-/**************************************************************************************************/
-int TrialSwap2::sim1(vector<vector<int> > &co_matrix){
- try {
- vector<int> randRow;
- vector<vector<int> > tmpmatrix;
- int nrows = co_matrix.size();
- int ncols = co_matrix[0].size();
-
- //clear co_matrix
- // for(i=0;i<nrows;i++)
- // {
- // co_matrix.clear();
- // }
-
- //cout << "building matrix" << endl;
- for(int i=0;i<nrows;i++){
- if (m->control_pressed) { break; }
-
- for(int j=0;j<ncols;j++){
- double randNum = rand() / double(RAND_MAX);
- //cout << randNum << endl;
-
- if(randNum > 0.5) {
- randRow.push_back(1);
- }else{
- randRow.push_back(0);
- }
- }
- tmpmatrix.push_back(randRow);
- randRow.clear();
- //cout << endl;
- }
- co_matrix = tmpmatrix;
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim1");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/*
- *row sums fixed, columns equiprobable
- */
-void TrialSwap2::sim2(vector<vector<int> > &co_matrix)
-{
- try {
-
- for(int i=0;i<co_matrix.size();i++)
- {
- if (m->control_pressed) { break; }
- random_shuffle( co_matrix[i].begin(), co_matrix[i].end() );
- }
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim2");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int TrialSwap2::sim2plus(vector<int> rowtotal, vector<vector<int> > &co_matrix)
-{
- try {
- int nrows = co_matrix.size();
- int ncols = co_matrix[0].size();
- double cellprob = 1.0/ncols;
- vector<double> cellprobvec;
- vector<int> tmprow;
- vector<vector<int> > tmpmatrix;
- //double randNum;
-
- double start = 0.0;
-
- for(int i=0; i<ncols; i++)
- {
- if (m->control_pressed) { return 0; }
- cellprobvec.push_back(start + cellprob);
- start = cellprobvec[i];
- }
-
- for(int i=0; i<nrows; i++)
- {
- tmprow.assign(ncols, 0);
-
- while( accumulate( tmprow.begin(), tmprow.end(), 0 ) < rowtotal[i])
- {
- if (m->control_pressed) { return 0; }
- double randNum = rand() / double(RAND_MAX);
- //cout << randNum << endl;
- if(randNum <= cellprobvec[0])
- {
- tmprow[0] = 1;
- continue;
- }
- for(int j=1;j<ncols;j++)
- {
- //cout << range[j] << endl;
- if(randNum <= cellprobvec[j] && randNum > cellprobvec[j-1] && tmprow[j] != 1)
- {
- tmprow[j] = 1;
- }
- }
- }
- tmpmatrix.push_back(tmprow);
- tmprow.clear();
- }
- co_matrix = tmpmatrix;
- tmpmatrix.clear();
- cellprobvec.clear();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim2plus");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/*
- * same as sim2 but using initmatrix which is the initial co-occurrence matrix before transposition
- * may have to be changed depending on what matrix 'seed' is used. One way to use is to transpose
- * every null matrix before using an index and use the random matrix as a seed for the next null.
- */
-/**************************************************************************************************/
-void TrialSwap2::sim3(vector<vector<int> > &initmatrix)
-{
- try {
- for(int i=0;i<initmatrix.size();i++)
- {
- if (m->control_pressed) { break; }
- random_shuffle( initmatrix[i].begin(), initmatrix[i].end() );
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim3");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/*
- *
- *
- *
- */
-/**************************************************************************************************/
-int TrialSwap2::sim4(vector<int> columntotal, vector<int> rowtotal, vector<vector<int> > &co_matrix)
-{
- try {
- vector<double> colProb;
- vector<int> tmprow;//(ncols, 7);
- vector<vector<int> > tmpmatrix;
- vector<double> range;
- vector<double> randNums;
- int ncols = columntotal.size();
- int nrows = rowtotal.size();
- tmprow.clear();
-
- double colSum = accumulate( columntotal.begin(), columntotal.end(), 0 );
- //cout << "col sum: " << colSum << endl;
- for(int i=0;i<ncols;i++)
- {
- if (m->control_pressed) { return 0; }
- colProb.push_back(columntotal[i]/colSum);
- }
-
- double start = 0.0;
-
- for(int i=0;i<ncols;i++)
- {
- if (m->control_pressed) { return 0; }
- range.push_back(start + colProb[i]);
- start = range[i];
- }
-
- for(int i=0;i<nrows;i++)
- {
- tmprow.assign(ncols, 0);
- if (m->control_pressed) { return 0; }
-
- while ( accumulate( tmprow.begin(), tmprow.end(), 0 ) < rowtotal[i])
- {
- if (m->control_pressed) { return 0; }
-
- double randNum = rand() / double(RAND_MAX);
- if(randNum <= range[0])
- {
- tmprow[0] = 1;
- continue;
- }
- for(int j=1;j<ncols;j++)
- {
- if(randNum <= range[j] && randNum > range[j-1] && tmprow[j] != 1)
- {
- tmprow[j] = 1;
- }
-
- }
- }
- tmpmatrix.push_back(tmprow);
- tmprow.clear();
- }
-
- co_matrix = tmpmatrix;
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim4");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/*
- * inverse of sim4, MUST BE TRANSPOSED BEFORE CO-OCCURRENCE ANALYSIS
- *
- *
- */
-/**************************************************************************************************/
-int TrialSwap2::sim5(vector<int> initcolumntotal,vector<int> initrowtotal, vector<vector<int> > &initmatrix)
-{
- try {
- vector<double> colProb;
- vector<int> tmprow;//(ncols, 7);
- vector<vector<int> > tmpmatrix;
- vector<double> range;
- vector<double> randNums;
- int ncols = initcolumntotal.size();
- int nrows = initrowtotal.size();
-
- tmprow.clear();
-
- double colSum = accumulate( initcolumntotal.begin(), initcolumntotal.end(), 0 );
- //cout << "col sum: " << colSum << endl;
- for(int i=0;i<ncols;i++)
- {
- if (m->control_pressed) { return 0; }
- colProb.push_back(initcolumntotal[i]/colSum);
- }
-
- double start = 0.0;
-
- for(int i=0;i<ncols;i++)
- {
- if (m->control_pressed) { return 0; }
- range.push_back(start + colProb[i]);
- start = range[i];
- }
-
- for(int i=0;i<nrows;i++)
- {
- tmprow.assign(ncols, 0);
- if (m->control_pressed) { return 0; }
-
- while ( accumulate( tmprow.begin(), tmprow.end(), 0 ) < initrowtotal[i])
- {
- if (m->control_pressed) { return 0; }
-
- double randNum = rand() / double(RAND_MAX);
- if(randNum <= range[0])
- {
- tmprow[0] = 1;
- continue;
- }
- for(int j=1;j<ncols;j++)
- {
- if(randNum <= range[j] && randNum > range[j-1] && tmprow[j] != 1)
- {
- tmprow[j] = 1;
- }
-
- }
- }
- tmpmatrix.push_back(tmprow);
- tmprow.clear();
- }
-
- initmatrix = tmpmatrix;
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim5");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/*
- *
- *
- *
- */
-/**************************************************************************************************/
-int TrialSwap2::sim6(vector<int> columntotal, vector<vector<int> > &co_matrix)
-{
- try {
- vector<vector<int> > tmpmatrix;
- vector<double> colProb;
- vector<int> tmprow;
- vector<double> range;
- int ncols = columntotal.size();
- int nrows = co_matrix.size();
-
- int colSum = accumulate( columntotal.begin(), columntotal.end(), 0 );
-
- for(int i=0;i<ncols;i++)
- {
- if (m->control_pressed) { return 0; }
- colProb.push_back(columntotal[i]/double (colSum));
- }
-
- double start = 0.0;
-
- for(int i=0;i<ncols;i++)
- {
- if (m->control_pressed) { return 0; }
- range.push_back(start + colProb[i]);
- start = range[i];
- }
-
- for(int i=0;i<nrows;i++)
- {
- if (m->control_pressed) { return 0; }
- tmprow.assign(ncols, 0);
- int tmprowtotal;
- tmprowtotal = (rand() / double (RAND_MAX)) * 10;
- while ( tmprowtotal > ncols) {
- if (m->control_pressed) { return 0; }
- tmprowtotal = (rand() / double (RAND_MAX)) * 10;
- }
- //cout << tmprowtotal << endl;
- //cout << accumulate( tmprow.begin(), tmprow.end(), 0 ) << endl;
-
- while ( accumulate( tmprow.begin(), tmprow.end(), 0 ) < tmprowtotal)
- {
- if (m->control_pressed) { return 0; }
- double randNum = rand() / double(RAND_MAX);
- //cout << randNum << endl;
- if(randNum <= range[0])
- {
- tmprow[0] = 1;
- continue;
- }
- for(int j=1;j<ncols;j++)
- {
- //cout << range[j] << endl;
- if(randNum <= range[j] && randNum > range[j-1] && tmprow[j] != 1)
- {
- tmprow[j] = 1;
- }
-
- }
-
-
- }
-
- tmpmatrix.push_back(tmprow);
- tmprow.clear();
- }
-
- co_matrix = tmpmatrix;
- tmpmatrix.clear();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim6");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/*
- * MUST BE TRANSPOSED BEFORE CO-OCCURRENCE ANALYSIS
- *
- *
- */
-/**************************************************************************************************/
-int TrialSwap2::sim7(vector<int> initrowtotal, vector<vector<int> > &co_matrix)
-{
- try {
- vector<vector<double> > probmatrix;
- vector<vector<int> > tmpmatrix;
- vector<double> colProb;
- vector<double> probrow;
- vector<int> tmprow;
- vector<double> range;
- double nc;
- int ncols = co_matrix[0].size(); int nrows = co_matrix.size();
-
- tmpmatrix.assign(nrows, vector<int>(ncols, 0.));
-
- int rowsum = accumulate( initrowtotal.begin(), initrowtotal.end(), 0 );
-
- nc = rowsum * ncols;
- //cout << nc << endl;
-
- //assign null matrix based on probabilities
-
- double start = 0.0; // don't reset start -- probs should be from 0-1 thoughout the entire matrix
-
- for(int i=0;i<nrows;i++)
- {
- if (m->control_pressed) { return 0; }
- //cout << initrowtotal[i]/double(nc) << endl;
- double cellprob = initrowtotal[i]/double(nc);
- //cout << cellprob << endl;
- for(int j=0;j<ncols;j++)
- {
-
- probrow.push_back(start + cellprob);
- //cout << probrow[j] << endl;
- //cout << start << endl;
- start = start + cellprob;
- }
- probmatrix.push_back(probrow);
- probrow.clear();
- }
-
-
- //while(tmprowsum < rowsum)
- //for(int k=0;k<rowsum;k++)
- int k = 0;
- while(k < rowsum)
- {
- if (m->control_pressed) { return 0; }
- done:
- //cout << k << endl;
- //tmprowsum = accumulate( tmprowtotal.begin(), tmprowtotal.end(), 0 );
- double randNum = rand() / double(RAND_MAX);
- //cout << randNum << "+" << endl;
- //special case for the first entry
- if(randNum <= probmatrix[0][0] && tmpmatrix[0][0] != 1)
- {
- tmpmatrix[0][0] = 1;
- k++;
- //cout << k << endl;
- continue;
- }
-
-
- for(int i=0;i<nrows;i++)
- {
- if (m->control_pressed) { return 0; }
- for(int j=0;j<ncols;j++)
- {
- //cout << probmatrix[i][j] << endl;
- if(randNum <= probmatrix[i][j] && randNum > probmatrix[i][j-1] && tmpmatrix[i][j] != 1)
- {
- tmpmatrix[i][j] = 1;
- k++;
- //cout << k << endl;
- goto done;
- }
- //else
- //k = k-1;
- }
-
- }
-
- }
-
- co_matrix = tmpmatrix;
- return 0;
- //build probibility matrix
- /* for(int i=0;i<nrows;i++)
- {
- for(int j=0;j<ncols;j++)
- {
- probrow.push_back(rowtotal[i]/nc);
- }
- probmatrix.pushback(probrow);
- probrow.clear;
- }
- */
-
- /* int colSum = accumulate( initcolumntotal.begin(), initcolumntotal.end(), 0 );
-
- for(int i=0;i<ncols;i++)
- {
- colProb.push_back(initcolumntotal[i]/double (colSum));
- }
-
- double start = 0.0;
-
- for(int i=0;i<ncols;i++)
- {
- range.push_back(start + colProb[i]);
- start = range[i];
- }
-
- for(int i=0;i<nrows;i++)
- {
- tmprow.assign(ncols, 0);
- int tmprowtotal;
- tmprowtotal = (rand() / double (RAND_MAX)) * 10;
- while ( tmprowtotal > ncols)
- tmprowtotal = (rand() / double (RAND_MAX)) * 10;
- //cout << tmprowtotal << endl;
- //cout << accumulate( tmprow.begin(), tmprow.end(), 0 ) << endl;
-
- while ( accumulate( tmprow.begin(), tmprow.end(), 0 ) < tmprowtotal)
- {
- double randNum = rand() / double(RAND_MAX);
- //cout << randNum << endl;
- if(randNum <= range[0])
- {
- tmprow[0] = 1;
- continue;
- }
- for(int j=1;j<ncols;j++)
- {
- //cout << range[j] << endl;
- if(randNum <= range[j] && randNum > range[j-1] && tmprow[j] != 1)
- {
- tmprow[j] = 1;
- }
- }
- }
-
- tmpmatrix.push_back(tmprow);
- tmprow.clear();
- }
-
- initmatrix = tmpmatrix;
- */
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim7");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/*
- *
- *
- *
- */
-/**************************************************************************************************/
-int TrialSwap2::sim8(vector<int> columntotal, vector<int> rowtotal, vector<vector<int> > &co_matrix)
-{
- try {
- double prob;
- double start = 0.0;
- int ncols = columntotal.size(); int nrows = rowtotal.size();
- double probarray[nrows * ncols];
- double randnum;
- int grandtotal;
- int total = 0;
-
- //double colSum = accumulate( columntotal.begin(), columntotal.end(), 0 );
- double rowSum = accumulate( rowtotal.begin(), rowtotal.end(), 0 );
-
- if (m->control_pressed) { return 0; }
-
- //cout << "rowsum: " << rowSum << endl;
-
- grandtotal = rowSum;
-
- //create probability matrix with each site being between 0 and 1
- for (int i=0;i<nrows;i++) {
- if (m->control_pressed) { return 0; }
- for (int j=0;j<ncols;j++) {
- prob = (rowtotal[i] * columntotal[j])/(rowSum*rowSum);
- if (prob == 0.0)
- probarray[ncols * i + j] = -1;
- else
- probarray[ncols * i + j] = start + prob;
- //probmatrixrow.pushback(start + prob);
- start += prob;
- }
- }
- //cout << "prbarray" << endl;
- //for(int i=0;i<(nrows*ncols);i++)
- //cout << probarray[i] << " ";
- //cout << endl;
-
- //generate random muber between 0 and 1 and interate through probarray until found
- while (total < grandtotal) {
- if (m->control_pressed) { return 0; }
- randnum = rand() / double(RAND_MAX);
- //cout << "rand num: " << randnum << endl;
- if((randnum <= probarray[0]) && (probarray[0] != 2) ) {
- probarray[0] = 2;
- total++;
- continue;
- }
- for(int i=1;i<(nrows*ncols);i++) {
- if (m->control_pressed) { return 0; }
- if((randnum <= probarray[i]) && (randnum > probarray[i-1]) && (probarray[i] != 2) ) {
- probarray[i] = 2;
- total++;
- break;
- }
- else
- continue;
- }
- }
- //cout << "prbarray" << endl;
- //for(int i=0;i<(nrows*ncols);i++)
- //cout << probarray[i] << " ";
- //cout << endl;
- for(int i=0;i<nrows;i++) {
- if (m->control_pressed) { return 0; }
- for(int j=0;j<ncols;j++) {
- if(probarray[ncols * i + j] == 2)
- co_matrix[i][j] = 1;
- else
- co_matrix[i][j] = 0;
- }
- }
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TrialSwap2", "sim8");
- exit(1);
- }
-}
-/**************************************************************************************************/
-double TrialSwap2::calc_c_score (vector<vector<int> > &co_matrix,vector<int> rowtotal)