exit(1);
}
}
+/***********************************************************************/
+int VecCalc::sumElements(vector<int> vec){
+ try {
+ return sumElements(vec,0);
+ }
+ 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);
+ }
+}
+/***********************************************************************/
+int VecCalc::sumElements(vector<int> vec, int index){
+ try {
+ int 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::sumElements(vector<double> vec){
try {
}
}
/***********************************************************************/
+int VecCalc::numNZ(vector<int> vec){
+ try {
+ int 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::numNZ(vector<double> vec){
try {
double numNZ = 0;
}
}
/***********************************************************************/
-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.
return k/(1-k)*pow(1-k, spec)/(1-pow(1-k, spec));
}
/***********************************************************************/
-void GeometricSeries::doGeomTest(vector<double> vec)//vec = the data vector
+/*void GeometricSeries::doGeomTest(vector<double> vec)//vec = the data vector
{ try {
VecCalc vecCalc;
vec = vecCalc.quicksort(vec);//Sorts vec
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.
}
/***********************************************************************/
-void LogSD::doLogSD(vector<double> indVec, vector<double> specVec) //indVec = individuals vector, specVec = species vector
+/*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 << "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 {
/***********************************************************************/
double TDTable::getConfLimit(int row, int col) //Rows are the degrees of freedom
{ try {
- //Confidence Level .80 .90 .95 .98 .99 .998 .999
+ //Found on http://www.vgtu.lt/leidiniai/elektroniniai/Probability.pdf/Table%203.pdf
+
+ //Confidence Level .90 .95 .975 .99 .995 .999 .9995
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}};
+ {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) {
exit(1);
}
}
+
+/***********************************************************************/
+double KOSTable::getConfLimit(int index) //Table of Critical values for N = 4-20 for One-Sample Kolmogorov-Smirnov Test
+{ try {
+ //Confidence Level = .05
+ //Sample size = 4-20.
+ //Found on http://www.utdallas.edu/~herve/MolinAbdi1998-LillieforsTechReport.pdf
+
+ double values[21] = {.9011,
+ .6372,
+ .5203,
+ .4506,
+ 0.3754,
+ 0.3427,
+ 0.3245,
+ 0.3041,
+ 0.2875,
+ 0.2744,
+ 0.2616,
+ 0.2506,
+ 0.2426,
+ 0.2337,
+ 0.2257,
+ 0.2196,
+ 0.2128,
+ 0.2071,
+ 0.2018,
+ 0.1965,
+ 0.1920,
+ };
+ return values[index];
+ }
+ 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
{
projects / mothur.git / blobdiff