-/*int main(int argc, char *argv[])
-{
- srand (time(0));
- char* input_filename = argv[1];
- std::ifstream infile (input_filename);
-
- //skip the first line of headers
- getline(infile, line);
- //get the first line of data
- getline(infile, line);
-
- nrows = 0;
- ncols = 0;
-
- //int numspaces = 0;
- char nextChar;
-
- for (int i=0; i<int(line.length()); i++)
- {
- nextChar = line.at(i); // gets a character
- if (isspace(line[i]))
- ncols++;
- }
-
- ncols = ncols-3;
-
- cout << "number of OTUs: ";
- cout << ncols << endl;
-
- infile.close();
-
- std::ifstream infile2 (input_filename);
-
- //skip first line of headers
- getline(infile2, line);
-
- while (!infile2.eof())
- {
- getline(infile2, line);
- if (!line.empty())
- nrows++;
- }
-
- cout << "number of sites: ";
- cout << nrows << endl;
-
- infile2.close();
-
- std::ifstream infile3 (input_filename);
-
- //skip first line
- getline(infile3, line);
-
- //variables that depend on info from initial matrix
- vector<vector<int> > co_matrix;//[nrows][ncols];
- vector<vector<int> > initmatrix;
- vector<int> tmprow;
- vector<double> stats;
- int tmpnrows = nrows;
-
- for (int row1=0; row1<nrows; row1++) // first line was skipped when counting, so we can start from 0
- {
- //ignore first 3 cols in each row, data starts on the 3th col
- for (int i = 0; i < 3; i++)
- infile3 >> tmp;
-
- for (int col=0; col<ncols; col++)
- {
- infile3 >> tmp;
- //cout << tmp << endl;
- if (atoi(tmp.c_str()) > 0)
- tmprow.push_back(1);
- else
- tmprow.push_back(0);
- }
- if (accumulate( tmprow.begin(), tmprow.end(), 0 ) == 0)
- {
- tmpnrows--;
- }
- else
- initmatrix.push_back(tmprow);
- //add the row to the matrix
- //initmatrix.push_back(tmprow);
- tmprow.clear();
- //cout << tmprow << endl;
- }
-
- infile3.close();
- nrows = tmpnrows;
-
- //print init matrix
- /* cout << "original matrix:" << endl;
-
- for (int i = 0; i < nrows; i++)
- {
- for (int j = 0; j < ncols; j++)
- {
- cout << initmatrix[i][j];
- }
- cout << endl;
- } */
-
- //for (i=0;i<ncols;i++)
- //cout << "col "<< i<< ": " << columntotal[i] << endl;
-
- //co_matrix is now initmatrix and newmatrix is now co_matrix
-
- //remove cols where sum is 0
-
- //transpose matrix
- /* int newmatrows = ncols;
- int newmatcols = nrows;
- int initcols = ncols; //for the combo metric
- int initrows = nrows; //for the combo metric
- //swap for transposed matrix
- nrows = newmatrows;//ncols;
- ncols = newmatcols;//nrows;
-
- vector<int> columntotal(ncols, 0);
- vector<int> initcolumntotal(ncols, 0);
- vector<int> initrowtotal(nrows, 0);
- vector<int> rowtotal(nrows, 0);
-
- transpose_matrix(initmatrix,co_matrix);
- //remove degenerate rows and cols
-
- //cout << "transposed matrix:" << endl;
- int rowcount = 0;
- for (int i = 0; i < nrows; i++)
- {
- for (int j = 0; j < ncols; j++)
- {
- if (co_matrix[i][j] == 1)
- {
- rowcount++;
- columntotal[j]++;
- }
- //cout << co_matrix[i][j];
- }
- //cout << " row total: " << rowcount << endl;
- //cout << endl;
- rowtotal[i] = rowcount;
- rowcount = 0;
- }
-
- initcolumntotal = rowtotal;
- initrowtotal = columntotal;
-
- cout << endl;
-
- runs = atol(argv[2]);
- int metric = atol(argv[3]);
- int nullModel = atol(argv[4]);
- double initscore;
- update_row_col_totals(co_matrix, rowtotal, columntotal, ncols, nrows);
- //do initial metric: checker, c score, v ratio or combo
- switch(metric)
- {
- case 1:
- //c score
- initscore = calc_c_score(co_matrix, rowtotal);
- cout << "initial c score: " << initscore << endl;
- //print_matrix(co_matrix, nrows, ncols);
- break;
-
- case 2:
- //checker
- initscore = calc_checker(co_matrix, rowtotal);
- cout << "initial checker score: " << initscore << endl;
- break;
-
- case 3:
- //v ratio
- initscore = calc_vratio(nrows, ncols, rowtotal, columntotal);
- cout << "initial v ratio: " << initscore << endl;
- break;
-
- case 4:
- //combo
- initscore = calc_combo(initrows, initcols, initmatrix);
- cout << "initial combo score: " << initscore << endl;
- //set co_matrix equal to initmatrix because combo requires row comparisons
- co_matrix = initmatrix;
- break;
-
- case 5:
- //test!
-
- //print_matrix(co_matrix, nrows, ncols);
- //sim1(nrows, ncols, co_matrix);
- //sim2(nrows, ncols, co_matrix);
- //sim3(initrows, initcols, initmatrix);
- //sim4(columntotal, rowtotal, co_matrix);
- //sim5(initcolumntotal, initmatrix);
- //sim6(columntotal, co_matrix);
- //sim7(initcolumntotal, initmatrix);
- sim8(columntotal, rowtotal, co_matrix);
- //print_matrix(initmatrix, initrows, initcols);
- //print_matrix(co_matrix, nrows, ncols);
-
- break;
-
- default:
- cout << "no metric selected!" << endl;
- return 1;
-
- }
-
- //matrix initialization
- //havel_hakimi(nrows, ncols, rowtotal, columntotal, co_matrix);
- //sum_of_square(nrows, ncols, rowtotal, columntotal, co_matrix);
- //co-matrix is now a random matrix with the same row and column totals as the initial matrix
-
- //null matrix burn in
- cout << "initializing null matrix...";
- for(int l=0;l<10000;l++)
- {
- //swap_checkerboards (co_matrix);
- //if(l%10 == 0)
- switch(nullModel)
- {
- case 1:
- //
- sim1(nrows, ncols, co_matrix);
- break;
-
- case 2:
- //sim2
- sim2(nrows, ncols, co_matrix);
- //sim2plus(nrows, ncols, initrowtotal, co_matrix);
- break;
-
- case 3:
- //sim3
- sim3(initrows, initcols, initmatrix);
- //transpose_matrix(initmatrix,co_matrix);
- co_matrix = initmatrix;
- break;
-
- case 4:
- //sim4
- sim4(columntotal, rowtotal, co_matrix);
- break;
-
- case 5:
- //sim5
- sim5(initcolumntotal, initrowtotal, initmatrix);
- transpose_matrix(initmatrix,co_matrix);
- //co_matrix = initmatrix;
- break;
-
- case 6:
- sim6(columntotal, co_matrix);
- break;
-
- case 7:
- //sim7(ncols, nrows, initrowtotal, co_matrix);
- //transpose_matrix(initmatrix,co_matrix);
- //co_matrix = initmatrix;
- break;
-
- case 8:
- sim8(columntotal, rowtotal, co_matrix);
- break;
-
- case 9:
- //swap_checkerboards
- swap_checkerboards (co_matrix);
- break;