//burn-in for sim9
if(matrix == "sim9") {
- for(int i=0;i<10000;i++) trial.swap_checkerboards (co_matrix, rowtotal, columntotal, ncols, nrows);
+ for(int i=0;i<10000;i++) trial.swap_checkerboards (co_matrix, ncols, nrows);
}
//populate null matrix from probability matrix, do this a lot.
- for(int i=0;i<runs;i++){
+ for(int k=0;k<runs;k++){
nullmatrix.clear();
//zero-fill the null matrix
nullmatrix.assign(nrows, vector<int>(ncols, 0));
else if(matrix == "sim4") {
for(int i=0;i<nrows;i++) {
- previous = 0.0;
count = 0;
while(count < rowtotal[i]) {
+ previous = 0.0;
randnum = rand() / double(RAND_MAX);
for(int j=0;j<ncols;j++) {
current = probabilityMatrix[ncols * i + j];
//swap_checkerboards takes the original matrix and swaps checkerboards
else if(matrix == "sim9") {
- trial.swap_checkerboards (co_matrix, rowtotal, columntotal, ncols, nrows);
+ trial.swap_checkerboards (co_matrix, ncols, nrows);
}
else {
m->mothurOut("[ERROR]: No null model selected!\n\n"); m->control_pressed = true;
}
}
/**************************************************************************************************/
-int TrialSwap2::swap_checkerboards (vector<vector<int> > &co_matrix, vector<int> rowtotal, vector<int> columntotal, int ncols, int nrows)
+int TrialSwap2::swap_checkerboards (vector<vector<int> > &co_matrix, int ncols, int nrows)
{
try {
- int ncols = co_matrix[0].size(); int nrows = co_matrix.size();
+ //int ncols = co_matrix[0].size(); int nrows = co_matrix.size();
int i, j, k, l;
i = m->getRandomIndex(nrows-1);
while((j = m->getRandomIndex(nrows-1) ) == i ) {;if (m->control_pressed) { return 0; }}
double calc_pvalue_lessthan (vector<double>, double);
double calc_pvalue_greaterthan (vector<double>, double);
- void swap_checkerboards (vector<vector<int> > &, vector<int>, vector<int>, int, int);
+ int swap_checkerboards (vector<vector<int> > &, int, int);
int calc_combo (int, int, vector<vector<int> > &);
double calc_vratio (int, int, vector<int>, vector<int>);
int calc_checker (vector<vector<int> > &, vector<int>, int, int);