Ejemplo n.º 1
0
int main(void) {
 igraph_real_t avg_path;
 igraph_t graph;
 igraph_vector_t dimvector;
 igraph_vector_t edges;
 int i;

 igraph_vector_init(&dimvector, 2);
 VECTOR(dimvector)[0]=30;
 VECTOR(dimvector)[1]=30;
 igraph_lattice(&graph, &dimvector, 0, IGRAPH_UNDIRECTED, 0, 1);
 igraph_rng_seed(igraph_rng_default(), 42);
 igraph_vector_init(&edges, 20);
 for (i=0; i<igraph_vector_size(&edges); i++) {
 VECTOR(edges)[i] = rand() % (int)igraph_vcount(&graph);
 }
 igraph_average_path_length(&graph, &avg_path, IGRAPH_UNDIRECTED, 1);
 printf("Average path length (lattice): %f\n", (double) avg_path);
 igraph_add_edges(&graph, &edges, 0);
 igraph_average_path_length(&graph, &avg_path, IGRAPH_UNDIRECTED, 1);
 printf("Average path length (randomized lattice): %f\n", (double) avg_path);

 igraph_vector_destroy(&dimvector);
 igraph_vector_destroy(&edges);
 igraph_destroy(&graph);
 return 0;
}
Ejemplo n.º 2
0
int main() {
  
  igraph_t g;
  igraph_vs_t vertices;
  igraph_vector_t result1, result2;

  igraph_rng_seed(igraph_rng_default(), 42);
  
  igraph_vector_init(&result1, 0);
  igraph_vector_init(&result2, 0);

  igraph_erdos_renyi_game(&g, IGRAPH_ERDOS_RENYI_GNP, 100, .1,
			  IGRAPH_UNDIRECTED, IGRAPH_NO_LOOPS);

  igraph_vs_seq(&vertices, 0, 99);

  igraph_transitivity_local_undirected(&g, &result1, igraph_vss_all(),
				       IGRAPH_TRANSITIVITY_NAN);
  igraph_transitivity_local_undirected(&g, &result2, vertices,
				       IGRAPH_TRANSITIVITY_NAN);
  
  if (!igraph_vector_all_e(&result1, &result2)) {
    igraph_vector_print(&result1);
    igraph_vector_print(&result2);
    return 1;
  }

  igraph_vector_destroy(&result1);
  igraph_vector_destroy(&result2);
  igraph_vs_destroy(&vertices);
  igraph_destroy(&g);
  
  return 0;
}
int main() {
  
  igraph_matrix_t A;
  igraph_vector_t values;
  igraph_matrix_t vectors;
  int i, j;
  igraph_eigen_which_t which;

  igraph_rng_seed(igraph_rng_default(), 42 * 42);
  
  igraph_matrix_init(&A, DIM, DIM);
  igraph_matrix_init(&vectors, 0, 0);
  igraph_vector_init(&values, 0);

  /* All eigenvalues and eigenvectors */

  for (i=0; i<DIM; i++) {
    for (j=i; j<DIM; j++) {
      MATRIX(A, i, j) = MATRIX(A, j, i) = 
	igraph_rng_get_integer(igraph_rng_default(), 1, 10);
    }
  }

  which.pos=IGRAPH_EIGEN_LM;
  which.howmany=5;
  igraph_eigen_matrix_symmetric(&A, /*sA=*/ 0, /*fun=*/ 0, DIM, /*extra=*/ 0,
				IGRAPH_EIGEN_LAPACK, &which, /*options=*/ 0,
				/*storage=*/ 0, &values, &vectors);
  igraph_vector_print(&values);
  check_ev(&A, &values, &vectors);

  which.howmany=8;
  igraph_eigen_matrix_symmetric(&A, /*sA=*/ 0, /*fun=*/ 0, DIM, /*extra=*/ 0,
				IGRAPH_EIGEN_LAPACK, &which, /*options=*/ 0,
				/*storage=*/ 0, &values, &vectors);
  igraph_vector_print(&values);
  check_ev(&A, &values, &vectors);

  which.pos=IGRAPH_EIGEN_BE;
  which.howmany=5;
  igraph_eigen_matrix_symmetric(&A, /*sA=*/ 0, /*fun=*/ 0, DIM, /*extra=*/ 0,
				IGRAPH_EIGEN_LAPACK, &which, /*options=*/ 0,
				/*storage=*/ 0, &values, &vectors);
  igraph_vector_print(&values);
  check_ev(&A, &values, &vectors);

  which.pos=IGRAPH_EIGEN_SM;
  which.howmany=5;
  igraph_eigen_matrix_symmetric(&A, /*sA=*/ 0, /*fun=*/ 0, DIM, /*extra=*/ 0,
				IGRAPH_EIGEN_LAPACK, &which, /*options=*/ 0,
				/*storage=*/ 0, &values, &vectors);
  igraph_vector_print(&values);
  check_ev(&A, &values, &vectors);
  
  igraph_vector_destroy(&values);
  igraph_matrix_destroy(&vectors);
  igraph_matrix_destroy(&A);  

  return 0;
}
Ejemplo n.º 4
0
int main() {
  
  const int nodes=10, skip=3;
  igraph_matrix_t mat2;
  igraph_vector_complex_t values, values2;
  igraph_matrix_complex_t vectors, vectors2;
  igraph_eigen_which_t which;
  int i;

  igraph_rng_seed(igraph_rng_default(), 42);
  igraph_matrix_init(&mat2, nodes, nodes);
  for (i=0; i<nodes; i++) {
    int j;
    for (j=0; j<nodes; j++) {
      MATRIX(mat2, i, j) = igraph_rng_get_integer(igraph_rng_default(), 1, 10);
    }
  }

  igraph_vector_complex_init(&values, 0);
  igraph_matrix_complex_init(&vectors, 0, 0);
  which.pos=IGRAPH_EIGEN_LI;
  which.howmany=nodes;
  igraph_eigen_matrix(&mat2, /*sparsemat=*/ 0, /*fun=*/ 0, nodes, 
		      /*extra=*/ 0, IGRAPH_EIGEN_LAPACK, &which,
		      /*options=*/ 0, /*storage=*/ 0, &values, &vectors);
  
  igraph_vector_complex_init(&values2, 0);
  igraph_matrix_complex_init(&vectors2, 0, 0);
  which.pos=IGRAPH_EIGEN_SI;
  which.howmany=nodes;
  igraph_eigen_matrix(&mat2, /*sparsemat=*/ 0, /*fun=*/ 0, nodes, 
		      /*extra=*/ 0, IGRAPH_EIGEN_LAPACK, &which, 
		      /*options=*/ 0, /*storage=*/ 0, &values2, &vectors2);

  igraph_vector_complex_print(&values);
  igraph_vector_complex_print(&values2);

  for (i=0; i<nodes; i++) { 
    int j;
    igraph_real_t d=
      igraph_complex_abs(igraph_complex_sub(VECTOR(values)[i],
					    VECTOR(values2)[nodes-i-1]));
    if (d > 1e-15) { DUMP(); return 2; }
    for (j=0; j<nodes; j++) { 
      igraph_real_t d=
	igraph_complex_abs(igraph_complex_sub(MATRIX(vectors, j, i), 
					      MATRIX(vectors2, j,
						     nodes-i-1)));
      if (d > 1e-15) { DUMP(); return 3; }
    }
  }

  igraph_vector_complex_destroy(&values);
  igraph_matrix_complex_destroy(&vectors);
  igraph_vector_complex_destroy(&values2);
  igraph_matrix_complex_destroy(&vectors2);
  igraph_matrix_destroy(&mat2);
  
  return 0;
}
Ejemplo n.º 5
0
int main() {
  igraph_t karate;
  igraph_vector_t parents, weights;

  igraph_rng_seed(igraph_rng_default(), 42);
  
  igraph_small(&karate, 34, IGRAPH_UNDIRECTED,
               0,1,0,2,0,3,0,4,0,5,0,6,0,7,0,8,0,10,0,11,0,12,0,13,
               0,17,0,19,0,21,0,31,
               1,2,1,3,1,7,1,13,1,17,1,19,1,21,1,30,
               2,3,2,7,2,27,2,28,2,32,2,9,2,8,2,13,
               3,7,3,12,3,13,
               4,6,4,10,
               5,6,5,10,5,16,
               6,16,
               8,30,8,32,8,33,
               9,33,
               13,33,
               14,32,14,33,
               15,32,15,33,
               18,32,18,33,
               19,33,
               20,32,20,33,
               22,32,22,33,
               23,25,23,27,23,32,23,33,23,29,
               24,25,24,27,24,31,
               25,31,
               26,29,26,33,
               27,33,
               28,31,28,33,
               29,32,29,33,
               30,32,30,33,
               31,32,31,33,
               32,33,
               -1);
  
  igraph_vector_init(&parents, 0);
  igraph_vector_init(&weights, 0);
  igraph_hrg_consensus(&karate, &parents, &weights, /* hrg= */ 0, 
		       /* start= */ 0, /* num_samples= */ 100);

  /* Check */
  igraph_vector_print(&parents);
  igraph_vector_print(&weights);

  igraph_vector_destroy(&parents);
  igraph_vector_destroy(&weights);
  igraph_destroy(&karate);

#ifdef __APPLE__
  return 0;
#else
  return 77;
#endif
}
Ejemplo n.º 6
0
int main(void)
{
	igraph_integer_t diameter;
	igraph_t graph;
	igraph_rng_seed(igraph_rng_default(), 42);
	igraph_erdos_renyi_game(&graph, IGRAPH_ERDOS_RENYI_GNP, 1000, 5.0/1000, IGRAPH_UNDIRECTED, IGRAPH_NO_LOOPS);
	igraph_diameter(&graph, &diameter, 0, 0, 0, IGRAPH_UNDIRECTED, 1);
	printf("Diameter of a random graph with average degree 5: %d\n", (int) diameter);

	igraph_destroy(&graph);
	return 0;
}
Ejemplo n.º 7
0
int main() {
  igraph_t small, big;
  igraph_matrix_t small_coords, big_coords, merged_coords;
  igraph_vector_ptr_t graph_ptr, coords_ptr;
  igraph_arpack_options_t arpack_opts;

  /* To make things reproducible */
  igraph_rng_seed(igraph_rng_default(), 42);
  
  igraph_small(&big, 10, IGRAPH_UNDIRECTED, 
	       0,1, 1,2, 2,3, 3,4, 4,5, 5,6, 6,7, 7,8, 8,9, 9,0,
	       -1);
  
  igraph_small(&small, 3, IGRAPH_UNDIRECTED,
	       0,1, 1,2, 2,0,
	       -1);

  igraph_arpack_options_init(&arpack_opts);

  igraph_matrix_init(&big_coords, 0, 0);
  igraph_layout_mds(&big, &big_coords, /*dist=*/ 0, /*dim=*/ 2,
		    &arpack_opts);
  
  igraph_matrix_init(&small_coords, 0, 0);
  igraph_layout_mds(&small, &small_coords, /*dist=*/ 0, /*dim=*/ 2,
		    &arpack_opts);
  
  igraph_vector_ptr_init(&graph_ptr, 2);
  igraph_vector_ptr_init(&coords_ptr, 2);
  igraph_matrix_init(&merged_coords, 0, 0);
  VECTOR(graph_ptr)[0] = &big; 
  VECTOR(graph_ptr)[1] = &small;
  VECTOR(coords_ptr)[0] = &big_coords;
  VECTOR(coords_ptr)[1] = &small_coords;
  
  igraph_layout_merge_dla(&graph_ptr, &coords_ptr, &merged_coords);
  
  igraph_matrix_print(&merged_coords);
  
  igraph_matrix_destroy(&merged_coords);
  igraph_matrix_destroy(&small_coords);
  igraph_matrix_destroy(&big_coords);
  igraph_vector_ptr_destroy(&graph_ptr);
  igraph_vector_ptr_destroy(&coords_ptr);
  igraph_destroy(&small);
  igraph_destroy(&big);
  
#ifdef __APPLE__
  return 0;
#else
  return 77;
#endif
}
Ejemplo n.º 8
0
int main() {
  igraph_t graph;
  igraph_vector_ptr_t cliques;
  igraph_rng_t rng;
  igraph_rng_init(&rng, &igraph_rngtype_mt19937);

  igraph_rng_seed(&rng, 42);
  igraph_rng_seed(igraph_rng_default(), 42);
  igraph_erdos_renyi_game(&graph, IGRAPH_ERDOS_RENYI_GNP,
  			  /*n=*/ 100, /*p=*/ 0.7, /*directed=*/ 0,
  			  /*loops=*/ 0, &rng);

  igraph_vector_ptr_init(&cliques, 0);
  
  igraph_maximal_cliques(&graph, &cliques, /*min_size=*/ 15,
			 /*max_size=*/ 0);
  
  print_and_destroy(&cliques);
  igraph_destroy(&graph);
  igraph_rng_destroy(&rng);

  return 0;
}
Ejemplo n.º 9
0
int main() {
    igraph_t g;
    igraph_vector_ptr_t res;
    igraph_integer_t i, n;

    igraph_rng_seed(igraph_rng_default(), 42);

    igraph_erdos_renyi_game(&g, IGRAPH_ERDOS_RENYI_GNM, 100, 3000, /* directed = */ 0, /* loops= */ 0);

    igraph_vector_ptr_init(&res, 0);

    BENCH("1 Cliques in random graph with 100 vertices and 3000 edges",
        igraph_cliques(&g, &res, /* min_size= */ 0, /* max_size= */ 0);
    );
Ejemplo n.º 10
0
int main() {
  
  igraph_matrix_t A;
  igraph_matrix_t vectors_left, vectors_right;
  igraph_vector_t values_real, values_imag;
  int i, j;
  int info=1;
  int ilo, ihi;
  igraph_real_t abnrm;
  
  igraph_rng_seed(igraph_rng_default(), 42);
  
  igraph_matrix_init(&A, DIM, DIM);
  igraph_matrix_init(&vectors_left, 0, 0);
  igraph_matrix_init(&vectors_right, 0, 0);
  igraph_vector_init(&values_real, 0);
  igraph_vector_init(&values_imag, 0);

  for (i=0; i<DIM; i++) {
    for (j=0; j<DIM; j++) {
      MATRIX(A, i, j) = igraph_rng_get_integer(igraph_rng_default(), 1, 10);
    }
  }
  
  igraph_lapack_dgeevx(IGRAPH_LAPACK_DGEEVX_BALANCE_BOTH,
		       &A, &values_real, &values_imag, 
		       &vectors_left, &vectors_right, &ilo, &ihi,
		       /*scale=*/ 0, &abnrm, /*rconde=*/ 0, 
		       /*rcondv=*/ 0, &info);

  if (check_ev(&A, &values_real, &values_imag, 
	       &vectors_left, &vectors_right, /*tol=*/ 1e-8)) {
    return 1;
  }
  
  /* igraph_matrix_print(&A); */
  /* igraph_vector_print(&values_real); */
  /* igraph_vector_print(&values_imag); */
  /* igraph_matrix_print(&vectors_left); */
  /* igraph_matrix_print(&vectors_right); */
  
  igraph_vector_destroy(&values_imag);
  igraph_vector_destroy(&values_real);
  igraph_matrix_destroy(&vectors_right);
  igraph_matrix_destroy(&vectors_left);
  igraph_matrix_destroy(&A);

  return 0;
}
Ejemplo n.º 11
0
int main() {
    igraph_t graph;
    igraph_vector_t walk, weights;
    igraph_integer_t ec, i;

    igraph_rng_seed(igraph_rng_default(), 137);

    igraph_vector_init(&walk, 0);
    igraph_vector_init(&weights, 0);

    /* This directed graph has loop edges.
       It also has multi-edges when considered as undirected. */
    igraph_de_bruijn(&graph, 3, 2);
    ec = igraph_ecount(&graph);

    /* unweighted, directed */
    igraph_random_edge_walk(&graph, NULL, &walk, 0, IGRAPH_OUT, 1000, IGRAPH_RANDOM_WALK_STUCK_RETURN);
    assert(igraph_vector_size(&walk) == 1000);

    /* unweighted, undirected */
    igraph_random_edge_walk(&graph, NULL, &walk, 0, IGRAPH_ALL, 1000, IGRAPH_RANDOM_WALK_STUCK_RETURN);
    assert(igraph_vector_size(&walk) == 1000);

    igraph_vector_resize(&weights, ec);
    for (i=0; i < ec; ++i)
        VECTOR(weights)[i] = igraph_rng_get_unif01(igraph_rng_default());

    /* weighted, directed */
    igraph_random_edge_walk(&graph, &weights, &walk, 0, IGRAPH_OUT, 1000, IGRAPH_RANDOM_WALK_STUCK_RETURN);
    assert(igraph_vector_size(&walk) == 1000);

    /* weighted, undirecetd */
    igraph_random_edge_walk(&graph, &weights, &walk, 0, IGRAPH_ALL, 1000, IGRAPH_RANDOM_WALK_STUCK_RETURN);
    assert(igraph_vector_size(&walk) == 1000);

    igraph_destroy(&graph);

    /* 1-vertex graph, should get stuck */
    igraph_empty(&graph, 1, /* directed = */ 0);
    igraph_random_edge_walk(&graph, NULL, &walk, 0, IGRAPH_OUT, 1000, IGRAPH_RANDOM_WALK_STUCK_RETURN);
    assert(igraph_vector_size(&walk) == 0);
    igraph_destroy(&graph);

    igraph_vector_destroy(&weights);
    igraph_vector_destroy(&walk);

    return 0;
}
Ejemplo n.º 12
0
int main() {
  igraph_t graph;
  igraph_t full, tree;
  igraph_hrg_t hrg;
  igraph_t dendrogram;
  // int i, j;
  // igraph_vector_t neis;

  igraph_rng_seed(igraph_rng_default(), 42);

  // We need attributes
  igraph_i_set_attribute_table(&igraph_cattribute_table);
  
  igraph_full(&full, 10, /*directed=*/ 0, /*loops=*/ 0);
  igraph_tree(&tree, 15, /*children=*/ 2, /*type=*/ IGRAPH_TREE_UNDIRECTED);
  igraph_disjoint_union(&graph, &full, &tree);
  igraph_add_edge(&graph, 0, 10);
  
  igraph_destroy(&full);
  igraph_destroy(&tree);

  // Fit
  igraph_hrg_init(&hrg, igraph_vcount(&graph));
  igraph_hrg_fit(&graph, &hrg, /*start=*/ 0, /*steps=*/ 0);

  // Create a graph from it
  igraph_hrg_dendrogram(&dendrogram, &hrg);

  // Print the tree, with labels
  // igraph_vector_init(&neis, 0);
  // for (i=0; i<igraph_vcount(&graph)-1; i++) {
  //   printf("Vertex # %2i, ", (int) (i+igraph_vcount(&graph)));
  //   igraph_neighbors(&dendrogram, &neis, i+igraph_vcount(&graph), IGRAPH_OUT);
  //   printf("left: # %2i, right: # %2i, ", (int) VECTOR(neis)[0], 
  // 	   (int) VECTOR(neis)[1]);
  //   printf("prob: %6.2g\n", 
  // 	   VAN(&dendrogram, "probability", i+igraph_vcount(&graph)));
  // }
  // igraph_vector_destroy(&neis);

  igraph_destroy(&dendrogram);
  igraph_hrg_destroy(&hrg);
  igraph_destroy(&graph);

  return 0;
}
Ejemplo n.º 13
0
int main() {
  igraph_matrix_t mat;
  igraph_sparsemat_t spmat, spmat2;
  int i;
  igraph_real_t m1, m2;
  
  igraph_rng_seed(igraph_rng_default(), 42);

  igraph_sparsemat_init(&spmat, DIM1, DIM2, 20);
  igraph_sparsemat_entry(&spmat, 1, 2, -1.0);
  igraph_sparsemat_entry(&spmat, 3, 2, 10.0);
  for (i=0; i<10; i++) {
    igraph_sparsemat_entry(&spmat, INT(DIM1-1), INT(DIM2-1), 1.0);
  } 
  igraph_sparsemat_entry(&spmat, 1, 2, -1.0);
  igraph_sparsemat_entry(&spmat, 3, 2, 10.0);
  
  igraph_sparsemat_compress(&spmat, &spmat2);
  igraph_matrix_init(&mat, 0, 0);
  igraph_sparsemat_as_matrix(&mat, &spmat2);
  m1=igraph_sparsemat_min(&spmat2);
  m2=igraph_matrix_min(&mat);
  if (m1 != m2) {
    printf("%f %f\n", m1, m2);
    return 1; 
  }
  m1=igraph_sparsemat_max(&spmat2);
  m2=igraph_matrix_max(&mat);
  if (m1 != m2) {
    printf("%f %f\n", m1, m2);
    return 2;
  }

  igraph_sparsemat_minmax(&spmat2, &m1, &m2);
  if (m1 != igraph_matrix_min(&mat)) { return 3; }
  if (m2 != igraph_matrix_max(&mat)) { return 4; }

  igraph_matrix_destroy(&mat);
  igraph_sparsemat_destroy(&spmat);
  igraph_sparsemat_destroy(&spmat2);
  
  return 0;
}
Ejemplo n.º 14
0
int main() {

  int nodes=10;
  igraph_t g;
  igraph_matrix_t L, R;
  igraph_sparsemat_t Lsparse, Rsparse;
  igraph_matrix_t V, V3;
  igraph_matrix_complex_t V2;
  igraph_sparsemat_t stochastic, stochasticT;
  igraph_vector_t groups;
  igraph_eigen_which_t which;
  igraph_vector_t p, selcol;

  igraph_matrix_init(&L, 0, 0);
  igraph_matrix_init(&R, 0, 0);
  igraph_matrix_init(&V, 0, 0);
  igraph_matrix_init(&V3, 0, 0);
  igraph_vector_init(&groups, 0);
  igraph_vector_init(&selcol, 1);
    
  igraph_rng_seed(igraph_rng_default(), 42);
  
  igraph_tree(&g, 10, /* children= */ 3, IGRAPH_TREE_UNDIRECTED);
  
  igraph_sparsemat_init(&stochastic, nodes, nodes, igraph_ecount(&g)*2);
  igraph_matrix_complex_init(&V2, 0, 0);
  igraph_vector_init(&p, 0);
  
  igraph_rng_seed(igraph_rng_default(), 42);

  igraph_get_stochastic_sparsemat(&g, &stochastic, /*column-wise=*/ 0);
  igraph_sparsemat_transpose(&stochastic, &stochasticT, /*values=*/ 1);

  which.pos=IGRAPH_EIGEN_LR;
  which.howmany=1;

  igraph_eigen_matrix(/*matrix=*/ 0, &stochasticT, /*fun=*/ 0, 10,
		      /*extra=*/ 0, /*algorithm=*/ IGRAPH_EIGEN_LAPACK,
		      &which, /*options=*/ 0, /*storage=*/ 0, 
		      /*values=*/ 0, &V2);
  igraph_matrix_complex_real(&V2, &V);
  /* `p' is always the eigenvector corresponding to the 1-eigenvalue */
  igraph_matrix_get_col(&V, &p, 0);

  which.howmany=3;
  igraph_eigen_matrix(/*matrix=*/ 0, &stochastic, /*fun=*/ 0, 10,
		      /*extra=*/ 0, /*algorithm=*/ IGRAPH_EIGEN_LAPACK,
		      &which, /*options=*/ 0, /*storage=*/ 0, 
		      /*values=*/ 0, &V2);
  igraph_matrix_complex_real(&V2, &V3);
  VECTOR(selcol)[0]=2;
  igraph_matrix_select_cols(&V3, &V, &selcol);

#define SEMI()								\
  do {									\
    igraph_scg_semiprojectors(&groups, IGRAPH_SCG_STOCHASTIC, &L, &R,	\
			      &Lsparse, &Rsparse, &p,			\
			      IGRAPH_SCG_NORM_ROW);			\
  } while(0)

#define PRINTRES()				\
  do {						\
    printf("----------------------\n");		\
    igraph_matrix_print(&L);			\
    printf("---\n");				\
    igraph_matrix_print(&R);			\
    printf("---\n");				\
  } while (0)

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_STOCHASTIC,
		      IGRAPH_SCG_OPTIMUM, &p, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_STOCHASTIC,
		      IGRAPH_SCG_INTERV_KM, &p, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_STOCHASTIC,
		      IGRAPH_SCG_INTERV, &p, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*(ignored) intervals=*/ 0, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_STOCHASTIC,
		      IGRAPH_SCG_EXACT, &p, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_vector_destroy(&p);
  igraph_vector_destroy(&selcol);
  igraph_vector_destroy(&groups);
  igraph_matrix_destroy(&L);
  igraph_matrix_destroy(&R);
  igraph_matrix_destroy(&V);
  igraph_matrix_destroy(&V3);
  igraph_matrix_complex_destroy(&V2);
  igraph_sparsemat_destroy(&stochasticT);
  igraph_sparsemat_destroy(&stochastic);
  igraph_destroy(&g);
  
#ifdef __APPLE__
  return 0;
#else
  return 77;
#endif
}
Ejemplo n.º 15
0
int main() {
    igraph_t graph;
    igraph_vector_t walk, weights;
    igraph_integer_t ec, i;

    igraph_rng_seed(igraph_rng_default(), 137);

    igraph_vector_init(&walk, 0);
    igraph_vector_init(&weights, 0);

    /* create a small graph, and a compatible weight vector */
    igraph_de_bruijn(&graph, 3, 2); /* 9 vertices, 27 edges, average degree: 6 */
    ec = igraph_ecount(&graph);

    igraph_vector_resize(&weights, ec);
    for (i=0; i < ec; ++i)
        VECTOR(weights)[i] = igraph_rng_get_unif01(igraph_rng_default());

    BENCH(" 1 Random edge walk,   directed,   unweighted, small graph  ",
        igraph_random_edge_walk(&graph, NULL, &walk, 0, IGRAPH_OUT, 50000000, IGRAPH_RANDOM_WALK_STUCK_RETURN)
    );

    BENCH(" 2 Random edge walk,   directed,   weighted,   small graph  ",
        igraph_random_edge_walk(&graph, &weights, &walk, 0, IGRAPH_OUT, 50000000, IGRAPH_RANDOM_WALK_STUCK_RETURN)
    );

    BENCH(" 3 Random vertex walk, directed,   unweighted, small graph  ",
        igraph_random_walk(&graph, &walk, 0, IGRAPH_OUT, 50000000, IGRAPH_RANDOM_WALK_STUCK_RETURN)
    );

    igraph_to_undirected(&graph, IGRAPH_TO_UNDIRECTED_EACH, NULL);

    BENCH(" 4 Random edge walk,   undirected, unweighted, small graph  ",
        igraph_random_edge_walk(&graph, NULL, &walk, 0, IGRAPH_OUT, 50000000, IGRAPH_RANDOM_WALK_STUCK_RETURN)
    );

    BENCH(" 5 Random edge walk,   undirected, weighted,   small graph  ",
        igraph_random_edge_walk(&graph, &weights, &walk, 0, IGRAPH_OUT, 50000000, IGRAPH_RANDOM_WALK_STUCK_RETURN)
    );

    BENCH(" 6 Random vertex walk, undirected, unweighted, small graph  ",
        igraph_random_walk(&graph, &walk, 0, IGRAPH_OUT, 50000000, IGRAPH_RANDOM_WALK_STUCK_RETURN)
    );

    igraph_destroy(&graph);

    /* create a big graph, and a compatible weight vector */
    igraph_de_bruijn(&graph, 8, 5); /* 32768 vertices, 262144 edges, average degree: 16 */
    ec = igraph_ecount(&graph);

    igraph_vector_resize(&weights, ec);
    for (i=0; i < ec; ++i)
        VECTOR(weights)[i] = igraph_rng_get_unif01(igraph_rng_default());

    BENCH(" 7 Random edge walk,   directed,   unweighted, large graph  ",
        igraph_random_edge_walk(&graph, NULL, &walk, 0, IGRAPH_OUT, 50000000, IGRAPH_RANDOM_WALK_STUCK_RETURN)
    );

    BENCH(" 8 Random edge walk,   directed,   weighted,   large graph  ",
        igraph_random_edge_walk(&graph, &weights, &walk, 0, IGRAPH_OUT, 50000000, IGRAPH_RANDOM_WALK_STUCK_RETURN)
    );

    BENCH(" 9 Random vertex walk, directed,   unweighted, large graph  ",
        igraph_random_walk(&graph, &walk, 0, IGRAPH_OUT, 50000000, IGRAPH_RANDOM_WALK_STUCK_RETURN)
    );

    igraph_to_undirected(&graph, IGRAPH_TO_UNDIRECTED_EACH, NULL);

    BENCH("10 Random edge walk,   undirected, unweighted, large graph  ",
        igraph_random_edge_walk(&graph, NULL, &walk, 0, IGRAPH_OUT, 50000000, IGRAPH_RANDOM_WALK_STUCK_RETURN)
    );

    BENCH("11 Random edge walk,   undirected, weighted,   large graph  ",
        igraph_random_edge_walk(&graph, &weights, &walk, 0, IGRAPH_OUT, 50000000, IGRAPH_RANDOM_WALK_STUCK_RETURN)
    );

    BENCH("12 Random vertex walk, undirected, unweighted, large graph  ",
        igraph_random_walk(&graph, &walk, 0, IGRAPH_OUT, 50000000, IGRAPH_RANDOM_WALK_STUCK_RETURN)
    );

    igraph_destroy(&graph);

    igraph_vector_destroy(&weights);
    igraph_vector_destroy(&walk);

    return 0;
}
Ejemplo n.º 16
0
int main() {

  igraph_t g;
  igraph_matrix_t L, R;
  igraph_sparsemat_t Lsparse, Rsparse;
  igraph_matrix_t adj, V;
  igraph_vector_t groups;
  igraph_eigen_which_t which;

  igraph_matrix_init(&L, 0, 0);
  igraph_matrix_init(&R, 0, 0);
  igraph_matrix_init(&adj, 0, 0);
  igraph_matrix_init(&V, 0, 0);
  igraph_vector_init(&groups, 0);
    
  igraph_rng_seed(igraph_rng_default(), 42);
  
  igraph_tree(&g, 10, /* children= */ 3, IGRAPH_TREE_UNDIRECTED);
  
  igraph_get_adjacency(&g, &adj, IGRAPH_GET_ADJACENCY_BOTH, /*eids=*/ 0);

  which.pos=IGRAPH_EIGEN_LM;
  which.howmany=1;
  igraph_eigen_matrix_symmetric(&adj, /*sparsemat=*/ 0, /*fun=*/ 0,
				igraph_vcount(&g), /*extra=*/ 0, 
				/*algorithm=*/ IGRAPH_EIGEN_LAPACK,
				&which, /*options=*/ 0, /*storage=*/ 0, 
				/*values=*/ 0, &V);

#define SEMI()								\
  do {									\
    igraph_scg_semiprojectors(&groups, IGRAPH_SCG_SYMMETRIC, &L, &R,	\
			      &Lsparse, &Rsparse, /*p=*/ 0,		\
			      IGRAPH_SCG_NORM_ROW);			\
  } while(0)

#define PRINTRES()				\
  do {						\
    printf("----------------------\n");		\
    igraph_matrix_print(&L);			\
    printf("---\n");				\
    igraph_matrix_print(&R);			\
    printf("---\n");				\
  } while (0)

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_SYMMETRIC,
		      IGRAPH_SCG_OPTIMUM, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 2, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_SYMMETRIC,
		      IGRAPH_SCG_INTERV_KM, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 2, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_SYMMETRIC,
		      IGRAPH_SCG_INTERV, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*(ignored) intervals=*/ 0, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_SYMMETRIC,
		      IGRAPH_SCG_EXACT, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_vector_destroy(&groups);
  igraph_matrix_destroy(&V);
  igraph_matrix_destroy(&adj);
  igraph_destroy(&g);
  
  return 0;
}
Ejemplo n.º 17
0
int main() {
  igraph_matrix_t A;
  igraph_matrix_t values, vectors;
  igraph_arpack_options_t options;
  cb2_data_t data = { &A };  
  int i, j;

  igraph_rng_seed(igraph_rng_default(), 42 * 42);

  igraph_matrix_init(&A, DIM, DIM);

  for (i=0; i<DIM; i++) {
    for (j=0; j<DIM; j++) {
      MATRIX(A, i, j) = igraph_rng_get_integer(igraph_rng_default(), -10, 10);
    }
  }
  
  igraph_arpack_options_init(&options);
  options.n=DIM;
  options.start=0;
  options.nev=4;
  options.ncv=9;
  options.which[0]='L' ; options.which[1]='M';

  igraph_matrix_init(&values, 0, 0);
  igraph_matrix_init(&vectors, options.n, 1);

  igraph_arpack_rnsolve(cb2, /*extra=*/ &data, &options, /*storage=*/ 0, 
			&values, &vectors);

  if (MATRIX(values, 2, 1) > 0) {
    MATRIX(values, 2, 1) = -MATRIX(values, 2, 1);
    MATRIX(values, 3, 1) = -MATRIX(values, 3, 1);    
  }

  igraph_matrix_print(&values);
  printf("---\n");
  igraph_matrix_print(&vectors);
  printf("---\n");

  /* -------------- */

  options.nev=3;
  options.which[0]='L' ; options.which[1]='M';

  igraph_arpack_rnsolve(cb2, /*extra=*/ &data, &options, /*storage=*/ 0, 
			&values, &vectors);

  if (MATRIX(values, 2, 1) > 0) {
    MATRIX(values, 2, 1) = -MATRIX(values, 2, 1);
  }

  igraph_matrix_print(&values);
  printf("---\n");
  igraph_matrix_print(&vectors);
  printf("---\n");

  /* -------------- */

  options.nev=3;
  options.which[0]='S' ; options.which[1]='R';

  igraph_arpack_rnsolve(cb2, /*extra=*/ &data, &options, /*storage=*/ 0, 
			&values, &vectors);

  igraph_matrix_print(&values);
  printf("---\n");
  igraph_matrix_print(&vectors);
  printf("---\n");

  /* -------------- */

  options.nev=3;
  options.which[0]='L' ; options.which[1]='I';

  igraph_arpack_rnsolve(cb2, /*extra=*/ &data, &options, /*storage=*/ 0, 
			&values, &vectors);

  igraph_matrix_print(&values);
  printf("---\n");
  igraph_matrix_print(&vectors);
  printf("---\n");

  /* -------------- */

  igraph_matrix_destroy(&values);
  igraph_matrix_destroy(&vectors);
  igraph_matrix_destroy(&A);
  
  return 0;
}
Ejemplo n.º 18
0
int main() {

  int nodes=10;
  igraph_t g;
  igraph_matrix_t L, R;
  igraph_sparsemat_t Lsparse, Rsparse;
  igraph_matrix_t V;
  igraph_matrix_complex_t V2;
  igraph_sparsemat_t laplacian;
  igraph_vector_t groups;
  igraph_eigen_which_t which;

  igraph_matrix_init(&L, 0, 0);
  igraph_matrix_init(&R, 0, 0);
  igraph_matrix_init(&V, 0, 0);
  igraph_matrix_complex_init(&V2, 0, 0);
  igraph_vector_init(&groups, 0);
    
  igraph_rng_seed(igraph_rng_default(), 42);
  
  igraph_tree(&g, 10, /* children= */ 3, IGRAPH_TREE_UNDIRECTED);
  
  igraph_sparsemat_init(&laplacian, nodes, nodes, igraph_ecount(&g)*2);
  
  igraph_rng_seed(igraph_rng_default(), 42);

  igraph_laplacian(&g, /*res=*/ 0, /*sparseres=*/ &laplacian, 
		   /*normalized=*/ 0, /*weights=*/ 0);

  which.pos=IGRAPH_EIGEN_LM;
  which.howmany=1;

  igraph_eigen_matrix(/*matrix=*/ 0, &laplacian, /*fun=*/ 0, 10,
		      /*extra=*/ 0, /*algorithm=*/ IGRAPH_EIGEN_LAPACK,
		      &which, /*options=*/ 0, /*storage=*/ 0, 
		      /*values=*/ 0, &V2);
  igraph_matrix_complex_real(&V2, &V);

#define SEMI()								\
  do {									\
    igraph_scg_semiprojectors(&groups, IGRAPH_SCG_LAPLACIAN, &L, &R,	\
			      &Lsparse, &Rsparse, /*p=*/ 0,		\
			      IGRAPH_SCG_NORM_ROW);			\
  } while(0)

#define PRINTRES()				\
  do {						\
    printf("----------------------\n");		\
    igraph_matrix_print(&L);			\
    printf("---\n");				\
    igraph_matrix_print(&R);			\
    printf("---\n");				\
    igraph_sparsemat_destroy(&Lsparse);         \
    igraph_sparsemat_destroy(&Rsparse);         \
  } while (0)

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_OPTIMUM, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 2, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_INTERV_KM, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 2, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_INTERV, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*(ignored) intervals=*/ 0, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_EXACT, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_matrix_destroy(&L);
  igraph_matrix_destroy(&R);
  igraph_matrix_destroy(&V);
  igraph_matrix_complex_destroy(&V2);
  igraph_vector_destroy(&groups);
  igraph_sparsemat_destroy(&laplacian);
  igraph_destroy(&g);
  
  return 0;
}
Ejemplo n.º 19
0
int main() {

  const int nodes=10;
  igraph_t g;
  igraph_matrix_t V;
  igraph_matrix_complex_t V2;
  igraph_sparsemat_t laplacian;
  igraph_vector_t groups;
  igraph_eigen_which_t which;

  igraph_tree(&g, nodes, /* children= */ 3, IGRAPH_TREE_UNDIRECTED);

  igraph_sparsemat_init(&laplacian, nodes, nodes, igraph_ecount(&g)*2);
  igraph_matrix_complex_init(&V2, 0, 0);
  igraph_matrix_init(&V, 0, 0);
  igraph_vector_init(&groups, 0);
  
  igraph_rng_seed(igraph_rng_default(), 42);

  igraph_sparsemat_init(&laplacian, 0, 0, 0);
  igraph_laplacian(&g, /*res=*/ 0, /*sparseres=*/ &laplacian, 
		   /*normalized=*/ 0, /*weights=*/ 0);

  which.pos=IGRAPH_EIGEN_LR;
  which.howmany=1;

  igraph_eigen_matrix(/*matrix=*/ 0, &laplacian, /*fun=*/ 0, nodes,
		      /*extra=*/ 0, /*algorithm=*/ IGRAPH_EIGEN_LAPACK,
		      &which, /*options=*/ 0, /*storage=*/ 0, 
		      /*values=*/ 0, &V2);
  igraph_matrix_complex_real(&V2, &V);

  /* ------------ */
  
  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_OPTIMUM, /*p=*/ 0, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  /* ------------ */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_INTERV_KM, /*p=*/ 0, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  /* ------------ */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_INTERV, /*p=*/ 0, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  /* ------------ */

  igraph_scg_grouping(&V, &groups, /*(ignored) intervals=*/ 0, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_EXACT, /*p=*/ 0, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  /* ------------ */  

  igraph_vector_destroy(&groups);
  igraph_matrix_destroy(&V);
  igraph_matrix_complex_destroy(&V2);
  igraph_sparsemat_destroy(&laplacian);
  igraph_destroy(&g);

#ifdef __APPLE__
  return 0;
#else
  return 77;
#endif
}
Ejemplo n.º 20
0
int main() {
  
  igraph_t g, g2, cli;
  igraph_vector_t perm;
  igraph_vector_ptr_t cliques;
  igraph_integer_t no;
  int i;

  igraph_rng_seed(igraph_rng_default(), 42);
  
  /* Create a graph that has a random component, plus a number of 
     relatively small cliques */
  
  igraph_vector_init_seq(&perm, 0, NODES-1);
  igraph_erdos_renyi_game(&g, IGRAPH_ERDOS_RENYI_GNM, NODES, NODES, 
        /*directed=*/ 0, /*loops=*/ 0, igraph_rng_default());
  igraph_full(&cli, CLIQUE_SIZE, /*directed=*/ 0, /*loops=*/ 0);

  for (i=0; i<NO_CLIQUES; i++) {
    /* Permute vertices of g */
    permutation(&perm);
    igraph_permute_vertices(&g, &g2, &perm);
    igraph_destroy(&g);
    g=g2;
    
    /* Add a clique */
    igraph_union(&g2, &g, &cli, /*edge_map1=*/ 0, /*edge_map2=*/ 0);
    igraph_destroy(&g);
    g=g2;
  }
  igraph_simplify(&g, /*multiple=*/ 1, /*loop=*/ 0, /*edge_comb=*/ 0);
  
  igraph_vector_destroy(&perm);
  igraph_destroy(&cli);
  
  /* Find the maximal cliques */
  
  igraph_vector_ptr_init(&cliques, 0);
  igraph_maximal_cliques(&g, &cliques, /*min_size=*/ 3,
       /*max_size=*/ 0 /*no limit*/);
  igraph_maximal_cliques_count(&g, &no, /*min_size=*/ 3, 
       /*max_size=*/ 0 /*no limit*/);

  if (no != igraph_vector_ptr_size(&cliques)) { return 1; }
  
  /* Print and destroy them */

  print_and_destroy_cliques(&cliques);
  
  /* Clean up */

  igraph_vector_ptr_destroy(&cliques);
  igraph_destroy(&g);

  /* Build a triangle with a loop (thanks to Emmanuel Navarro) */

  igraph_small(&g, 3, IGRAPH_UNDIRECTED, 0, 1, 1, 2, 2, 0, 0, 0, -1);

  /* Find the maximal cliques */

  igraph_vector_ptr_init(&cliques, 0);
  igraph_maximal_cliques(&g, &cliques, /*min_size=*/ 3,
    /*max_size=*/ 0 /*no limit*/);
  igraph_maximal_cliques_count(&g, &no, /*min_size=*/ 3, 
       /*max_size=*/ 0 /*no limit*/);

  if (no != igraph_vector_ptr_size(&cliques)) { return 2; }

  /* Print and destroy them */

  print_and_destroy_cliques(&cliques);
  
  /* Clean up */

  igraph_vector_ptr_destroy(&cliques);
  igraph_destroy(&g);

  return 0;
}
Ejemplo n.º 21
0
int main(int argc,char*argv[])
{
	if(argc!=2)
	{
		cout<<"USAGE:SIS datafile  "<<endl;
		exit(1);
	}
	//define the entry

	string networkname(argv[1]); //network name

	double a=1;
	double alpha=0.4;
	double beta=0.1;
	int game_rounds=500; //MC rounds
	int aver_rounds=10;  //do average
	double delta=1;//delta


	string output_name_pre;  //the network name 
	for(int i=0;i!=networkname.size()-4;i++)
	{
		output_name_pre.push_back(networkname[i]);
	}

	//random generator
	//to initialize the random seed
	igraph_rng_init(mrng,&igraph_rngtype_mt19937);

	unsigned long idum;  // random number seed
	idum=(unsigned long)time(NULL);
	igraph_rng_seed(mrng,idum);

	//construct the graph
	igraph_t network;
   
	gen_graph(&network,networkname);
	int nwsize=igraph_vcount(&network);  //the size of the network
   
   
	//to generate the name of the output file
	//output file name
	string resname("res.txt");
	string totalname=output_name_pre+resname;	
	FILE *outfile;
	outfile = fopen(totalname.c_str(), "w");
	
	//construct the population
	for(a=-6;a<6.1;a+=0.1 )
	{
		population popu(output_name_pre,&network,delta,0.01,a,2,3*nwsize,3*nwsize);
		double res=0;
		popu.population_dynamics(&res,alpha,beta,1000);
		fprintf(outfile,"%f\t%f\n",a,res/ nwsize);
		fflush(outfile);
	}
	fclose(outfile);
/*  
	igraph_t network;
	int nwsize = igraph_vcount(&network);  //the size of the network
	igraph_watts_strogatz_game(&network, 1, 500, 4, 0.1, false, false);
	string output_name_pre("small_world");
	population test(output_name_pre,&network, 1, 0.01, 1, 0, 3 * nwsize, 3 * nwsize);
	test.initial_state();

	double res = 0;

	test.population_dynamics(&res,0.3,0.1,300);
*/
	//for (a=-5;a!=5;a+=0.2)
	//
	//{

 //       population test(&network,delta,0.01,a,type,3*nwsize,3*nwsize);
	//	vector<double> average_rres;

	//	for(int i=0;i!=aver_rounds;++i)
	//	{
	//		double rres=0;
	//		test.initial_state();
	//		test.population_dynamics(&rres,0.4,0.1,game_rounds);
	////		printf("%f\n", rres);
	//		average_rres.push_back(rres);

	//	}
	//	fprintf(outfile,"%f\t%f\n",a,double (accumulate(average_rres.begin(),\
	//		average_rres.end(),0)/average_rres.size()));
	//	fflush(outfile);
	//}
	//fclose(outfile);
	igraph_destroy(&network);
	return 0;
}
Ejemplo n.º 22
0
int main() {
  igraph_t g;
  igraph_vector_t weights;

  igraph_rng_seed(igraph_rng_default(), 42);

  /* Two triangles connected by one edge */
  printf("# Two triangles connected by one edge\n");
  igraph_small(&g, 0, IGRAPH_UNDIRECTED,
                      0, 1, 1, 2, 2, 0,
                      3, 4, 4, 5, 5, 3,
                      0, 5,
                      -1);
  infomap_test(&g);
  igraph_destroy(&g);
  //return 0;

  /* Two 4-cliques with one commun vertex (vertex 3) */
  printf("# Two 4-cliques (0123 and 4567) connected by two edges (0-4 and 1-5)\n");
  igraph_small(&g, 0, IGRAPH_UNDIRECTED,
                      0, 1,  0, 2,  0, 3,  1, 2,  1, 3,  2, 3, // 4-clique 0,1,2,3
                      7, 4,  7, 5,  7, 6,  4, 5,  4, 6,  5, 6, // 4-clique 4,5,6,7
                      0, 4,  1, 5, //8, 0, 8, 4,
                      -1);
  infomap_test(&g);

  printf("# Two 4-cliques (0123 and 4567) connected by two edges (0-4 and 1-5)\n");
  igraph_add_edge(&g, 0, 4);
  igraph_add_edge(&g, 1, 5);
  infomap_test(&g);
  igraph_destroy(&g);
  
  /* Zachary Karate club -- this is just a quick smoke test */
  printf("# Zachary Karate club\n");
  igraph_small(&g, 0, IGRAPH_UNDIRECTED,
               0,  1,  0,  2,  0,  3,  0,  4,  0,  5, //0,  5, 0,  5, 0,  5,
               0,  6,  0,  7,  0,  8,  0, 10,  0, 11,
               0, 12,  0, 13,  0, 17,  0, 19,  0, 21,
               0, 31,  1,  2,  1,  3,  1,  7,  1, 13,
               1, 17,  1, 19,  1, 21,  1, 30,  2,  3,
               2,  7,  2,  8,  2,  9,  2, 13,  2, 27,
               2, 28,  2, 32,  3,  7,  3, 12,  3, 13,
               4,  6,  4, 10,  5,  6,  5, 10,  5, 16,
               6, 16,  8, 30,  8, 32,  8, 33,  9, 33,
               13, 33, 14, 32, 14, 33, 15, 32, 15, 33,
               18, 32, 18, 33, 19, 33, 20, 32, 20, 33,
               22, 32, 22, 33, 23, 25, 23, 27, 23, 29,
               23, 32, 23, 33, 24, 25, 24, 27, 24, 31,
               25, 31, 26, 29, 26, 33, 27, 33, 28, 31,
               28, 33, 29, 32, 29, 33, 30, 32, 30, 33,
               31, 32, 31, 33, 32, 33,
               -1);
  infomap_test(&g);
  igraph_destroy(&g);
  
  /* Flow.net that come in infomap_dir.tgz  */
  printf("# Flow (from infomap_dir.tgz)\n");
  igraph_small(&g, 0, IGRAPH_DIRECTED,
              0, 1,     1, 2,    2, 3,    3, 0,    1, 4,
              4, 5,     5, 6,    6, 7,    7, 4,    5, 8,
              8, 9,     9, 10,  10, 11,  11, 8,    9, 12,
              12, 13,  13, 14,  14, 15,  15, 12,  13, 0,
               -1);
  infomap_test(&g);
  igraph_destroy(&g);

  /* MultiphysChemBioEco40W_weighted_dir.net */
  printf("# MultiphysChemBioEco40W_weighted_dir.net (from infomap_dir.tgz)\n");
  igraph_small(&g, 0, IGRAPH_DIRECTED,
          1, 0,  2, 0,  3, 0,  4, 0,  5, 0,  6, 0,  7, 0,
          8, 0,  9, 0,  16, 0,  18, 0,  0, 1,  2, 1,  3, 1,
          5, 1,  6, 1,  7, 1,  9, 1,  10, 1,  16, 1,  18, 1,
          0, 2,  3, 2,  4, 2,  5, 2,  6, 2,  7, 2,  0, 3,
          1, 3,  2, 3,  4, 3,  5, 3,  6, 3,  7, 3,  8, 3,
          9, 3,  10, 3,  11, 3,  13, 3,  14, 3,  16, 3,  17, 3,
          18, 3,  19, 3,  26, 3,  30, 3,  1, 4,  3, 4,  5, 4,
          6, 4,  13, 4,  18, 4,  0, 5,  1, 5,  2, 5,  3, 5,
          6, 5,  7, 5,  9, 5,  1, 6,  3, 6,  7, 6,  9, 6,
          16, 6,  0, 7,  1, 7,  2, 7,  3, 7,  5, 7,  6, 7,
          9, 7,  3, 8,  5, 8,  3, 9,  7, 9,  12, 10,  13, 10,
          14, 10,  15, 10,  16, 10,  17, 10,  18, 10,  19, 10,
          21, 10,  3, 11,  18, 11,  10, 12,  14, 12,  16, 12,
          17, 12,  18, 12,  3, 13,  10, 13,  14, 13,  16, 13,
          10, 14,  12, 14,  13, 14,  15, 14,  16, 14,  17, 14,
          18, 14,  10, 15,  14, 15,  18, 15,  0, 16,  2, 16,
          3, 16,  6, 16,  10, 16,  12, 16,  13, 16,  14, 16,
          17, 16,  18, 16,  10, 17,  12, 17,  14, 17,  18, 17,
          3, 18,  10, 18,  12, 18,  14, 18,  15, 18,  16, 18,
          17, 18,  19, 18,  21, 18,  11, 19,  16, 19,  17, 19,
          16, 20,  18, 20,  21, 20,  22, 20,  23, 20,  24, 20,
          25, 20,  26, 20,  27, 20,  28, 20,  29, 20,  3, 21,
          14, 21,  18, 21,  20, 21,  22, 21,  23, 21,  24, 21,
          25, 21,  26, 21,  27, 21,  28, 21,  29, 21,  35, 21,
          36, 21,  38, 21,  18, 22,  20, 22,  21, 22,  23, 22,
          24, 22,  25, 22,  26, 22,  27, 22,  29, 22,  3, 23,
          20, 23,  21, 23,  22, 23,  24, 23,  25, 23,  26, 23,
          27, 23,  28, 23,  29, 23,  35, 23,  38, 23,  39, 23,
          20, 24,  21, 24,  23, 24,  25, 24,  26, 24,  27, 24,
          28, 24,  29, 24,  9, 25,  20, 25,  21, 25,  22, 25,
          23, 25,  24, 25,  26, 25,  27, 25,  28, 25,  29, 25,
          18, 26,  20, 26,  21, 26,  22, 26,  23, 26,  25, 26,
          27, 26,  28, 26,  29, 26,  30, 26,  32, 26,  35, 26,
          36, 26,  38, 26,  39, 26,  3, 27,  14, 27,  20, 27,
          21, 27,  22, 27,  23, 27,  24, 27,  25, 27,  26, 27,
          28, 27,  29, 27,  38, 27,  3, 28,  18, 28,  20, 28,
          21, 28,  23, 28,  24, 28,  25, 28,  26, 28,  27, 28,
          29, 28,  35, 28,  14, 29,  16, 29,  18, 29,  20, 29,
          21, 29,  22, 29,  23, 29,  24, 29,  25, 29,  26, 29,
          27, 29,  28, 29,  31, 30,  32, 30,  33, 30,  34, 30,
          35, 30,  36, 30,  38, 30,  39, 30,  30, 31,  32, 31,
          34, 31,  36, 31,  30, 32,  34, 32,  35, 32,  36, 32,
          30, 33,  32, 33,  34, 33,  35, 33,  36, 33,  38, 33,
          30, 34,  31, 34,  32, 34,  33, 34,  35, 34,  36, 34,
          38, 34,  39, 34,  26, 35,  30, 35,  32, 35,  33, 35,
          34, 35,  36, 35,  38, 35,  39, 35,  30, 36,  34, 36,
          35, 36,  38, 36,  39, 36,  34, 37,  26, 38,  30, 38,
          32, 38,  33, 38,  34, 38,  35, 38,  36, 38,  39, 38,
          26, 39,  30, 39,  33, 39,  34, 39,  35, 39,  36, 39,
          38, 39,
          -1);
  igraph_vector_init_real(&weights, 306,
          5.0,  3.0,  130.0,  4.0,  15.0,  9.0,
          7.0,  1.0,  1.0,  3.0,  1.0,  1.0,
          1.0,  34.0,  38.0,  2.0,  23.0,  1.0,
          1.0,  3.0,  2.0,  2.0,  16.0,  1.0,
          3.0,  1.0,  3.0,  63.0,  92.0,  72.0,
          25.0,  447.0,  121.0,  65.0,  4.0,  16.0,
          35.0,  1.0,  19.0,  1.0,  78.0,  1.0,
          45.0,  1.0,  3.0,  1.0,  1.0,  25.0,
          1.0,  3.0,  1.0,  1.0,  3.0,  36.0,
          19.0,  136.0,  41.0,  96.0,  1.0,  7.0,
          26.0,  1.0,  2.0,  2.0,  3.0,  2.0,  2.0,
          23.0,  52.0,  4.0,  1.0,  2.0,  1.0,  3.0,
          1.0,  11.0,  2.0,  17.0,  1.0,  5.0,  18.0,
          86.0,  5.0,  1.0,  1.0,  1.0,  6.0,  1.0,
          2.0,  2.0,  20.0,  4.0,  5.0,  1.0,  5.0,
          12.0,  4.0,  1.0,  1.0,  4.0,  9.0,  40.0,
          2.0,  1.0,  4.0,  1.0,  1.0,  48.0,  2.0,
          18.0,  1.0,  7.0,  2.0,  2.0,  53.0,  25.0,
          9.0,  1.0,  23.0,  8.0,  62.0,  29.0,  35.0,
          4.0,  34.0,  35.0,  3.0,  1.0,  24.0,  1.0,
          6.0,  2.0,  2.0,  22.0,  7.0,  2.0,  5.0,
          14.0,  3.0,  28.0,  14.0,  20.0,  3.0,  1.0,
          5.0,  77.0,  20.0,  25.0,  35.0,  55.0,  35.0,
          115.0,  68.0,  105.0,  2.0,  2.0,  2.0,  4.0,
          2.0,  17.0,  12.0,  3.0,  3.0,  11.0,  10.0,
          7.0,  2.0,  12.0,  31.0,  11.0,  5.0,  11.0,
          65.0,  39.0,  17.0,  26.0,  3.0,  4.0,  2.0,
          3.0,  6.0,  4.0,  8.0,  1.0,  7.0,  7.0,
          6.0,  1.0,  39.0,  42.0,  9.0,  6.0,  9.0,
          5.0,  45.0,  43.0,  26.0,  1.0,  2.0,  6.0,
          2.0,  15.0,  3.0,  9.0,  2.0,  1.0,  1.0,
          1.0,  4.0,  2.0,  9.0,  2.0,  1.0,  2.0,
          28.0,  80.0,  10.0,  18.0,  13.0,  17.0,
          28.0,  40.0,  76.0,  1.0,  2.0,  1.0,  11.0,
          37.0,  5.0,  11.0,  14.0,  4.0,  14.0,  10.0,
          1.0,  1.0,  1.0,  1.0,  41.0,  121.0,  6.0,
          21.0,  12.0,  30.0,  6.0,  141.0,  43.0,  2.0,
          12.0,  6.0,  35.0,  10.0,  7.0,  2.0,  12.0,
          6.0,  2.0,  11.0,  1.0,  7.0,  6.0,  5.0,  3.0,
          1.0,  2.0,  1.0,  1.0,  1.0,  1.0,  67.0,  9.0,
          9.0,  11.0,  10.0,  21.0,  7.0,  12.0,  9.0,
          16.0,  7.0,  4.0,  11.0,  17.0,  37.0,  32.0,
          9.0,  2.0,  2.0,  5.0,  4.0,  2.0,  7.0,  3.0,
          3.0,  5.0,  8.0,  14.0,  3.0,  38.0,  3.0,  9.0,
          2.0,  8.0,  21.0,  18.0,  58.0);
  infomap_weighted_test(&g, &weights);
  igraph_vector_destroy(&weights);
  igraph_destroy(&g);
  
   /* Two triangles connected by one edge */
  printf("# Wiktionary english verbs (synonymy 2008)\n");
  FILE *wikt = fopen("wikti_en_V_syn.elist", "r");
  igraph_read_graph_edgelist(&g, wikt, 0, 0);
  fclose(wikt);
  gsumary(&g);
  infomap_test(&g);
  igraph_destroy(&g);
  
#ifdef __APPLE__
  return 0;
#else
  return 77;
#endif
}
Ejemplo n.º 23
0
int main(int argc, char* argv[])
{
    if (argc != 9)
    {
        cout << "Usage: ./release/fixating <Update Rule: \"Bd\", \"dB\"> <integer: population size> <\"directed\" or \"undirected\"> <double: fitness of mutant> <category of graph: \"complete\", \"ER\", \"BB\", \"WS\", \"geo\", or \"custom\" > <secondary parameter for the category of graph: \"GNM\" or \"GNP\" for Erdos Reny, double power of preference for Barabasi, int dimension for small world, bool periodic for geometric, , adjacency matrix for custom> <tertiary parameter for the category of graph: probability for every edge in Erdos-Reny GNP and geometric, number of edges for Erdos-Reny GNM, m for barabasi, probability of rewiring for small world, 0 for custom> <output: \"probability\", \"conditional\", \"unconditional\", or \"all\">" << endl;
        return -1;
    }
    //   ---------- If you want to stop time, uncomment all comments with //CLOCK//
    //CLOCK//
    std::clock_t start;
    //CLOCK//
    double bt = 0;
    //CLOCK//
    double st = 0;
    //counting variable for the graph generators
    int counts = 0;
    const unsigned int popSize = atoi(argv[2]);
    if (popSize > 23)
    {
        cout << "Code only possible for population size up to 23... aborting..." << endl;
        return -1;
    }
    const unsigned int numStates = 1 << popSize;

    string update = argv[1];
    if (update != "dB" && update != "Bd")
    {
        cout << "Only \"Bd\" or \"dB\" possible for update rule!... aborting..." << endl;
        return -1;
    }

    float fitnessMutants = atof(argv[4]);
    string direction = argv[3];
    string category = argv[5];
    igraph_t graph;
    int admat[popSize * popSize];

    string output = argv[8];
    if (output != "probability" && output != "conditional" && output != "unconditional" && output != "all")
    {
        cout << "Only \"probability\", \"unconditional\", \"conditional\" or \"all\" possible for output!... aborting..." << endl;
        return -1;
    }



    // ----------   Code snippet for fully connected graph   ----------
    if (category == "complete")
    {
        if (direction == "undirected")
        {
            igraph_full(&graph, popSize, false, false);
        }
        else if (direction == "directed")
        {
            igraph_full(&graph, popSize, true, false);
        }
        else
        {
            cout << "Only \"directed\" and \"undirected\" possible for direction of graph!... aborting..." << endl;
            return -1;
        }
    }


    // ----------   Code snippet for random graph   ----------
    else if (category == "ER")
    {
        string gn = argv[6];

        igraph_rng_seed(igraph_rng_default(), std::clock());
        igraph_bool_t isConnected = 0;

        if (direction == "directed")
        {
            while ((isConnected == 0) & (counts < maxcount))
            {
                if (gn == "GNP")
                {
                    double edgeprob = atof(argv[7]);
                    if ((edgeprob > 1) || (edgeprob < 0))
                    {
                        cout << "probabilities larger than 1 or smaller than 0 ...aborting..." << endl;
                        return -1;
                    }
                    igraph_erdos_renyi_game(&graph, IGRAPH_ERDOS_RENYI_GNP,
                                            popSize, edgeprob,
                                            true, false);
                }
                else if (gn == "GNM")
                {
                    int edgenumber = atoi(argv[7]);
                    if ((edgenumber < 1) || (edgenumber > popSize*(popSize-1)))
                    {
                        cout << "number of edges must be greater than 1 and smaller than N*(N-1) ...aborting..." << endl;
                        return -1;
                    }

                    igraph_erdos_renyi_game(&graph, IGRAPH_ERDOS_RENYI_GNM,
                                            popSize, edgenumber,
                                            true, false);
                }
                else
                {
                    cout << "Only \"GNM\" and \"GNP\" possible ... aborting..." << endl;
                }
                igraph_is_connected(&graph, &isConnected, IGRAPH_STRONG);

                counts++;
            }
            if (counts == maxcount)
            {
                cout << "Probability or number of edges too low... Did not find a connected graph after "<< maxcount <<" attempts... aborting..." << endl;
                return -1;
            }
        }
        else if (direction == "undirected")
        {
            int counts = 0;
            while ((isConnected == 0) & (counts < maxcount))
            {
                if (gn == "GNP")
                {
                    double edgeprob = atof(argv[7]);
                    if ((edgeprob > 1) || (edgeprob < 0))
                    {
                        cout << "probabilities larger than 1 or smaller than 0 ...aborting..." << endl;
                        return -1;
                    }
                    igraph_erdos_renyi_game(&graph, IGRAPH_ERDOS_RENYI_GNP,
                                            popSize, edgeprob,
                                            false, false);
                }
                else if (gn == "GNM")
                {
                    int edgenumber = atoi(argv[7]);
                    if ((edgenumber < 1) || (edgenumber > popSize*(popSize-1)/2))
                    {
                        cout << "number of edges must be greater than 1 and smaller than N*(N-1)/2 ...aborting..." << endl;
                        return -1;
                    }
                    igraph_erdos_renyi_game(&graph, IGRAPH_ERDOS_RENYI_GNM,
                                            popSize, edgenumber,
                                            false, false);
                }
                else
                {
                    cout << "Only \"GNM\" and \"GNP\" possible ... aborting..." << endl;
                }
                igraph_is_connected(&graph, &isConnected, IGRAPH_STRONG);
                counts++;
            }
            if (counts == maxcount)
            {
                cout << "Probability or number of edges too low... Did not find a connected graph after "<< maxcount <<" attempts... aborting..." << endl;
                return -1;
            }
        }
        else
        {
            cout << "Only \"directed\" and \"undirected\" possible for direction of graph!... aborting..." << endl;
            return -1;
        }
    }

//---------------------------- Code snippet for small world network --------------------------------//
    else if (category == "WS")
    {
        igraph_rng_seed(igraph_rng_default(), std::clock());
        igraph_bool_t isConnected = 0;

        double edgeprob = atof(argv[7]);
        if ((edgeprob > 1) || (edgeprob < 0))
        {
            cout << "probabilities larger than 1 or smaller than 0 ...aborting..." << endl;
            return -1;
        }

        int dim = atoi(argv[6]);
        int latSize = pow(popSize,1/double(dim));

        if (direction == "directed")
        {
            while ((isConnected == 0) & (counts < maxcount))
            {
                igraph_watts_strogatz_game(&graph, dim,
                                           latSize, 1,
                                           edgeprob, 0,
                                           0);
                igraph_is_connected(&graph, &isConnected, IGRAPH_STRONG);
                counts++;
            }
        }
        else if (direction == "undirected")
        {
            while ((isConnected == 0) & (counts < maxcount))
            {
                igraph_watts_strogatz_game(&graph, dim,
                                           latSize, 1,
                                           edgeprob, 0,
                                           0);
                igraph_is_connected(&graph, &isConnected, IGRAPH_STRONG);
                counts++;
            }
        }
        else
        {
            cout << "Only \"directed\" and \"undirected\" possible for direction of graph!... aborting..." << endl;
            return -1;
        }
        if (counts == maxcount)
        {
            cout << "Did not find a connected graph after "<< maxcount <<" attempts... aborting..." << endl;
            return -1;
        }
    }

//---------------------------- Code snippet for geometric generator --------------------------------//
    else if(category == "geo")
    {
        igraph_rng_seed(igraph_rng_default(), std::clock());
        igraph_bool_t isConnected = 0;
        double edgeprob = atof(argv[7]);
        if ((edgeprob > 1) || (edgeprob < 0))
        {
            cout << "probabilities larger than 1 or smaller than 0 ...aborting..." << endl;
            return -1;
        }
        bool torus = (atoi(argv[6]) == 1);
        double radius = sqrt(edgeprob/3.14);
        if (direction == "directed")
        {
            while ((isConnected == 0) & (counts < maxcount))
            {
                igraph_grg_game(&graph, popSize,
                                radius, torus,
                                0, 0);
                igraph_is_connected(&graph, &isConnected, IGRAPH_STRONG);
                counts++;
            }
        }
        else if (direction == "undirected")
        {
            while ((isConnected == 0) & (counts < maxcount))
            {
                igraph_grg_game(&graph, popSize,
                                radius, torus,
                                0, 0);
                igraph_is_connected(&graph, &isConnected, IGRAPH_STRONG);
                counts++;
            }
        }
        else
        {
            cout << "Only \"directed\" and \"undirected\" possible for direction of graph!... aborting..." << endl;
            return -1;
        }
        if (counts == maxcount)
        {
            cout << "Probability or number of edges too low... Did not find a connected graph after "<< maxcount <<" attempts... aborting..." << endl;
            return -1;
        }
    }
//---------------------------- Code snippet for barabasi generator --------------------------------//
    else if(category == "BB")
    {
        double power = atof(argv[6]);
        int m = atoi(argv[7]);

        igraph_rng_seed(igraph_rng_default(), std::clock());
        igraph_bool_t isConnected = 0;
        if (direction == "directed")
        {
            cout << "directed Barabasi-Albert never creates connected graphs, use undirected instead! aborting..." << endl;
            return -1;

        }
        else if (direction == "undirected")
        {
            while ((isConnected == 0) & (counts < maxcount))
            {
                igraph_barabasi_game(&graph, popSize,
                                     power,
                                     m,
                                     0,
                                     0,
                                     1.0,
                                     false,
                                     IGRAPH_BARABASI_PSUMTREE,
                                     0);
                igraph_is_connected(&graph, &isConnected, IGRAPH_STRONG);
                counts++;
            }
        }
        else
        {
            cout << "Only \"directed\" and \"undirected\" possible for direction of graph!... aborting..." << endl;
            return -1;
        }
        if (counts == maxcount)
        {
            cout << "Did not find a connected graph after "<< maxcount <<" attempts... aborting..." << endl;
            return -1;
        }
    }
    // ----------   Code snippet for custom graph   ----------
    else if(category == "custom")
    {
        std::string admats = argv[6];
        if (admats.size() != popSize*popSize)
        {
            cout << "adjacency matrix has the wrong size... aborting..." << endl;
            return -1;
        }
        std::vector<int> ints;
        std::transform(std::begin(admats), std::end(admats), std::back_inserter(ints),
                       [](char c)
        {
            return c - '0';
        }
                      );
        std::copy(ints.begin(), ints.end(), admat);
    }

    else
    {
        cout << "Only \"complete\", \"ER\", \"BB\", \"WS\", or \"geo\" as categories... aborting..." << endl;
        return -1;
    }


    // ----------   Here the adjacency matrix gets copied into an array  ----------

    if(category!="custom")
    {
        igraph_matrix_t admatv;
        igraph_matrix_init(&admatv, 0,0);
        igraph_get_adjacency( &graph, &admatv,IGRAPH_GET_ADJACENCY_BOTH,false);
        for(unsigned int i = 0 ; i < popSize ; i++)
        {
            for(unsigned int k = 0 ; k < popSize ; k++)
            {
                admat[ i*popSize + k] = MATRIX(admatv,i,k );
            }
        }

        igraph_destroy(&graph);
        igraph_matrix_destroy(&admatv);
    }
    for (unsigned int i=0; i<popSize; i++) {

        for (unsigned int j=0; j<popSize; j++) {
            // If you want to print the adjacency matrix:
            cout<<admat[i * popSize + j]<<" ";
        }
    }
    cout<<endl;
    t_vectorFP data;
    t_vectorInt row;
    t_vectorInt col;
    data.reserve(popSize * numStates);
    row.reserve(popSize * numStates);
    col.reserve(popSize * numStates);

    //CLOCK//
    start = std::clock();
    createTransitionMatrix(popSize, numStates, fitnessMutants, update, admat, data, row, col);


    std::vector<T> tripletList;
    tripletList.reserve(popSize * numStates);

    for( unsigned int j = 0 ; j < data.size() ; j++)
    {
        tripletList.push_back(T(col.at(j),row.at(j),data.at(j)));
    }

    SpMat mat(numStates,numStates);
    mat.setFromTriplets(tripletList.begin(), tripletList.end());

    // Stopping time after creating transition matrix
    //CLOCK//
    bt = ( std::clock() - start ) / (double) CLOCKS_PER_SEC;

    //for (int i = 0; i<data.size(); i++)
    //    cout<<"unconditional: transition prob from state "<<row[i]<<" to state "<<col[i]<<" is "<<data[i]<<endl;
    string s1;



    /*   ----------   No distinguishing between "probability", "unconditional" time, and "conditional" time   ----------    */

    float * fixProbAllStates = static_cast<float*> (malloc(numStates * sizeof(float)));
    fixProb(mat, popSize, numStates, fixProbAllStates);

    // Stopping time after solving fixation probabilities
    //CLOCK//
    st = ( std::clock() - start) / (double) CLOCKS_PER_SEC - bt;

    float probOne = 0.0;
    for(unsigned int i = 0; i < popSize; i++)
    {
        int j = 1 << i;

        probOne = probOne + fixProbAllStates[j];

    }
    probOne = probOne / (float)(popSize);

    cout << "fixation probability:" << probOne << endl;
    /*   ----------   Printing the fixation probability starting from all states   ----------    */
    /*
    for(unsigned int i = 0; i < numStates; i++)
    {
        bitset<23> b1(i);
        s1 =  b1.to_string();
        cout<<"fixation probability in state ";
        cout<< s1.substr(23-popSize,popSize);
        cout <<" is "<<fixProbAllStates[i]<<endl;
    }
    */
    if((output == "unconditional")||(output == "all"))
    {
        float * uncondFixTimeAllStates = static_cast<float*> (malloc(numStates * sizeof(float)));
        // Stopping the time for solving for unconditional fixation time
        //CLOCK// start = std::clock();
        //CLOCK// bt = ( std::clock() - start ) / (double) CLOCKS_PER_SEC;
        time(mat, popSize, numStates, uncondFixTimeAllStates);
        //CLOCK//

        float avUncondTime = 0.0;
        for(unsigned int i = 0 ; i < popSize ; i++)
        {
            int j = 1 << i;
            avUncondTime = avUncondTime + uncondFixTimeAllStates[j];
        }
        avUncondTime = avUncondTime / (float)(popSize);

        free(uncondFixTimeAllStates);

        cout<< "unconditional fixation time:" << avUncondTime << endl;
    }
    /*   ----------   Printing the average unconditional fixation time starting from all states   ----------    */

    //for(unsigned int i = 0; i < numStates; i++)
    //{
    //    bitset<23> b1(i);
    //    s1 =  b1.to_string();
    //cout<<"Unconditional fixation time in state ";
    //cout<< s1.substr (23-popSize,popSize);
    //cout <<" is "<<uncondFixTimeAllStates[i]<<endl;
    //}

    //float * fixProbAllStates = (float*) malloc(numStates * sizeof(float));
    //fixProb(mat, popSize, numStates, fixProbAllStates);
    if((output == "conditional")||(output == "all"))
    {
        createConditionalTransitionMatrix(popSize, numStates, fixProbAllStates, data, row, col);

        std::vector<T> tripletListCond;
        tripletListCond.reserve(popSize * numStates);

        for( unsigned int j = 0 ; j < data.size() ; j++)
        {
            tripletListCond.push_back(T(col.at(j),row.at(j),data.at(j)));
        }

        SpMat conditionalMatrix(numStates,numStates);
        conditionalMatrix.setFromTriplets(tripletListCond.begin(), tripletListCond.end());


        float * condFixTimeAllStates = static_cast<float*> (malloc(numStates * sizeof(float)));
        time(conditionalMatrix, popSize, numStates, condFixTimeAllStates);


        float avCondTime = 0.0;
        for(unsigned int i = 0 ; i < popSize ; i++)
        {
            int j = 1 << i;
            avCondTime = avCondTime + condFixTimeAllStates[j];
        }
        avCondTime = avCondTime / (float)(popSize);

        free(condFixTimeAllStates);
        cout << "conditional fixation time:" << avCondTime << endl;
    }

    free(fixProbAllStates);
    /*   ----------   Printing the average conditional fixation time starting from all states   ----------    */

    //for(unsigned int i = 0; i < numStates; i++)
    //{
    //bitset<23> b1(i);
    //s1 =  b1.to_string();
    //cout<<"Conditional fixation time in state ";
    //cout<< s1.substr (23-popSize,popSize);
    //cout <<" is "<<condFixTimeAllStates[i]<<endl;
    //}

    st = ( std::clock() - start) / (double) CLOCKS_PER_SEC - bt;
    //CLOCK//
    cout<<"building time: "<< bt <<'\n';
    //CLOCK//
    cout<<"solving time: "<< st << "\n\n";

}
Ejemplo n.º 24
0
int main() {
  igraph_real_t d;
  igraph_vector_t u, v;
  int ret;
  long int i, k, n;

  /********************************
   * Example usage
   ********************************/

  /* Sequences with one element. Such sequences are trivially permuted.
   * The result of any Fisher-Yates shuffle on a sequence with one element
   * must be the original sequence itself.
   */
  n = 1;
  igraph_vector_init(&v, n);
  igraph_rng_seed(igraph_rng_default(), time(0));
  k = R_INTEGER(-1000, 1000);
  VECTOR(v)[0] = k;
  igraph_vector_shuffle(&v);
  if (VECTOR(v)[0] != k) {
    return 1;
  }
  d = R_UNIF(-1000.0, 1000.0);

  VECTOR(v)[0] = d;
  igraph_vector_shuffle(&v);
  if (VECTOR(v)[0] != d) {
    return 2;
  }
  igraph_vector_destroy(&v);

  /* Sequences with multiple elements. A Fisher-Yates shuffle of a sequence S
   * is a random permutation \pi(S) of S. Thus \pi(S) must have the same
   * length and elements as the original sequence S. A major difference between
   * S and its random permutation \pi(S) is that the order in which elements
   * appear in \pi(S) is probably different from how elements are ordered in S.
   * If S has length n = 1, then both \pi(S) and S are equivalent sequences in
   * that \pi(S) is merely S and no permutation has taken place. If S has
   * length n > 1, then there are n! possible permutations of S. Assume that
   * each such permutation is equally likely to appear as a result of the
   * Fisher-Yates shuffle. As n increases, the probability that S is different
   * from \pi(S) also increases. We have a probability of 1 / n! that S and
   * \pi(S) are equivalent sequences.
   */
  n = 100;
  igraph_vector_init(&u, n);
  igraph_vector_init(&v, n);

  for (i = 0; i < n; i++) {
    k = R_INTEGER(-1000, 1000);
    VECTOR(u)[i] = k;
    VECTOR(v)[i] = k;
  }

  igraph_vector_shuffle(&v);
  /* must have same length */
  if (igraph_vector_size(&v) != n) {
    return 3;
  }
  if (igraph_vector_size(&u) != igraph_vector_size(&v)) {
    return 4;
  }
  /* must have same elements */
  igraph_vector_sort(&u);
  igraph_vector_sort(&v);
  if (!igraph_vector_all_e(&u, &v)) {
    return 5;
  }
  igraph_vector_destroy(&u);
  igraph_vector_destroy(&v);

  /* empty sequence */
  igraph_vector_init(&v, 0);
  ret = igraph_vector_shuffle(&v);
  igraph_vector_destroy(&v);

  return ret == 0 ? 0 : 6;
}