//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;