+++ /dev/null
-#include "trialswap2.h"
-
-
-//The sum_of_squares, havel_hakimi and calc_c_score algorithms have been adapted from I. Miklos and J. Podani. 2004. Randomization of presence-absence matrices: comments and new algorithms. Ecology 85:86-92.
-
-
-double TrialSwap2::calc_c_score (vector<vector<int> > &co_matrix, vector<int> rowtotal, int ncols, int nrows)
-{
- try {
- double cscore = 0.0;
- double maxD;
- double D;
- double normcscore = 0.0;
- int nonzeros = 0;
- //int ncols = co_matrix[0].size(); int nrows = rowtotal.size();
- vector<vector<double> > s; s.resize(nrows);
- for (int i = 0; i < nrows; i++) { s[i].resize(nrows,0.0); }//only fill half the matrix
-
-
- for(int i=0;i<nrows-1;i++)
- {
-
- for(int j=i+1;j<nrows;j++)
- {
- if (m->control_pressed) { return 0; }
- for(int k=0;k<ncols;k++)
- {
- if((co_matrix[i][k]==1)&&(co_matrix[j][k]==1)) //if both are 1s ie co-occurrence
- s[i][j]++; //s counts co-occurrences
- }
-
- //rowtotal[i] = A, rowtotal[j] = B, ncols = P, s[i][j] = J
- cscore += (rowtotal[i]-s[i][j])*(rowtotal[j]-s[i][j]);///(nrows*(nrows-1)/2);
- D = (rowtotal[i]-s[i][j])*(rowtotal[j]-s[i][j]);
-
- if(ncols < (rowtotal[i] + rowtotal[j]))
- {
- maxD = (ncols-rowtotal[i])*(ncols-rowtotal[j]);
- }
- else
- {
- maxD = rowtotal[i] * rowtotal[j];
- }
-
- if(maxD != 0)
- {
- normcscore += D/maxD;
- nonzeros++;
- }
- }
- }
-
- cscore = cscore/(double)(nrows*(nrows-1)/2);
- //cout << "normalized c score: " << normcscore/nonzeros << endl;
-
- return cscore;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "calc_c_score");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int TrialSwap2::calc_checker (vector<vector<int> > &co_matrix, vector<int> rowtotal, int ncols, int nrows)
-{
- try {
- int cunits=0;
- //int s[nrows][ncols];
- //int ncols = co_matrix[0].size(); int nrows = rowtotal.size();
- vector<vector<int> > s; s.resize(nrows);
- for (int i = 0; i < nrows; i++) { s[i].resize(nrows,0); }//only fill half the matrix
-
- for(int i=0;i<nrows-1;i++)
- {
- for(int j=i+1;j<nrows;j++)
- {
- if (m->control_pressed) { return 0; }
- //s[i][j]=0;
- for(int k=0;k<ncols;k++)
- {
- //cout << s[i][j] << endl;
- //iterates through the row and counts co-occurrences. The total number of co-occurrences for each row pair is kept in matrix s at location s[i][j].
- if((co_matrix[i][k]==1)&&(co_matrix[j][k]==1)) //if both are 1s ie co-occurrence
- s[i][j]++; //s counts co-occurrences
-
- }
- //cout << "rowtotal: " << rowtotal[i] << endl;
- //cout << "co-occurrences: " << s[i][j] << endl;
- //cunits+=(rowtotal[i]-s[i][j])*(rowtotal[j]-s[i][j]);
- if (s[i][j] == 0)
- {
- cunits+=1;
- }
- //cunits+=s[i][j];
- }
- }
-
- return cunits;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "calc_checker");
- exit(1);
- }
-}
-/**************************************************************************************************/
-double TrialSwap2::calc_vratio (int nrows, int ncols, vector<int> rowtotal, vector<int> columntotal)
-{
- try {
- //int nrows = rowtotal.size();
- //int ncols = columntotal.size();
- int sumCol = accumulate(columntotal.begin(), columntotal.end(), 0 );
- // int sumRow = accumulate(rowtotal.begin(), rowtotal.end(), 0 );
-
- double colAvg = (double) sumCol / (double) ncols;
- // double rowAvg = (double) sumRow / (double) nrows;
-
- double p = 0.0;
-
- // double totalRowVar = 0.0;
- double rowVar = 0.0;
- double colVar = 0.0;
-
- for(int i=0;i<nrows;i++)
- {
- if (m->control_pressed) { return 0; }
- p = (double) rowtotal[i]/(double) ncols;
- rowVar += p * (1.0-p);
- }
-
- for(int i=0;i<ncols;i++)
- {
- if (m->control_pressed) { return 0; }
- colVar += pow(((double) columntotal[i]-colAvg),2);
- }
-
- colVar = (1.0/(double)ncols) * colVar;
-
- return colVar/rowVar;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "calc_vratio");
- exit(1);
- }
-
-}
-/**************************************************************************************************/
-int TrialSwap2::calc_combo (int nrows, int ncols, vector<vector<int> > &nullmatrix)
-{
- try {
- //need to transpose so we can compare rows (row-major order)
- int tmpnrows = nrows;
- vector<vector<int> > tmpmatrix;
-
- vector<int> tmprow;
- if(!tmpmatrix.empty())
- tmpmatrix.clear();
- for (int i=0;i<ncols;i++)
- {
- for (int j=0;j<nrows;j++)
- {
- tmprow.push_back(nullmatrix[j][i]);
- }
-
- tmpmatrix.push_back(tmprow);
- tmprow.clear();
- }
-
- int unique = 0;
- int match = 0;
- for(int j=0;j<ncols;j++)
- {
- match = 0;
- for(int i=j+1;i<=ncols;i++)
- {
- //comparing matrix rows
- if( (tmpmatrix[j] == tmpmatrix[i]))
- {
- match++;
- break;
- }
- }
-
- //on the last iteration of a previously matched row it will add itself because it doesn't match any following rows, so that combination is counted
- if (match == 0)
- unique++;
- }
- return unique;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "calc_combo");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int TrialSwap2::swap_checkerboards (vector<vector<int> > &co_matrix, int ncols, int nrows)
-{
- try {
- //do 100 runs to make sure enough swaps are happening. This does NOT mean that there will be 1000 swaps, but that is the theoretical max.
- for(int a=0;a<1000;a++){
- int i, j, k, l;
- i = m->getRandomIndex(nrows-1);
- while((j = m->getRandomIndex(nrows-1) ) == i ) {;if (m->control_pressed) { return 0; }}
- k = m->getRandomIndex(ncols-1);
- while((l = m->getRandomIndex(ncols-1)) == k ) {;if (m->control_pressed) { return 0; }}
-
- if((co_matrix[i][k]*co_matrix[j][l]==1 && co_matrix[i][l]+co_matrix[j][k]==0)||(co_matrix[i][k]+co_matrix[j][l]==0 && co_matrix[i][l]*co_matrix[j][k]==1)) //checking for checkerboard value and swap
- {
- co_matrix[i][k]=1-co_matrix[i][k];
- co_matrix[i][l]=1-co_matrix[i][l];
- co_matrix[j][k]=1-co_matrix[j][k];
- co_matrix[j][l]=1-co_matrix[j][l];
-
- }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "swap_checkerboards");
- exit(1);
- }
-}
-/**************************************************************************************************/
-double TrialSwap2::calc_pvalue_greaterthan (vector<double> scorevec, double initialscore)
-{
- try {
- int runs = scorevec.size();
- double p = 0.0;
- for( int i=0;i<runs;i++)
- {
- if (m->control_pressed) { return 0; }
- if(scorevec[i]>=initialscore)
- p++;
- }
- return p/(double)runs;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "calc_pvalue_greaterthan");
- exit(1);
- }
-}
-/**************************************************************************************************/
-double TrialSwap2::calc_pvalue_lessthan (vector<double> scorevec, double initialscore)
-{
- try {
- int runs = scorevec.size();
- double p = 0.0;
- for( int i=0;i<runs;i++)
- {
- if (m->control_pressed) { return 0; }
- if(scorevec[i]<=initialscore)
- p++;
- }
- return p/(double)runs;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "calc_pvalue_lessthan");
- exit(1);
- }
-}
-/**************************************************************************************************/
-double TrialSwap2::t_test (double initialscore, int runs, double nullMean, vector<double> scorevec)
-{
- try {
- double t;
- double sampleSD;
- double sum = 0;
-
- for(int i=0;i<runs;i++)
- {
- if (m->control_pressed) { return 0; }
- sum += pow((scorevec[i] - nullMean),2);
- //cout << "scorevec[" << i << "]" << scorevec[i] << endl;
- }
-
- m->mothurOut("nullMean: " + toString(nullMean)); m->mothurOutEndLine();
-
- m->mothurOut("sum: " + toString(sum)); m->mothurOutEndLine();
-
- sampleSD = sqrt( (1/runs) * sum );
-
- m->mothurOut("samplSD: " + toString(sampleSD)); m->mothurOutEndLine();
-
- t = (nullMean - initialscore) / (sampleSD / sqrt(runs));
-
- return t;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "t_test");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int TrialSwap2::print_matrix(vector<vector<int> > &matrix, int nrows, int ncols)
-{
- try {
- m->mothurOut("matrix:"); m->mothurOutEndLine();
-
- for (int i = 0; i < nrows; i++)
- {
- if (m->control_pressed) { return 0; }
- for (int j = 0; j < ncols; j++)
- {
- m->mothurOut(toString(matrix[i][j]));
- }
- m->mothurOutEndLine();
- }
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "print_matrix");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-
-
-
-
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