
+ }
+ cExpSpec = vecCalc.genCVec(expSpec);
+
+ // Statistical Analysis
+ double dTStat = vecCalc.findDStat(cObsSpec, cExpSpec, numSpec);
+ cout << "D Test Statistic = " << dTStat << "\n";
+ cout << ".05 confidence value = " << .89196/sqrt(numSpec) << "\n";
+ cout << ".01 confidence value = " << 1.0471/sqrt(numSpec) << "\n\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the LogSD class Function doLogSD. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the LogSD class function doLogSD. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+void QStatistic::doQStat(vector<double> vec)//vec = The data vector.
+{ try {
+ VecCalc vecCalc;
+ vector<double> cVec = vecCalc.genCSVec(vec);
+ vector<int> q = vecCalc.findQuartiles(cVec);//q.at(0) is the index of the first quartile; q.at(1) is the index of the second quartile.
+ vector<double> nDupVec = vecCalc.remDup(vec);//nDupVec only contains one of every unique element in cVec.
+ double Q;
+ if(q.at(0) != 0)//The case if neither quartile is 0 or 1
+ Q = (.5*(cVec.at(q.at(0))-cVec.at(q.at(0)-1)) + (cVec.at(q.at(1)-1)-cVec.at(q.at(0))) + .5*(cVec.at(q.at(1))-cVec.at(q.at(1)-1)))/log(nDupVec.at(nDupVec.size()-1-q.at(1))/nDupVec.at(nDupVec.size()-1-q.at(0)));
+ else if(q.at(0) == 0 && (q.at(1) == 0 || q.at(1) == 1))//The case if the quartiles are both at index 0 or one is at 0 and the other at 1.
+ Q = (.5*cVec.at(0) + .5*(cVec.at(1)-cVec.at(0)))/log(nDupVec.at(nDupVec.size()-2)/nDupVec.at(nDupVec.size()-1));
+ else if(q.at(0) == 0 && q.at(1) > 1) //The case if the lower quartile is at index 0 and upper quartile index is above index 1.
+ Q = (.5*cVec.at(0) + (cVec.at(q.at(1)-1)-cVec.at(q.at(0))) + .5*(cVec.at(q.at(1))-cVec.at(q.at(1)-1)))/log(nDupVec.at(nDupVec.size()-1-q.at(1))/nDupVec.at(nDupVec.size()-1));
+
+ cout << "Q = " << Q << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the QStatistic class Function doQStat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the QStatistic class function doQStat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double SSBPDiversityIndices::getShan(vector<double> vec)//vec = The data vector.
+{ try {
+ VecCalc vecCalc;
+ double nz = vecCalc.numNZ(vec);
+ double nSum = vecCalc.sumElements(vec);
+ double H = 0;
+ for(int i = 0; i < nz; i++)
+ H += vec.at(i)/nSum*log(vec.at(i)/nSum);
+ H *= -1;
+ return H;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SSBPDiversityIndices class Function getShan. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SSBPDiversityIndices class function getShan. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double SSBPDiversityIndices::getSimp(vector<double> vec)//vec = The data vector.
+{ try {
+ VecCalc vecCalc;
+ double nSum = vecCalc.sumElements(vec);
+ double D = 0;
+ for(int j = 0; j < vec.size(); j++)
+ D += vec.at(j)*(vec.at(j)-1)/(nSum*(nSum-1));
+ return D;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SSBPDiversityIndices class Function getSimp. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SSBPDiversityIndices class function getSimp. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double SSBPDiversityIndices::getBP(vector<double> vec)//vec = The data vector.
+{ try {
+ VecCalc vecCalc;
+ double nSum = vecCalc.sumElements(vec);
+ return vecCalc.findMax(vec)/nSum;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SSBPDiversityIndices class Function getBP. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SSBPDiversityIndices class function getBP. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+void SSBPDiversityIndices::doSSBP(vector<double> vec)//vec = The data vector.
+{ try {
+ VecCalc vecCalc;
+ double nz = vecCalc.numNZ(vec);
+
+ //Shannon index
+ double H = getShan(vec);
+ cout << "H = " << H << "\n";
+ cout << "Eveness = " << H/log(nz) << "\n\n";
+
+ //Simpson index
+ double D = getSimp(vec);
+ cout << "D diversity = " << 1/D << "\n";
+ cout << "Eveness = " << 1/D/nz << "\n\n";
+
+ //Berger-Parker index
+ double BP = getBP(vec);
+ cout << "BP index = " << BP << "\n\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SSBPDiversityIndices class Function doSSBP. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SSBPDiversityIndices class function doSSBP. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+double TDTable::getConfLimit(int row, int col) //Rows are the degrees of freedom
+{ try {
+ //Confidence Level .80 .90 .95 .98 .99 .998 .999
+ double values[33][7] = {{3.078, 6.314, 12.706, 31.821, 63.656, 318.289, 636.578},
+ {1.886, 2.920, 4.303, 6.965, 9.925, 22.328, 31.600},
+ {1.638, 2.353, 3.182, 4.541, 5.841, 10.214, 12.924},
+ {1.533, 2.132, 2.776, 3.747, 4.604, 7.173, 8.610},
+ {1.476, 2.015, 2.571, 3.365, 4.032, 5.894, 6.869},
+ {1.440, 1.943, 2.447, 3.143, 3.707, 5.208, 5.959},
+ {1.415, 1.895, 2.365, 2.998, 3.499, 4.785, 5.408},
+ {1.397, 1.860, 2.306, 2.896, 3.355, 4.501, 5.041},
+ {1.383, 1.833, 2.262, 2.821, 3.250, 4.297, 4.781},
+ {1.372, 1.812, 2.228, 2.764, 3.169, 4.144, 4.587},
+ {1.363, 1.796, 2.201, 2.718, 3.106, 4.025, 4.437},
+ {1.356, 1.782, 2.179, 2.681, 3.055, 3.930, 4.318},
+ {1.350, 1.771, 2.160, 2.650, 3.012, 3.852, 4.221},
+ {1.345, 1.761, 2.145, 2.624, 2.977, 3.787, 4.140},
+ {1.341, 1.753, 2.131, 2.602, 2.947, 3.733, 4.073},
+ {1.337, 1.746, 2.120, 2.583, 2.921, 3.686, 4.015},
+ {1.333, 1.740, 2.110, 2.567, 2.898, 3.646, 3.965},
+ {1.330, 1.734, 2.101, 2.552, 2.878, 3.610, 3.922},
+ {1.328, 1.729, 2.093, 2.539, 2.861, 3.579, 3.883},
+ {1.325, 1.725, 2.086, 2.528, 2.845, 3.552, 3.850},
+ {1.323, 1.721, 2.080, 2.518, 2.831, 3.527, 3.819},
+ {1.321, 1.717, 2.074, 2.508, 2.819, 3.505, 3.792},
+ {1.319, 1.714, 2.069, 2.500, 2.807, 3.485, 3.768},
+ {1.318, 1.711, 2.064, 2.492, 2.797, 3.467, 3.745},
+ {1.316, 1.708, 2.060, 2.485, 2.787, 3.450, 3.725},
+ {1.315, 1.706, 2.056, 2.479, 2.779, 3.435, 3.707},
+ {1.314, 1.703, 2.052, 2.473, 2.771, 3.421, 3.689},
+ {1.313, 1.701, 2.048, 2.467, 2.763, 3.408, 3.674},
+ {1.311, 1.699, 2.045, 2.462, 2.756, 3.396, 3.660},
+ {1.310, 1.697, 2.042, 2.457, 2.750, 3.385, 3.646},
+ {1.296, 1.671, 2.000, 2.390, 2.660, 3.232, 3.460},
+ {1.289, 1.658, 1.980, 2.358, 2.617, 3.160, 3.373},
+ {1.282, 1.645, 1.960, 2.326, 2.576, 3.091, 3.291}};
+ return values[row][col];
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the TDTable class Function getConfLimit. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the TDTable class function getConfLimit. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************
+void TrunLN::doTrunLN(vector<double> indVec, vector<double> specVec) //indVec = individuals vector, specVec = species vector
+{
+ VecCalc vecCalc;
+ double numSpec = vecCalc.sumElements(specVec); //numSpec = The total number of species
+ double numInd = vecCalc.sumElements(vecCalc.multVecs(indVec,specVec)); //numInd = The total number of individuals
+
+ double obsMean = 0;
+ for(int i = 0; i < indVec.size(); i++)
+ obsMean += log10(indVec.at(i));
+ obsMean /= numSpec; //obsMean = observed mean of the individuals vector
+ cout << "obsMean = " << obsMean << "\n";
+ double variance = 0;
+ for(int t = 0; t < indVec.size(); t++)
+ variance += pow(log10(indVec.at(t))-obsMean,2)/numSpec;
+
+ double rO = 0;
+ for(int k = 0; k < indVec.size(); k++)
+ rO += log10(indVec.at(k));
+ rO /= indVec.size();
+ double veilLine = .5;//The desired veil line.
+ double auxFunc = -(obsMean-rO)/(obsMean-log10(veilLine));
+ double uX = obsMean-auxFunc*(obsMean-log10(veilLine));
+ double vX = variance + auxFunc*pow(obsMean-log10(veilLine),2);
+ double z = (log10(veilLine)-uX)/pow(vX, .5);
+ double p = .5*(erf(z)+1);
+ double specRichness = numSpec/(1-p);
+
+ double numUnseen = .5*(erf((log10(.5)-uX)/pow(vX,.5))+1)*specRichness;
+
+
+ vector<double> cExp;
+ for(int i = 1; i < 8; i++)
+ {
+ double a = pow(10, i-1)+.5;
+ double b = log10(a);
+ double c = (b - uX)/pow(vX,.5);
+ double d = .5*(erf(c)+1);
+ double numS = d*specRichness;
+ double toPush = numS - numUnseen;
+ cExp.push_back(toPush);
+ }
+ vector<double> cObs;
+ double sumOct = 0;
+ for(int i = 0; i < 8; i++)
+ {
+ sumOct = 0;
+ for(int r = 0; r < indVec.size(); r++)
+ {
+ if(indVec.at(r) < pow(10, i-1)+.5)
+ sumOct += specVec.at(r);
+ else
+ {
+ cObs.push_back(sumOct);
+ sumOct = specVec.at(r);
+ r = indVec.size();
+ }
+ if(r == indVec.size()-1)
+ cObs.push_back(sumOct);
+ }
+ }
+
+ //Statistical Analysis
+ double d = vecCalc.findDStat(cExp, cObs, numSpec);
+ cout << "DStat = " << d << "\n";
+ cout << ".05 confidence value = " << .89196/sqrt(numSpec) << "\n";
+ cout << ".01 confidence value = " << 1.0471/sqrt(numSpec) << "\n\n";
+}
+/***********************************************************************/
projects / mothur.git / blobdiff