int main() {
igraph_t g;
int ret;
/* empty directed graph, zero vertices */
igraph_empty(&g, 0, 1);
if (igraph_vcount(&g) != 0) {
return 1;
}
if (igraph_ecount(&g) != 0) {
return 2;
}
igraph_destroy(&g);
/* empty undirected graph, zero vertices */
igraph_empty(&g, 0, 0);
if (igraph_vcount(&g) != 0) {
return 3;
}
if (igraph_ecount(&g) != 0) {
return 4;
}
igraph_destroy(&g);
/* empty directed graph, 20 vertices */
igraph_empty(&g, 20, 1);
if (igraph_vcount(&g) != 20) {
return 5;
}
if (igraph_ecount(&g) != 0) {
return 6;
}
igraph_destroy(&g);
/* empty undirected graph, 30 vertices */
igraph_empty(&g, 30, 0);
if (igraph_vcount(&g) != 30) {
return 7;
}
if (igraph_ecount(&g) != 0) {
return 8;
}
igraph_destroy(&g);
/* error: negative number of vertices */
igraph_set_error_handler(igraph_error_handler_ignore);
ret=igraph_empty(&g, -1, 0);
if (ret != IGRAPH_EINVAL) {
return 9;
}
return 0;
}
static void barabasi_game(igraph_t *graph, int population, int param, bool isDirected) {
vector<double> p (2*param+1, isDirected);
vector<int> id;
int i, j, from, to;
igraph_empty(graph, population, isDirected);
for (i = 0; i < 2*param+1; i++) {
for (j = i+1; j < 2*param+1; j++) {
from = j;
to = i;
igraph_add_edge (graph, from, to);
p[to]++;
if (!isDirected) p[from]++;
}
}
int k = 0;
for (i = 0; i < 2*param+1; i++) k += p[i];
fprintf (stderr, " awawa %lf\n", k/(double)(2*param+1));
for (; i < population; i++) {
Statistic::sample(p, param, id);
p.push_back(isDirected);
for (j = 0; j < param; j++) {
from = i;
to = id[j];
igraph_add_edge (graph, from, to);
p[to]++;
if (!isDirected) p[from]++;
}
}
k = 0;
for (i = 0; i < population; i++) k += p[i];
}
int main() {
igraph_t g;
igraph_vector_t v, weights;
long int i;
igraph_real_t value;
igraph_arpack_options_t options;
igraph_star(&g, 100, IGRAPH_STAR_UNDIRECTED, 0);
igraph_arpack_options_init(&options);
igraph_vector_init(&v, 0);
igraph_eigenvector_centrality(&g, &v, &value, /*directed=*/ 0,
/*scale=*/0, /*weights=*/0,
&options);
if (options.info != 0) {
return 1;
}
for (i=0; i<igraph_vector_size(&v); i++) {
printf(" %.3f", fabs(VECTOR(v)[i]));
}
printf("\n");
igraph_destroy(&g);
/* Special cases: check for empty graph */
igraph_empty(&g, 10, 0);
igraph_eigenvector_centrality(&g, &v, &value, 0, 0, 0, &options);
if (value != 0.0) {
return 1;
}
for (i=0; i<igraph_vector_size(&v); i++) {
printf(" %.2f", fabs(VECTOR(v)[i]));
}
printf("\n");
igraph_destroy(&g);
/* Special cases: check for full graph, zero weights */
igraph_full(&g, 10, 0, 0);
igraph_vector_init(&weights, 45);
igraph_vector_fill(&weights, 0);
igraph_eigenvector_centrality(&g, &v, &value, 0, 0, &weights, &options);
igraph_vector_destroy(&weights);
if (value != 0.0) {
return 2;
}
for (i=0; i<igraph_vector_size(&v); i++) {
printf(" %.2f", fabs(VECTOR(v)[i]));
}
printf("\n");
igraph_destroy(&g);
igraph_vector_destroy(&v);
return 0;
}
/* Erdos-Renyi : G(n,M)
*/
igraph_t *ggen_generate_erdos_gnm(gsl_rng *r, unsigned long n, unsigned long m)
{
igraph_matrix_t adj;
igraph_t *g = NULL;
int err;
unsigned long i,j;
unsigned long added_edges = 0;
ggen_error_start_stack();
if(r == NULL)
GGEN_SET_ERRNO(GGEN_EINVAL);
if(m > (n*(n-1)/2))
GGEN_SET_ERRNO(GGEN_EINVAL);
g = malloc(sizeof(igraph_t));
GGEN_CHECK_ALLOC(g);
GGEN_FINALLY3(free,g,1);
if(m == 0 || n <= 1)
{
GGEN_CHECK_IGRAPH(igraph_empty(g,n,1));
goto end;
}
if(m == (n*(n-1))/2)
{
GGEN_CHECK_IGRAPH(igraph_full_citation(g,n,1));
goto end;
}
GGEN_CHECK_IGRAPH(igraph_matrix_init(&adj,n,n));
GGEN_FINALLY(igraph_matrix_destroy,&adj);
igraph_matrix_null(&adj);
while(added_edges < m) {
GGEN_CHECK_GSL_DO(i = gsl_rng_uniform_int(r,n));
GGEN_CHECK_GSL_DO(j = gsl_rng_uniform_int(r,n));
if(i < j && igraph_matrix_e(&adj,i,j) == 0)
{
igraph_matrix_set(&adj,i,j,1);
added_edges++;
}
}
GGEN_CHECK_IGRAPH(igraph_adjacency(g,&adj,IGRAPH_ADJ_DIRECTED));
end:
ggen_error_clean(1);
return g;
ggen_error_label:
return NULL;
}
VALUE cIGraph_alloc(VALUE klass){
igraph_t *graph = malloc(sizeof(igraph_t));
VALUE obj;
igraph_empty(graph, 0, 1);
obj = Data_Wrap_Struct(klass, cIGraph_mark, cIGraph_free, graph);
return obj;
}
int main() {
igraph_t g;
igraph_vector_t v;
int ret;
/* without edges */
igraph_empty(&g, 5, IGRAPH_DIRECTED);
igraph_add_vertices(&g, 2, 0);
igraph_add_vertices(&g, 3, 0);
igraph_add_vertices(&g, 1, 0);
igraph_add_vertices(&g, 4, 0);
if (igraph_vcount(&g) != 15) {
return 1;
}
igraph_delete_vertices(&g, igraph_vss_1(2));
if (igraph_vcount(&g) != 14) {
return 2;
}
igraph_destroy(&g);
igraph_vector_init(&v, 8);
VECTOR(v)[0]=0; VECTOR(v)[1]=1;
VECTOR(v)[2]=1; VECTOR(v)[3]=2;
VECTOR(v)[4]=2; VECTOR(v)[5]=3;
VECTOR(v)[6]=2; VECTOR(v)[7]=2;
igraph_create(&g, &v, 0, 0);
igraph_vector_destroy(&v);
/* resize vector */
igraph_delete_vertices(&g, igraph_vss_1(2));
if (igraph_vcount(&g) != 3) {
return 3;
}
if (igraph_ecount(&g) != 1) {
return 4;
}
/* error test */
igraph_set_error_handler(igraph_error_handler_ignore);
ret=igraph_delete_vertices(&g, igraph_vss_1(3));
if (ret != IGRAPH_EINVVID) {
return 5;
}
igraph_destroy(&g);
return 0;
}
int igraph_create_bipartite(igraph_t *graph, const igraph_vector_bool_t *types,
const igraph_vector_t *edges,
igraph_bool_t directed) {
igraph_integer_t no_of_nodes=
(igraph_integer_t) igraph_vector_bool_size(types);
long int no_of_edges=igraph_vector_size(edges);
igraph_real_t min_edge=0, max_edge=0;
igraph_bool_t min_type=0, max_type=0;
long int i;
if (no_of_edges % 2 != 0) {
IGRAPH_ERROR("Invalid (odd) edges vector", IGRAPH_EINVEVECTOR);
}
no_of_edges /= 2;
if (no_of_edges != 0) {
igraph_vector_minmax(edges, &min_edge, &max_edge);
}
if (min_edge < 0 || max_edge >= no_of_nodes) {
IGRAPH_ERROR("Invalid (negative) vertex id", IGRAPH_EINVVID);
}
/* Check types vector */
if (no_of_nodes != 0) {
igraph_vector_bool_minmax(types, &min_type, &max_type);
if (min_type < 0 || max_type > 1) {
IGRAPH_WARNING("Non-binary type vector when creating a bipartite graph");
}
}
/* Check bipartiteness */
for (i=0; i<no_of_edges*2; i+=2) {
long int from=(long int) VECTOR(*edges)[i];
long int to=(long int) VECTOR(*edges)[i+1];
long int t1=VECTOR(*types)[from];
long int t2=VECTOR(*types)[to];
if ( (t1 && t2) || (!t1 && !t2) ) {
IGRAPH_ERROR("Invalid edges, not a bipartite graph", IGRAPH_EINVAL);
}
}
IGRAPH_CHECK(igraph_empty(graph, no_of_nodes, directed));
IGRAPH_FINALLY(igraph_destroy, graph);
IGRAPH_CHECK(igraph_add_edges(graph, edges, 0));
IGRAPH_FINALLY_CLEAN(1);
return 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;
}
int GraphRepresentation::buildIGraphTopology() {
int source_vertex_id, destination_vertex_id;
igraph_i_set_attribute_table(&igraph_cattribute_table);
igraph_empty(&igraph, 0, true);
//cout << "iGraph: number of nodes: " << dm->number_of_nodes << endl;
//cout << "iGraph: number number_of_connections nodes: " << dm->number_of_connections << endl;
for (int i = 0; i < dm->network_nodes.size(); i++) {
NetworkNode *nn = dm->network_nodes[i];
for (int j = 0; j < nn->connections.size(); j++) {
NetworkConnection *nc = nn->connections[j];
map <string, int>::iterator index_it;
/*find that node - if exists*/
index_it = reverse_node_index.find(nc->src_label);
/*check if the source node exists in the reverse index*/
if (index_it == reverse_node_index.end()) {
/*it does not exist...add it*/
source_vertex_id = igraph_vcount(&igraph);
igraph_add_vertices(&igraph, 1, 0);
reverse_node_index.insert(pair<string, int>(nc->src_label, source_vertex_id));
igraph_cattribute_VAS_set(&igraph, "NODEID", source_vertex_id, nc->src_label.c_str());
//cout << "added node " << nc->src_label << " in the igraph" << endl;
} else {
source_vertex_id = (*index_it).second;
}
index_it = reverse_node_index.find(nc->dst_label);
/*check if the destination node exists in the reverse index*/
if (index_it == reverse_node_index.end()) {
/*it does not exist...add it*/
destination_vertex_id = igraph_vcount(&igraph);
igraph_add_vertices(&igraph, 1, 0);
reverse_node_index.insert(pair<string, int>(nc->dst_label, destination_vertex_id));
igraph_cattribute_VAS_set(&igraph, "NODEID", destination_vertex_id, nc->dst_label.c_str());
//cout << "added node " << nc->dst_label << " in the igraph" << endl;
} else {
destination_vertex_id = (*index_it).second;
}
/*add an edge in the graph*/
igraph_add_edge(&igraph, source_vertex_id, destination_vertex_id);
igraph_cattribute_EAS_set(&igraph, "LID", igraph_ecount(&igraph) - 1, nc->LID.to_string().c_str());
reverse_edge_index.insert(pair<string, int>(nc->LID.to_string(), igraph_ecount(&igraph) - 1));
}
}
for (int i = 0; i < dm->network_nodes.size(); i++) {
NetworkNode *nn = dm->network_nodes[i];
igraph_cattribute_VAS_set(&igraph, "iLID", i, nn->iLid.to_string().c_str());
}
}
/* Erdos-Renyi : G(n,p)
*/
igraph_t *ggen_generate_erdos_gnp(gsl_rng *r, unsigned long n, double p)
{
igraph_matrix_t m;
igraph_t *g = NULL;
int err;
unsigned long i,j;
ggen_error_start_stack();
if(r == NULL)
GGEN_SET_ERRNO(GGEN_EINVAL);
if(p < 0.0 || p > 1.0)
GGEN_SET_ERRNO(GGEN_EINVAL);
g = malloc(sizeof(igraph_t));
GGEN_CHECK_ALLOC(g);
GGEN_FINALLY3(free,g,1);
if(p == 0.0)
{
GGEN_CHECK_IGRAPH(igraph_empty(g,n,1));
goto end;
}
if(p == 1.0)
{
GGEN_CHECK_IGRAPH(igraph_full_citation(g,n,1));
goto end;
}
GGEN_CHECK_IGRAPH(igraph_matrix_init(&m,n,n));
GGEN_FINALLY(igraph_matrix_destroy,&m);
for(i = 0; i < n; i++)
for(j = 0; j < n; j++)
if(i < j)
// coin flipping to determine if we add an edge or not
igraph_matrix_set(&m,i,j,gsl_ran_bernoulli(r,p));
else
igraph_matrix_set(&m,i,j,0);
GGEN_CHECK_IGRAPH(igraph_adjacency(g,&m,IGRAPH_ADJ_DIRECTED));
end:
ggen_error_clean(1);
return g;
ggen_error_label:
return NULL;
}
int main(int argc, char **argv) {
unsigned int i;
for (i=0; i<1000; ++i) {
igraph_t graph;
igraph_vector_t edges;
igraph_empty(&graph, 1001, 0);
igraph_vector_init(&edges, 2000);
igraph_add_edges(&graph, &edges, NULL);
igraph_destroy(&graph);
igraph_vector_destroy(&edges);
}
return 0;
}
static void SF2ER (igraph_t *graph, int N, int param, double alpha, bool isDirected) {
int i, j, k, m;
igraph_bool_t areconn;
vector<int> p (N, 0); //quantidade de arestas PA
int etot = 0, acc;
igraph_empty(graph, N, isDirected);
for (i = 0; i < 2*param+1; i++)
for (j = i+1; j < 2*param+1; j++) {
igraph_add_edge (graph, i, j);
p[j]++;
if (!isDirected) p[i]++;
etot += 1+(!isDirected);
}
for (; i < N; i++) {
for (m = param; m > 0; m--) {
if (Statistic::unif() < alpha) { //ER
do {
j = rand()%(N-1);
if (j >= i) j++;
igraph_are_connected(graph, i, j, &areconn);
//printf ("er %d\n", (int)areconn);
} while (areconn == 1);
igraph_add_edge (graph, i, j);
} else { //SF
do {
k = rand()%(etot-p[i]);
//printf ("%d %d %d\n", k, etot, p[i]);
acc = 0;
for (j = 0; j < N; j++) {
if (i == j) continue;
if (acc+p[j] >= k) break;
acc+=p[j];
}
igraph_are_connected(graph, i, j, &areconn);
//printf ("sf %d %d %d\n",k, (int)areconn, etot);
} while (areconn == 1);
igraph_add_edge (graph, i, j);
p[j]++;
if (!isDirected) p[i]++;
etot += 1+(!isDirected);
}
}
}
}
int main(int argc,char** argv)
{
igraph_vector_t *lp;
igraph_t g;
// all ggen methods should fail on incorrect arguments
assert(ggen_analyze_longest_path(NULL) == NULL);
// an empty graph as a longest path of zero
igraph_empty(&g,10,1);
lp = ggen_analyze_longest_path(&g);
assert(lp != NULL);
assert(igraph_vector_size(lp) == 0);
igraph_destroy(&g);
igraph_vector_destroy(lp);
free((void *)lp);
// a full dag as a longest path of containing all vertices
igraph_full_citation(&g,10,1);
lp = ggen_analyze_longest_path(&g);
assert(lp != NULL);
assert(igraph_vector_size(lp) == 10);
igraph_destroy(&g);
igraph_vector_destroy(lp);
free((void *)lp);
// a wrong graph (not dag) should fail
// graph is 0 -> 1 -> 2 and 2 -> 0
igraph_small(&g,10,1,0,1,1,2,2,0,-1);
assert(ggen_analyze_longest_path(&g) == NULL);
igraph_destroy(&g);
// a simple graph should work too
// graph is 0 -> 1 -> 2 and 0 -> 2
igraph_small(&g,10,1,0,1,1,2,0,2,-1);
lp = ggen_analyze_longest_path(&g);
assert(lp != NULL);
assert(igraph_vector_size(lp) == 3);
igraph_destroy(&g);
igraph_vector_destroy(lp);
free((void *)lp);
return 0;
}
igraph_t *ggen_generate_erdos_lbl(gsl_rng *r, unsigned long n, double p, unsigned long nbl)
{
igraph_t *g = NULL;
igraph_matrix_t m;
igraph_vector_t layers;
unsigned long i,j;
int err;
ggen_error_start_stack();
if(r == NULL)
GGEN_SET_ERRNO(GGEN_EINVAL);
if(p < 0.0 || p > 1.0)
GGEN_SET_ERRNO(GGEN_EINVAL);
if(nbl > n || nbl == 0)
GGEN_SET_ERRNO(GGEN_EINVAL);
g = malloc(sizeof(igraph_t));
GGEN_CHECK_ALLOC(g);
GGEN_FINALLY3(free,g,1);
if(p == 0.0)
{
GGEN_CHECK_IGRAPH(igraph_empty(g,n,1));
goto end;
}
if(p == 1.0 && nbl == n)
{
GGEN_CHECK_IGRAPH(igraph_full_citation(g,n,1));
goto end;
}
GGEN_CHECK_IGRAPH(igraph_matrix_init(&m,n,n));
GGEN_FINALLY(igraph_matrix_destroy,&m);
GGEN_CHECK_IGRAPH(igraph_vector_init(&layers,n));
GGEN_FINALLY(igraph_vector_destroy,&layers);
// asign to each vertex a layer
for(i = 0; i < n; i++)
{
GGEN_CHECK_GSL_DO(j = gsl_rng_uniform_int(r,nbl));
VECTOR(layers)[i] = j;
}
// create edges
for(i = 0; i < n; i++)
for(j = 0; j < n; j++)
// if the layer allocation allows the edge, we test for it
if(VECTOR(layers)[i]<VECTOR(layers)[j])
igraph_matrix_set(&m,i,j,gsl_ran_bernoulli(r,p));
else
igraph_matrix_set(&m,i,j,0);
//translate the matrix to a graph
GGEN_CHECK_IGRAPH(igraph_adjacency(g,&m,IGRAPH_ADJ_DIRECTED));
end:
ggen_error_clean(1);
return g;
ggen_error_label:
return NULL;
}
igraph_vector_t *ggen_analyze_lowest_single_ancestor(igraph_t *g)
{
unsigned long i,v,l,vid,r;
int err = 0;
igraph_vector_t toposort,itopo;
igraph_vector_t *lsa;
igraph_t tree;
igraph_vs_t vs;
igraph_vit_t vit;
lca_metadata md;
if(g == NULL)
return NULL;
err = igraph_vector_init(&toposort,igraph_vcount(g));
if(err) return NULL;
err = igraph_topological_sorting(g,&toposort,IGRAPH_OUT);
if(err) goto d_tp;
/* build a reverse index of the toposort */
err = igraph_vector_init(&itopo,igraph_vcount(g));
if(err) goto d_tp;
for(i = 0; i < igraph_vcount(g); i++)
{
v = VECTOR(toposort)[i];
VECTOR(itopo)[v] = i;
}
err = igraph_empty(&tree,1,IGRAPH_DIRECTED);
if(err) goto d_i;
lsa = calloc(1,sizeof(igraph_vector_t*));
if(lsa == NULL) goto cleanup;
err = igraph_vector_init(lsa,igraph_vcount(g));
if(err) goto f_l;
for(v = 1; v < igraph_vcount(g); v++)
{
vid = VECTOR(toposort)[v];
tree_lca_metadata_init(&tree,&md);
tree_lca_preprocessing(&tree,0,&md);
/* iterate over parents of v in g
* The lsa of a node is the LCA of all its parents in our
* special tree.
*/
igraph_vs_adj(&vs, vid, IGRAPH_IN);
igraph_vit_create(g,vs,&vit);
l = VECTOR(itopo)[IGRAPH_VIT_GET(vit)];
IGRAPH_VIT_NEXT(vit);
for(vit;!IGRAPH_VIT_END(vit); IGRAPH_VIT_NEXT(vit))
{
tree_lca_query(&tree,l,VECTOR(itopo)[IGRAPH_VIT_GET(vit)],&r,&md);
l = r;
}
igraph_vit_destroy(&vit);
igraph_vs_destroy(&vs);
tree_lca_metadata_free(&tree,&md);
// update tree
err = igraph_add_vertices(&tree,1,NULL);
if(err) goto d_l;
err = igraph_add_edge(&tree,l,v);
if(err) goto d_l;
VECTOR(*lsa)[vid] = VECTOR(toposort)[l];
}
goto cleanup;
d_l:
igraph_vector_destroy(lsa);
f_l:
free(lsa);
lsa = NULL;
cleanup:
igraph_destroy(&tree);
d_i:
igraph_vector_destroy(&itopo);
d_tp:
igraph_vector_destroy(&toposort);
return lsa;
}
igraph_vector_t * ggen_analyze_longest_antichain(igraph_t *g)
{
/* The following steps are implemented :
* - Convert our DAG to a specific bipartite graph B
* - solve maximum matching on B
* - conver maximum matching to min vectex cover
* - convert min vertex cover to antichain on G
*/
int err;
unsigned long i,vg,found,added;
igraph_t b,gstar;
igraph_vector_t edges,*res = NULL;
igraph_vector_t c,s,t,todo,n,next,l,r;
igraph_eit_t eit;
igraph_es_t es;
igraph_integer_t from,to;
igraph_vit_t vit;
igraph_vs_t vs;
igraph_real_t value;
if(g == NULL)
return NULL;
/* before creating the bipartite graph, we need all relations
* between any two vertices : the transitive closure of g */
err = igraph_copy(&gstar,g);
if(err) return NULL;
err = ggen_transform_transitive_closure(&gstar);
if(err) goto error;
/* Bipartite convertion : let G = (S,C),
* we build B = (U,V,E) with
* - U = V = S (each vertex is present twice)
* - (u,v) \in E iff :
* - u \in U
* - v \in V
* - u < v in C (warning, this means that we take
* transitive closure into account, not just the
* original edges)
* We will also need two additional nodes further in the code.
*/
vg = igraph_vcount(g);
err = igraph_empty(&b,vg*2,1);
if(err) goto error;
/* id and id+vg will be a vertex in U and its copy in V,
* iterate over gstar edges to create edges in b
*/
err = igraph_vector_init(&edges,igraph_ecount(&gstar));
if(err) goto d_b;
igraph_vector_clear(&edges);
err = igraph_eit_create(&gstar,igraph_ess_all(IGRAPH_EDGEORDER_ID),&eit);
if(err) goto d_edges;
for(IGRAPH_EIT_RESET(eit); !IGRAPH_EIT_END(eit); IGRAPH_EIT_NEXT(eit))
{
err = igraph_edge(&gstar,IGRAPH_EIT_GET(eit),&from,&to);
if(err)
{
igraph_eit_destroy(&eit);
goto d_edges;
}
to += vg;
igraph_vector_push_back(&edges,(igraph_real_t)from);
igraph_vector_push_back(&edges,(igraph_real_t)to);
}
igraph_eit_destroy(&eit);
err = igraph_add_edges(&b,&edges,NULL);
if(err) goto d_edges;
/* maximum matching on b */
igraph_vector_clear(&edges);
err = bipartite_maximum_matching(&b,&edges);
if(err) goto d_edges;
/* Let M be the max matching, and N be E - M
* Define T as all unmatched vectices from U as well as all vertices
* reachable from those by going left-to-right along N and right-to-left along
* M.
* Define L = U - T, R = V \inter T
* C:= L + R
* C is a minimum vertex cover
*/
err = igraph_vector_init_seq(&n,0,igraph_ecount(&b)-1);
if(err) goto d_edges;
err = vector_diff(&n,&edges);
if(err) goto d_n;
err = igraph_vector_init(&c,vg);
if(err) goto d_n;
igraph_vector_clear(&c);
/* matched vertices : S */
err = igraph_vector_init(&s,vg);
if(err) goto d_c;
igraph_vector_clear(&s);
for(i = 0; i < igraph_vector_size(&edges); i++)
{
err = igraph_edge(&b,VECTOR(edges)[i],&from,&to);
if(err) goto d_s;
igraph_vector_push_back(&s,from);
}
/* we may have inserted the same vertex multiple times */
err = vector_uniq(&s);
if(err) goto d_s;
/* unmatched */
err = igraph_vector_init_seq(&t,0,vg-1);
if(err) goto d_s;
err = vector_diff(&t,&s);
if(err) goto d_t;
/* alternating paths
*/
err = igraph_vector_copy(&todo,&t);
if(err) goto d_t;
err = igraph_vector_init(&next,vg);
if(err) goto d_todo;
igraph_vector_clear(&next);
do {
vector_uniq(&todo);
added = 0;
for(i = 0; i < igraph_vector_size(&todo); i++)
{
if(VECTOR(todo)[i] < vg)
{
/* scan edges */
err = igraph_es_adj(&es,VECTOR(todo)[i],IGRAPH_OUT);
if(err) goto d_next;
err = igraph_eit_create(&b,es,&eit);
if(err)
{
igraph_es_destroy(&es);
goto d_next;
}
for(IGRAPH_EIT_RESET(eit); !IGRAPH_EIT_END(eit); IGRAPH_EIT_NEXT(eit))
{
if(igraph_vector_binsearch(&n,IGRAPH_EIT_GET(eit),NULL))
{
err = igraph_edge(&b,IGRAPH_EIT_GET(eit),&from,&to);
if(err)
{
igraph_eit_destroy(&eit);
igraph_es_destroy(&es);
goto d_next;
}
if(!igraph_vector_binsearch(&t,to,NULL))
{
igraph_vector_push_back(&next,to);
added = 1;
}
}
}
}
else
{
/* scan edges */
err = igraph_es_adj(&es,VECTOR(todo)[i],IGRAPH_IN);
if(err) goto d_next;
err = igraph_eit_create(&b,es,&eit);
if(err)
{
igraph_es_destroy(&es);
goto d_next;
}
for(IGRAPH_EIT_RESET(eit); !IGRAPH_EIT_END(eit); IGRAPH_EIT_NEXT(eit))
{
if(igraph_vector_binsearch(&edges,IGRAPH_EIT_GET(eit),NULL))
{
err = igraph_edge(&b,IGRAPH_EIT_GET(eit),&from,&to);
if(err)
{
igraph_eit_destroy(&eit);
igraph_es_destroy(&es);
goto d_next;
}
if(!igraph_vector_binsearch(&t,to,NULL))
{
igraph_vector_push_back(&next,from);
added = 1;
}
}
}
}
igraph_es_destroy(&es);
igraph_eit_destroy(&eit);
}
igraph_vector_append(&t,&todo);
igraph_vector_clear(&todo);
igraph_vector_append(&todo,&next);
igraph_vector_clear(&next);
} while(added);
err = igraph_vector_init_seq(&l,0,vg-1);
if(err) goto d_t;
err = vector_diff(&l,&t);
if(err) goto d_l;
err = igraph_vector_update(&c,&l);
if(err) goto d_l;
err = igraph_vector_init(&r,vg);
if(err) goto d_l;
igraph_vector_clear(&r);
/* compute V \inter T */
for(i = 0; i < igraph_vector_size(&t); i++)
{
if(VECTOR(t)[i] >= vg)
igraph_vector_push_back(&r,VECTOR(t)[i]);
}
igraph_vector_add_constant(&r,(igraph_real_t)-vg);
err = vector_union(&c,&r);
if(err) goto d_r;
/* our antichain is U - C */
res = malloc(sizeof(igraph_vector_t));
if(res == NULL) goto d_r;
err = igraph_vector_init_seq(res,0,vg-1);
if(err) goto f_res;
err = vector_diff(res,&c);
if(err) goto d_res;
goto ret;
d_res:
igraph_vector_destroy(res);
f_res:
free(res);
res = NULL;
ret:
d_r:
igraph_vector_destroy(&r);
d_l:
igraph_vector_destroy(&l);
d_next:
igraph_vector_destroy(&next);
d_todo:
igraph_vector_destroy(&todo);
d_t:
igraph_vector_destroy(&t);
d_s:
igraph_vector_destroy(&s);
d_c:
igraph_vector_destroy(&c);
d_n:
igraph_vector_destroy(&n);
d_edges:
igraph_vector_destroy(&edges);
d_b:
igraph_destroy(&b);
error:
igraph_destroy(&gstar);
return res;
}
void LayoutBuilder::produce(AbstractPetriNetBuilder *builder){
if(!attrTableAttached){
igraph_i_set_attribute_table(&igraph_cattribute_table);
attrTableAttached = true;
}
size_t V = places.size() + transitions.size();
size_t E = inArcs.size() + outArcs.size();
igraph_t graph;
// Create a directed graph
igraph_empty(&graph, V, true);
// Create vector with all edges
igraph_vector_t edges;
igraph_vector_init(&edges, E * 2);
// Add edges to vector
int i = 0;
for(ArcIter it = inArcs.begin(); it != inArcs.end(); it++){
VECTOR(edges)[i++] = numberFromName(it->start);
VECTOR(edges)[i++] = numberFromName(it->end);
}
for(ArcIter it = outArcs.begin(); it != outArcs.end(); it++){
VECTOR(edges)[i++] = numberFromName(it->start);
VECTOR(edges)[i++] = numberFromName(it->end);
}
// Add the edges to graph
igraph_add_edges(&graph, &edges, 0);
// Delete the vector with edges
igraph_vector_destroy(&edges);
// Arrays to store result in
double posx[V];
double posy[V];
// Provide current positions, if they're used at all
if(startFromCurrentPositions){
int i = 0;
for(PlaceIter it = places.begin(); it != places.end(); it++){
posx[i] = it->x;
posy[i] = it->y;
igraph_cattribute_VAN_set(&graph, "id", i, i);
i++;
}
for(TransitionIter it = transitions.begin(); it != transitions.end(); it++){
posx[i] = it->x;
posy[i] = it->y;
igraph_cattribute_VAN_set(&graph, "id", i, i);
i++;
}
}
// Decompose the graph, and layout subgraphs induvidually
igraph_vector_ptr_t subgraphs;
igraph_vector_ptr_init(&subgraphs, 0);
igraph_decompose(&graph, &subgraphs, IGRAPH_WEAK, -1, 0);
// Offset for places subgraphs
double offsetx = 0;
double offsety = 0;
// Layout, translate and extract results for each subgraph
for(int i = 0; i < igraph_vector_ptr_size(&subgraphs); i++){
//Get the subgraph
igraph_t* subgraph = (igraph_t*)VECTOR(subgraphs)[i];
// Allocate result matrix
igraph_matrix_t sublayout;
igraph_matrix_init(&sublayout, 0, 0);
// Vertex selector and iterator
igraph_vs_t vs;
igraph_vit_t vit;
// Select all and create iterator
igraph_vs_all(&vs);
igraph_vit_create(subgraph, vs, &vit);
// Initialize sublayout, using original positions
if(startFromCurrentPositions){
// Count vertices
int vertices = 0;
// Iterator over vertices to count them, hacked but it works
while(!IGRAPH_VIT_END(vit)){
vertices++;
IGRAPH_VIT_NEXT(vit);
}
//Reset vertex iterator
IGRAPH_VIT_RESET(vit);
// Resize sublayout
igraph_matrix_resize(&sublayout, vertices, 2);
// Iterator over vertices
while(!IGRAPH_VIT_END(vit)){
int subindex = (int)IGRAPH_VIT_GET(vit);
int index = (int)igraph_cattribute_VAN(subgraph, "id", subindex);
MATRIX(sublayout, subindex, 0) = posx[index];
MATRIX(sublayout, subindex, 1) = posy[index];
IGRAPH_VIT_NEXT(vit);
}
//Reset vertex iterator
IGRAPH_VIT_RESET(vit);
}
igraph_layout_kamada_kawai(subgraph, &sublayout, 1000, ((double)V)/4.0, 10, 0.99, V*V, startFromCurrentPositions);
// Other layout algorithms with reasonable parameters
//igraph_layout_kamada_kawai(subgraph, &sublayout, 1000, ((double)V)/4.0, 10, 0.99, V*V, startFromCurrentPositions);
//igraph_layout_grid_fruchterman_reingold(subgraph, &sublayout, 500, V, V*V, 1.5, V*V*V, V*V/4, startFromCurrentPositions);
//igraph_layout_fruchterman_reingold(subgraph, &sublayout, 500, V, V*V, 1.5, V*V*V, startFromCurrentPositions, NULL);
//igraph_layout_lgl(subgraph, &sublayout, 150, V, V*V, 1.5, V*V*V, sqrt(V), -1);
//Find min and max values:
double minx = DBL_MAX,
miny = DBL_MAX,
maxx = -DBL_MAX,
maxy = -DBL_MAX;
//Iterator over all vertices
while(!IGRAPH_VIT_END(vit)){
int subindex = (int)IGRAPH_VIT_GET(vit);
double x = MATRIX(sublayout, subindex, 0) * factor;
double y = MATRIX(sublayout, subindex, 1) * factor;
minx = minx < x ? minx : x;
miny = miny < y ? miny : y;
maxx = maxx > x ? maxx : x;
maxy = maxy > y ? maxy : y;
IGRAPH_VIT_NEXT(vit);
}
//Reset vertex iterator
IGRAPH_VIT_RESET(vit);
// Compute translation
double tx = margin - minx;
double ty = margin - miny;
// Decide whether to put it below or left of current content
if(maxx - minx + offsetx < maxy - miny + offsety){
tx += offsetx;
offsetx += maxx - minx + margin;
if(offsety < maxy - miny + margin)
offsety = maxy - miny + margin;
}else{
ty += offsety;
offsety += maxy - miny + margin;
if(offsetx < maxx - minx + margin)
offsetx = maxx - minx + margin;
}
// Translate and extract results
while(!IGRAPH_VIT_END(vit)){
int subindex = (int)IGRAPH_VIT_GET(vit);
int index = (int)igraph_cattribute_VAN(subgraph, "id", subindex);
double x = MATRIX(sublayout, subindex, 0) * factor;
double y = MATRIX(sublayout, subindex, 1) * factor;
posx[index] = x + tx;
posy[index] = y + ty;
IGRAPH_VIT_NEXT(vit);
}
// Destroy iterator and selector
igraph_vit_destroy(&vit);
igraph_vs_destroy(&vs);
// Destroy the sublayout
igraph_matrix_destroy(&sublayout);
// Destroy subgraph
igraph_destroy(subgraph);
free(VECTOR(subgraphs)[i]);
}
// Remove the attributes
igraph_cattribute_remove_v(&graph, "id");
// Destroy the graph
igraph_destroy(&graph);
// Insert results
i = 0;
for(PlaceIter it = places.begin(); it != places.end(); it++){
it->x = posx[i];
it->y = posy[i];
i++;
}
for(TransitionIter it = transitions.begin(); it != transitions.end(); it++){
it->x = posx[i];
it->y = posy[i];
i++;
}
// Produce variables
for(VarIter it = vars.begin(); it != vars.end(); it++)
builder->addVariable(it->name, it->initialValue, it->range);
for(BoolVarIter it = boolVars.begin(); it != boolVars.end(); it++)
builder->addBoolVariable(it->name, it->initialValue);
for(PlaceIter it = places.begin(); it != places.end(); it++)
builder->addPlace(it->name, it->tokens, it->x, it->y);
for(TransitionIter it = transitions.begin(); it != transitions.end(); it++)
builder->addTransition(it->name, it->conditions, it->assignments, it->x, it->y);
for(ArcIter it = inArcs.begin(); it != inArcs.end(); it++)
builder->addInputArc(it->start, it->end, it->weight);
for(ArcIter it = outArcs.begin(); it != outArcs.end(); it++)
builder->addInputArc(it->start, it->end, it->weight);
//Reset builder state (just in case some idoit decides to reuse it!
vars.clear();
boolVars.clear();
places.clear();
transitions.clear();
inArcs.clear();
outArcs.clear();
}
TMIgraph::TMIgraph() {
igraph_i_set_attribute_table(&igraph_cattribute_table);
igraph_empty(&graph, 0, true);
}
int igraph_forest_fire_game(igraph_t *graph, igraph_integer_t nodes,
igraph_real_t fw_prob, igraph_real_t bw_factor,
igraph_integer_t pambs, igraph_bool_t directed) {
igraph_vector_long_t visited;
long int no_of_nodes=nodes, actnode, i;
igraph_vector_t edges;
igraph_vector_t *inneis, *outneis;
igraph_i_forest_fire_data_t data;
igraph_dqueue_t neiq;
long int ambs=pambs;
igraph_real_t param_geom_out=1-fw_prob;
igraph_real_t param_geom_in=1-fw_prob*bw_factor;
if (fw_prob < 0) {
IGRAPH_ERROR("Forest fire model: 'fw_prob' should be between non-negative",
IGRAPH_EINVAL);
}
if (bw_factor < 0) {
IGRAPH_ERROR("Forest fire model: 'bw_factor' should be non-negative",
IGRAPH_EINVAL);
}
if (ambs < 0) {
IGRAPH_ERROR("Number of ambassadors ('ambs') should be non-negative",
IGRAPH_EINVAL);
}
if (fw_prob == 0 || ambs == 0) {
IGRAPH_WARNING("'fw_prob or ambs is zero, creating empty graph");
IGRAPH_CHECK(igraph_empty(graph, nodes, directed));
return 0;
}
IGRAPH_VECTOR_INIT_FINALLY(&edges, 0);
inneis=igraph_Calloc(no_of_nodes, igraph_vector_t);
if (!inneis) {
IGRAPH_ERROR("Cannot run forest fire model", IGRAPH_ENOMEM);
}
IGRAPH_FINALLY(igraph_free, inneis);
outneis=igraph_Calloc(no_of_nodes, igraph_vector_t);
if (!outneis) {
IGRAPH_ERROR("Cannot run forest fire model", IGRAPH_ENOMEM);
}
IGRAPH_FINALLY(igraph_free, outneis);
data.inneis=inneis;
data.outneis=outneis;
data.no_of_nodes=no_of_nodes;
IGRAPH_FINALLY(igraph_i_forest_fire_free, &data);
for (i=0; i<no_of_nodes; i++) {
IGRAPH_CHECK(igraph_vector_init(inneis+i, 0));
IGRAPH_CHECK(igraph_vector_init(outneis+i, 0));
}
IGRAPH_CHECK(igraph_vector_long_init(&visited, no_of_nodes));
IGRAPH_FINALLY(igraph_vector_long_destroy, &visited);
IGRAPH_DQUEUE_INIT_FINALLY(&neiq, 10);
RNG_BEGIN();
#define ADD_EDGE_TO(nei) \
if (VECTOR(visited)[(nei)] != actnode+1) { \
VECTOR(visited)[(nei)] = actnode+1; \
IGRAPH_CHECK(igraph_dqueue_push(&neiq, nei)); \
IGRAPH_CHECK(igraph_vector_push_back(&edges, actnode)); \
IGRAPH_CHECK(igraph_vector_push_back(&edges, nei)); \
IGRAPH_CHECK(igraph_vector_push_back(outneis+actnode, nei)); \
IGRAPH_CHECK(igraph_vector_push_back(inneis+nei, actnode)); \
}
IGRAPH_PROGRESS("Forest fire: ", 0.0, NULL);
for (actnode=1; actnode < no_of_nodes; actnode++) {
IGRAPH_PROGRESS("Forest fire: ", 100.0*actnode/no_of_nodes, NULL);
IGRAPH_ALLOW_INTERRUPTION();
/* We don't want to visit the current vertex */
VECTOR(visited)[actnode] = actnode+1;
/* Choose ambassador(s) */
for (i=0; i<ambs; i++) {
long int a=RNG_INTEGER(0, actnode-1);
ADD_EDGE_TO(a);
}
while (!igraph_dqueue_empty(&neiq)) {
long int actamb=(long int) igraph_dqueue_pop(&neiq);
igraph_vector_t *outv=outneis+actamb;
igraph_vector_t *inv=inneis+actamb;
long int no_in=igraph_vector_size(inv);
long int no_out=igraph_vector_size(outv);
long int neis_out=(long int) RNG_GEOM(param_geom_out);
long int neis_in=(long int) RNG_GEOM(param_geom_in);
/* outgoing neighbors */
if (neis_out >= no_out) {
for (i=0; i<no_out; i++) {
long int nei=(long int) VECTOR(*outv)[i];
ADD_EDGE_TO(nei);
}
} else {
long int oleft=no_out;
for (i=0; i<neis_out && oleft > 0; ) {
long int which=RNG_INTEGER(0, oleft-1);
long int nei=(long int) VECTOR(*outv)[which];
VECTOR(*outv)[which] = VECTOR(*outv)[oleft-1];
VECTOR(*outv)[oleft-1] = nei;
if (VECTOR(visited)[nei] != actnode+1) {
ADD_EDGE_TO(nei);
i++;
}
oleft--;
}
}
/* incoming neighbors */
if (neis_in >= no_in) {
for (i=0; i<no_in; i++) {
long int nei=(long int) VECTOR(*inv)[i];
ADD_EDGE_TO(nei);
}
} else {
long int ileft=no_in;
for (i=0; i<neis_in && ileft > 0; ) {
long int which=RNG_INTEGER(0, ileft-1);
long int nei=(long int) VECTOR(*inv)[which];
VECTOR(*inv)[which] = VECTOR(*inv)[ileft-1];
VECTOR(*inv)[ileft-1] = nei;
if (VECTOR(visited)[nei] != actnode+1) {
ADD_EDGE_TO(nei);
i++;
}
ileft--;
}
}
} /* while neiq not empty */
} /* actnode < no_of_nodes */
#undef ADD_EDGE_TO
RNG_END();
IGRAPH_PROGRESS("Forest fire: ", 100.0, NULL);
igraph_dqueue_destroy(&neiq);
igraph_vector_long_destroy(&visited);
igraph_i_forest_fire_free(&data);
igraph_free(outneis);
igraph_free(inneis);
IGRAPH_FINALLY_CLEAN(5);
IGRAPH_CHECK(igraph_create(graph, &edges, nodes, directed));
igraph_vector_destroy(&edges);
IGRAPH_FINALLY_CLEAN(1);
return 0;
}
int ggen_read_graph(igraph_t *g,FILE *input)
{
Agraph_t *cg;
Agnode_t *v;
Agedge_t *e;
igraph_vector_t edges;
igraph_vector_t vertices;
int err;
unsigned long esize;
unsigned long vsize;
unsigned long from, to;
igraph_integer_t eid;
Agsym_t *att;
/* read the graph */
cg = agread((void *)input,NULL);
if(!cg) return 1;
if(!agisdirected(cg))
{
error("Input graph is undirected\n");
err = 1;
goto error_d;
}
/* init edge array */
err = igraph_vector_init(&edges,2*agnedges(cg));
if(err) goto error_d;
err = igraph_vector_init(&vertices,agnnodes(cg));
if(err) goto error_de;
/* init igraph */
igraph_empty(g,agnnodes(cg),1);
/* asign id to each vertex */
vsize = 0;
for(v = agfstnode(cg); v; v = agnxtnode(cg,v))
VECTOR(vertices)[vsize++] = AGID(v);
/* loop through each edge */
esize = 0;
for(v = agfstnode(cg); v; v = agnxtnode(cg,v))
{
from = find_id(AGID(v),vertices,vsize);
for(e = agfstout(cg,v); e; e = agnxtout(cg,e))
{
to = find_id(AGID(aghead(e)),vertices,vsize);
VECTOR(edges)[esize++] = from;
VECTOR(edges)[esize++] = to;
}
}
/* finish the igraph */
err = igraph_add_edges(g,&edges,NULL);
if(err) goto error;
/* read graph properties */
att = agnxtattr(cg,AGRAPH,NULL);
while(att != NULL)
{
/* copy this attribute to igraph */
SETGAS(g,att->name,agxget(cg,att));
att = agnxtattr(cg,AGRAPH,att);
}
/* we keep the graph name using a special attribute */
SETGAS(g,GGEN_GRAPH_NAME_ATTR,agnameof(cg));
/* read vertex properties */
att = agnxtattr(cg,AGNODE,NULL);
while(att != NULL)
{
/* iterate over all vertices for this attribute */
for(v = agfstnode(cg); v; v = agnxtnode(cg,v))
{
from = find_id(AGID(v),vertices,vsize);
SETVAS(g,att->name,from,agxget(v,att));
}
att = agnxtattr(cg,AGNODE,att);
}
/* we keep each vertex name in a special attribute */
for(v = agfstnode(cg); v; v = agnxtnode(cg,v))
{
from = find_id(AGID(v),vertices,vsize);
SETVAS(g,GGEN_VERTEX_NAME_ATTR,from,agnameof(v));
}
/* read edges properties */
att = agnxtattr(cg,AGEDGE,NULL);
while(att != NULL)
{
/* the only way to iterate over all edges is to iterate
* over the vertices */
for(v = agfstnode(cg); v; v = agnxtnode(cg,v))
{
from = find_id(AGID(v),vertices,vsize);
for(e = agfstout(cg,v); e; e = agnxtout(cg,e))
{
to = find_id(AGID(aghead(e)),vertices,vsize);
igraph_get_eid(g,&eid,from,to,1,0);
SETEAS(g,att->name,eid,agxget(e,att));
}
}
att = agnxtattr(cg,AGEDGE,att);
}
goto cleanup;
error:
igraph_destroy(g);
cleanup:
igraph_vector_destroy(&vertices);
error_de:
igraph_vector_destroy(&edges);
error_d:
agclose(cg);
return err;
}
static void
rvine_trees_to_vine(dml_vine_t *vine, igraph_t **trees)
{
size_t n = vine->dim;
size_t *order_inv;
gsl_vector_short *B;
igraph_integer_t Cea, Ceb;
size_t x = 0, x_hat = 0, x_hat_hat = 0; // Initialized to avoid GCC warnings.
dml_copula_t *copula = NULL; // Initialized to avoid GCC warnings.
igraph_integer_t e; // Edge id.
igraph_integer_t a, b, aa, ab, ba, bb; // Vertex id.
igraph_t **last_trees = NULL;
igraph_t *graph = NULL;
gsl_vector_short *Ue, *Ua, *Ub;
// Set the number of trees of the vines.
vine->trees = n - 1;
while (trees[vine->trees - 1] == NULL) vine->trees--;
// Nothing to do for vines without trees.
if (vine->trees == 0) return;
// Selecting a structure for the trees that were truncated.
// Is this really necessary? Think a better solution.
if (vine->trees != n - 1) {
igraph_i_set_attribute_table(&igraph_cattribute_table);
last_trees = g_malloc_n(n - 1 - vine->trees, sizeof(igraph_t *));
graph = g_malloc(sizeof(igraph_t));
for (size_t k = vine->trees; k < n - 1; k++) { // Tree index.
igraph_empty(graph, n - k, IGRAPH_UNDIRECTED);
// Adding all "possible" edges.
for (a = 0; a < igraph_vcount(graph) - 1; a++) {
for (b = a + 1; b < igraph_vcount(graph); b++) {
// Checking the proximity condition.
igraph_edge(k <= vine->trees ? trees[k - 1] : last_trees[k - 1 - vine->trees], a, &aa, &ab);
igraph_edge(k <= vine->trees ? trees[k - 1] : last_trees[k - 1 - vine->trees], b, &ba, &bb);
if (aa == ba || aa == bb || ab == ba || ab == bb) {
igraph_add_edge(graph, a, b);
igraph_get_eid(graph, &e, a, b, IGRAPH_UNDIRECTED, 1);
// Variables "connected" by this edge and conditioned set.
Ua = EAP(k <= vine->trees ? trees[k - 1] : last_trees[k - 1 - vine->trees], "Ue", a);
Ub = EAP(k <= vine->trees ? trees[k - 1] : last_trees[k - 1 - vine->trees], "Ue", b);
Ue = gsl_vector_short_calloc(n);
for (size_t i = 0; i < n; i++) {
gsl_vector_short_set(Ue, i,
gsl_vector_short_get(Ua, i)
| gsl_vector_short_get(Ub, i));
if (gsl_vector_short_get(Ua, i)
&& !gsl_vector_short_get(Ub, i)) {
SETEAN(graph, "Cea", e, i + 1);
}
if (gsl_vector_short_get(Ub, i)
&& !gsl_vector_short_get(Ua, i)) {
SETEAN(graph, "Ceb", e, i + 1);
}
}
SETEAP(graph, "Ue", e, Ue);
}
}
}
// Compute the minimum weight spanning tree.
last_trees[k - vine->trees] = g_malloc(sizeof(igraph_t));
igraph_minimum_spanning_tree_unweighted(graph, last_trees[k - vine->trees]);
igraph_destroy(graph);
}
}
order_inv = g_malloc0_n(n, sizeof(size_t));
B = gsl_vector_short_calloc(n);
// for loop in line 2.
for (size_t i = 0; i < n - 1; i++) {
if (trees[n - i - 2] == NULL) {
for (e = 0; e < igraph_ecount(last_trees[n - i - 2 - vine->trees]); e++) {
x = EAN(last_trees[n - i - 2 - vine->trees], "Cea", e);
x_hat = EAN(last_trees[n - i - 2 - vine->trees], "Ceb", e);
if (!gsl_vector_short_get(B, x - 1)
&& !gsl_vector_short_get(B, x_hat - 1)) {
x_hat = 0;
copula = NULL;
break;
}
}
} else {
for (e = 0; e < igraph_ecount(trees[n - i - 2]); e++) {
x = EAN(trees[n - i - 2], "Cea", e);
x_hat = EAN(trees[n - i - 2], "Ceb", e);
if (!gsl_vector_short_get(B, x - 1)
&& !gsl_vector_short_get(B, x_hat - 1)) {
copula = EAP(trees[n - i - 2], "copula", e);
break;
}
}
}
// Line 4.
gsl_vector_short_set(B, x - 1, 1);
vine->order[n - i - 1] = x - 1;
order_inv[x - 1] = n - i;
vine->matrix[i][i] = x;
vine->matrix[i + 1][i] = x_hat;
vine->copulas[i + 1][i] = copula;
// for loop in line 5.
for (size_t k = i + 2; k < n; k++) {
if (trees[n - k - 1] != NULL) {
for (e = 0; e < igraph_ecount(trees[n - k - 1]); e++) {
Cea = EAN(trees[n - k - 1], "Cea", e);
Ceb = EAN(trees[n - k - 1], "Ceb", e);
if (x == Cea) {
x_hat_hat = Ceb;
if (!gsl_vector_short_get(B, x_hat_hat - 1)) {
// The pseudocode of the algorithm does not included
// this check. Invalid matrices were generated when
// x_hat_hat is set to an index already assigned
// to a diagonal entry.
copula = EAP(trees[n - k - 1], "copula", e);
break;
}
} else if (x == Ceb) {
x_hat_hat = Cea;
if (!gsl_vector_short_get(B, x_hat_hat - 1)) {
// Ibdem to the previous comment.
copula = EAP(trees[n - k - 1], "copula", e);
break;
}
}
}
vine->matrix[k][i] = x_hat_hat;
vine->copulas[k][i] = copula;
}
}
}
for (size_t i = 0; i < n; i++) {
if (!gsl_vector_short_get(B, i)) {
vine->matrix[n - 1][n - 1] = i + 1;
vine->order[0] = i;
order_inv[i] = 1;
break;
}
}
// Reorder the variables. The simulation algorithm assumes that the
// diagonal entries of the R-vine matrix are ordered from n to 1.
for (size_t i = 0; i < n; i++) {
for (size_t j = 0; j <= i; j++) {
if (vine->matrix[i][j] > 0) {
vine->matrix[i][j] = order_inv[vine->matrix[i][j] - 1];
}
}
}
if (vine->trees != n - 1) {
for (size_t i = 0; i < n - 1 - vine->trees; i++) {
for (e = 0; e < igraph_ecount(last_trees[i]); e++) {
Ue = EAP(last_trees[i], "Ue", e);
gsl_vector_short_free(Ue);
}
DELEA(last_trees[i], "Ue");
igraph_destroy(last_trees[i]);
g_free(last_trees[i]);
}
g_free(last_trees);
g_free(graph);
}
g_free(order_inv);
gsl_vector_short_free(B);
}
int main() {
igraph_t g;
igraph_vector_t v, res, reset, weights;
igraph_arpack_options_t arpack_options;
igraph_real_t value;
int ret;
igraph_pagerank_power_options_t power_options;
/* Test graphs taken from http://www.iprcom.com/papers/pagerank/ */
igraph_vector_init(&v, 10);
VECTOR(v)[0]=0; VECTOR(v)[1]=1;
VECTOR(v)[2]=1; VECTOR(v)[3]=2;
VECTOR(v)[4]=2; VECTOR(v)[5]=0;
VECTOR(v)[6]=3; VECTOR(v)[7]=2;
VECTOR(v)[8]=0; VECTOR(v)[9]=2;
igraph_create(&g, &v, 0, 1);
igraph_vector_init(&res, 0);
oldwarn=igraph_set_warning_handler(warning_handler_stdout);
igraph_pagerank_old(&g, &res, igraph_vss_all(), 1, 1000, 0.001, 0.85, 0);
print_vector(&res, stdout);
igraph_vector_destroy(&res);
igraph_vector_destroy(&v);
igraph_destroy(&g);
igraph_vector_init(&v, 28);
VECTOR(v)[ 0]=0; VECTOR(v)[ 1]=1;
VECTOR(v)[ 2]=0; VECTOR(v)[ 3]=2;
VECTOR(v)[ 4]=0; VECTOR(v)[ 5]=3;
VECTOR(v)[ 6]=1; VECTOR(v)[ 7]=0;
VECTOR(v)[ 8]=2; VECTOR(v)[ 9]=0;
VECTOR(v)[10]=3; VECTOR(v)[11]=0;
VECTOR(v)[12]=3; VECTOR(v)[13]=4;
VECTOR(v)[14]=3; VECTOR(v)[15]=5;
VECTOR(v)[16]=3; VECTOR(v)[17]=6;
VECTOR(v)[18]=3; VECTOR(v)[19]=7;
VECTOR(v)[20]=4; VECTOR(v)[21]=0;
VECTOR(v)[22]=5; VECTOR(v)[23]=0;
VECTOR(v)[24]=6; VECTOR(v)[25]=0;
VECTOR(v)[26]=7; VECTOR(v)[27]=0;
igraph_create(&g, &v, 0, 1);
igraph_vector_init(&res, 0);
igraph_pagerank_old(&g, &res, igraph_vss_all(), 1, 10000, 0.0001, 0.85, 0);
print_vector(&res, stdout);
igraph_vector_destroy(&res);
igraph_vector_destroy(&v);
igraph_destroy(&g);
igraph_set_warning_handler(oldwarn);
/* New PageRank */
igraph_star(&g, 11, IGRAPH_STAR_UNDIRECTED, 0);
igraph_vector_init(&res, 0);
igraph_arpack_options_init(&arpack_options);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, 0,
igraph_vss_all(), 0, 0.85, 0, &arpack_options);
print_vector(&res, stdout);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, 0,
igraph_vss_all(), 0, 0.85, 0, 0);
print_vector(&res, stdout);
/* Check twice more for consistency */
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, 0,
igraph_vss_all(), 0, 0.85, 0, &arpack_options);
print_vector(&res, stdout);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, 0,
igraph_vss_all(), 0, 0.85, 0, 0);
print_vector(&res, stdout);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, 0,
igraph_vss_all(), 0, 0.85, 0, &arpack_options);
print_vector(&res, stdout);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, 0,
igraph_vss_all(), 0, 0.85, 0, 0);
print_vector(&res, stdout);
/* Check personalized PageRank */
igraph_personalized_pagerank_vs(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, 0,
igraph_vss_all(), 0, 0.5,
igraph_vss_1(1), 0, &arpack_options);
print_vector(&res, stdout);
igraph_personalized_pagerank_vs(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, 0,
igraph_vss_all(), 0, 0.5,
igraph_vss_1(1), 0, 0);
print_vector(&res, stdout);
/* Errors */
power_options.niter = -1; power_options.eps=0.0001;
igraph_set_error_handler(igraph_error_handler_ignore);
igraph_set_warning_handler(igraph_warning_handler_ignore);
ret=igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_POWER, &res,
/*value=*/ 0, igraph_vss_all(), 1, 0.85,
/*weights=*/ 0, &power_options);
if (ret != IGRAPH_EINVAL) {
return 1;
}
power_options.niter=10000; power_options.eps=-1;
ret=igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_POWER, &res,
/*value=*/ 0, igraph_vss_all(), 1, 0.85,
/*weights=*/ 0, &power_options);
if (ret != IGRAPH_EINVAL) {
return 2;
}
power_options.niter=10000; power_options.eps=0.0001;
ret=igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_POWER, &res,
/*value=*/ 0, igraph_vss_all(), 1, 1.2,
/*weights=*/ 0, &power_options);
if (ret != IGRAPH_EINVAL) {
return 3;
}
igraph_vector_init(&reset, 2);
ret=igraph_personalized_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, 0,
igraph_vss_all(), 0, 0.85, &reset, 0,
&arpack_options);
if (ret != IGRAPH_EINVAL) {
return 4;
}
ret=igraph_personalized_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, 0,
igraph_vss_all(), 0, 0.85, &reset, 0, 0);
if (ret != IGRAPH_EINVAL) {
return 4;
}
igraph_vector_resize(&reset, 10);
igraph_vector_fill(&reset, 0);
ret=igraph_personalized_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK,
&res, 0, igraph_vss_all(), 0, 0.85,
&reset, 0, &arpack_options);
if (ret != IGRAPH_EINVAL) {
return 5;
}
ret=igraph_personalized_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK,
&res, 0, igraph_vss_all(), 0, 0.85,
&reset, 0, 0);
if (ret != IGRAPH_EINVAL) {
return 5;
}
igraph_vector_destroy(&reset);
igraph_destroy(&g);
igraph_set_error_handler(igraph_error_handler_abort);
/* Special cases: check for empty graph */
igraph_empty(&g, 10, 0);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, &value,
igraph_vss_all(), 1, 0.85, 0, &arpack_options);
if (value != 1.0) {
return 6;
}
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, &value,
igraph_vss_all(), 1, 0.85, 0, 0);
if (value != 1.0) {
return 6;
}
print_vector(&res, stdout);
igraph_destroy(&g);
/* Special cases: check for full graph, zero weights */
igraph_full(&g, 10, 0, 0);
igraph_vector_init(&v, 45);
igraph_vector_fill(&v, 0);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, &value,
igraph_vss_all(), 1, 0.85, &v, &arpack_options);
if (value != 1.0) {
return 7;
}
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, &value,
igraph_vss_all(), 1, 0.85, &v, 0);
if (value != 1.0) {
return 7;
}
igraph_vector_destroy(&v);
print_vector(&res, stdout);
igraph_destroy(&g);
/* Another test case for PageRank (bug #792352) */
igraph_small(&g, 9, 1, 0, 5, 1, 5, 2, 0, 3, 1, 5, 4, 5, 7, 6, 0, 8, 0, 8, 1, -1);
igraph_vector_init(&weights, 9);
VECTOR(weights)[0] = 4; VECTOR(weights)[1] = 5; VECTOR(weights)[2] = 5;
VECTOR(weights)[3] = 4; VECTOR(weights)[4] = 4; VECTOR(weights)[5] = 4;
VECTOR(weights)[6] = 3; VECTOR(weights)[7] = 4; VECTOR(weights)[8] = 4;
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, 0,
igraph_vss_all(), 1, 0.85, &weights, &arpack_options);
print_vector(&res, stdout);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, 0,
igraph_vss_all(), 1, 0.85, &weights, 0);
print_vector(&res, stdout);
igraph_vector_destroy(&weights);
igraph_destroy(&g);
igraph_vector_destroy(&res);
return 0;
}
int igraph_bipartite_game_gnm(igraph_t *graph, igraph_vector_bool_t *types,
igraph_integer_t n1, igraph_integer_t n2,
igraph_integer_t m, igraph_bool_t directed,
igraph_neimode_t mode) {
igraph_vector_t edges;
igraph_vector_t s;
int retval=0;
if (n1 < 0 || n2 < 0) {
IGRAPH_ERROR("Invalid number of vertices", IGRAPH_EINVAL);
}
if (m < 0) {
IGRAPH_ERROR("Invalid number of edges", IGRAPH_EINVAL);
}
if (types) {
long int i;
IGRAPH_CHECK(igraph_vector_bool_resize(types, n1 + n2));
igraph_vector_bool_null(types);
for (i=n1; i<n1+n2; i++) {
VECTOR(*types)[i] = 1;
}
}
if (m == 0 || n1 * n2 == 0) {
IGRAPH_CHECK(retval=igraph_empty(graph, n1 + n2, directed));
} else {
long int i;
double maxedges;
if (!directed || mode != IGRAPH_ALL) {
maxedges = n1 * n2;
} else {
maxedges = 2 * n1 * n2;
}
if (m > maxedges) {
IGRAPH_ERROR("Invalid number (too large) of edges", IGRAPH_EINVAL);
}
if (maxedges == m) {
IGRAPH_CHECK(retval=igraph_full_bipartite(graph, types, n1, n2,
directed, mode));
} else {
long int to, from;
IGRAPH_VECTOR_INIT_FINALLY(&edges, 0);
IGRAPH_VECTOR_INIT_FINALLY(&s, 0);
IGRAPH_CHECK(igraph_random_sample(&s, 0, maxedges-1, m));
IGRAPH_CHECK(igraph_vector_reserve(&edges, igraph_vector_size(&s)*2));
for (i=0; i<m; i++) {
if (!directed || mode != IGRAPH_ALL) {
to=(long) floor(VECTOR(s)[i]/n1);
from=(long) (VECTOR(s)[i] - ((igraph_real_t) to) * n1);
to += n1;
} else {
long int n1n2 = n1 * n2;
if (VECTOR(s)[i] < n1n2) {
to=(long) floor(VECTOR(s)[i]/n1);
from=(long) (VECTOR(s)[i] - ((igraph_real_t) to) * n1);
to += n1;
} else {
to=(long) floor( (VECTOR(s)[i]-n1n2) /n2);
from=(long) (VECTOR(s)[i] - n1n2 - ((igraph_real_t) to) * n2);
from += n1;
}
}
if (mode != IGRAPH_IN) {
igraph_vector_push_back(&edges, from);
igraph_vector_push_back(&edges, to);
} else {
igraph_vector_push_back(&edges, to);
igraph_vector_push_back(&edges, from);
}
}
igraph_vector_destroy(&s);
IGRAPH_FINALLY_CLEAN(1);
IGRAPH_CHECK(retval=igraph_create(graph, &edges, n1+n2, directed));
igraph_vector_destroy(&edges);
IGRAPH_FINALLY_CLEAN(1);
}
}
return retval;
}
int igraph_bipartite_game_gnp(igraph_t *graph, igraph_vector_bool_t *types,
igraph_integer_t n1, igraph_integer_t n2,
igraph_real_t p, igraph_bool_t directed,
igraph_neimode_t mode) {
int retval=0;
igraph_vector_t edges, s;
int i;
if (p < 0.0 || p > 1.0) {
IGRAPH_ERROR("Invalid connection probability", IGRAPH_EINVAL);
}
if (types) {
IGRAPH_CHECK(igraph_vector_bool_resize(types, n1 + n2));
igraph_vector_bool_null(types);
for (i=n1; i<n1+n2; i++) {
VECTOR(*types)[i] = 1;
}
}
if (p == 0 || n1 * n2 < 1) {
IGRAPH_CHECK(retval=igraph_empty(graph, n1 + n2, directed));
} else if (p == 1.0) {
IGRAPH_CHECK(retval=igraph_full_bipartite(graph, types, n1, n2, directed,
mode));
} else {
long int to, from, slen;
double maxedges, last;
if (!directed || mode != IGRAPH_ALL) {
maxedges = n1 * n2;
} else {
maxedges = 2 * n1 * n2;
}
IGRAPH_VECTOR_INIT_FINALLY(&edges, 0);
IGRAPH_VECTOR_INIT_FINALLY(&s, 0);
IGRAPH_CHECK(igraph_vector_reserve(&s, (long) (maxedges*p*1.1)));
RNG_BEGIN();
last=RNG_GEOM(p);
while (last < maxedges) {
IGRAPH_CHECK(igraph_vector_push_back(&s, last));
last += RNG_GEOM(p);
last += 1;
}
RNG_END();
slen=igraph_vector_size(&s);
IGRAPH_CHECK(igraph_vector_reserve(&edges, slen * 2));
for (i=0; i<slen; i++) {
if (!directed || mode != IGRAPH_ALL) {
to=(long) floor(VECTOR(s)[i]/n1);
from=(long) (VECTOR(s)[i] - ((igraph_real_t) to) * n1);
to += n1;
} else {
long int n1n2 = n1 * n2;
if (VECTOR(s)[i] < n1n2) {
to=(long) floor(VECTOR(s)[i]/n1);
from=(long) (VECTOR(s)[i] - ((igraph_real_t) to) * n1);
to += n1;
} else {
to=(long) floor( (VECTOR(s)[i]-n1n2) /n2);
from=(long) (VECTOR(s)[i] - n1n2 - ((igraph_real_t) to) * n2);
from += n1;
}
}
if (mode != IGRAPH_IN) {
igraph_vector_push_back(&edges, from);
igraph_vector_push_back(&edges, to);
} else {
igraph_vector_push_back(&edges, to);
igraph_vector_push_back(&edges, from);
}
}
igraph_vector_destroy(&s);
IGRAPH_FINALLY_CLEAN(1);
IGRAPH_CHECK(retval=igraph_create(graph, &edges, n1+n2, directed));
igraph_vector_destroy(&edges);
IGRAPH_FINALLY_CLEAN(1);
}
return retval;
}
/* Fan-in/ Fan-out method
*/
igraph_t *ggen_generate_fifo(gsl_rng *r, unsigned long n, unsigned long od, unsigned long id)
{
igraph_t *g = NULL;
igraph_vector_t available_od;
igraph_vector_t out_degrees;
igraph_vector_t vertices;
igraph_vector_t choice;
igraph_vector_t edges;
unsigned long max;
unsigned long i,j,k;
unsigned long vcount = 1;
int err;
ggen_error_start_stack();
if(r == NULL)
GGEN_SET_ERRNO(GGEN_EINVAL);
if(id == 0 || od == 0 || od > n || id > n)
GGEN_SET_ERRNO(GGEN_EINVAL);
g = malloc(sizeof(igraph_t));
GGEN_CHECK_ALLOC(g);
GGEN_FINALLY3(free,g,1);
GGEN_CHECK_IGRAPH(igraph_empty(g,1,1));
GGEN_FINALLY3(igraph_destroy,g,1);
GGEN_CHECK_IGRAPH(igraph_vector_init(&available_od,n));
GGEN_FINALLY(igraph_vector_destroy,&available_od);
GGEN_CHECK_IGRAPH(igraph_vector_init(&out_degrees,n));
GGEN_FINALLY(igraph_vector_destroy,&out_degrees);
GGEN_CHECK_IGRAPH(igraph_vector_init(&vertices,n));
GGEN_FINALLY(igraph_vector_destroy,&vertices);
GGEN_CHECK_IGRAPH(igraph_vector_init(&choice,n));
GGEN_FINALLY(igraph_vector_destroy,&choice);
GGEN_CHECK_IGRAPH(igraph_vector_init(&edges,n*2));
GGEN_FINALLY(igraph_vector_destroy,&edges);
while(vcount < n)
{
// never trigger errors as it doesn't allocate or free memory
igraph_vector_resize(&available_od,vcount);
igraph_vector_resize(&out_degrees,vcount);
igraph_vector_resize(&vertices,vcount);
// compute the available out degree of each vertex
GGEN_CHECK_IGRAPH(igraph_degree(g,&out_degrees,igraph_vss_all(),IGRAPH_OUT,0));
// fill available with od and substract out_degrees
igraph_vector_fill(&available_od,od);
GGEN_CHECK_IGRAPH(igraph_vector_sub(&available_od,&out_degrees));
if(gsl_ran_bernoulli(r,0.5)) //Fan-out Step
{
// find max
max = igraph_vector_max(&available_od);
// register all vertices having max as outdegree
j = 0;
for (i = 0; i < vcount; i++)
if(VECTOR(available_od)[i] == max)
VECTOR(vertices)[j++] = i;
// choose randomly a vertex among availables
GGEN_CHECK_GSL_DO(i = gsl_rng_uniform_int(r,j));
// how many children ?
GGEN_CHECK_GSL_DO(j = gsl_rng_uniform_int(r,max));
j = j+1;
// create all new nodes and add edges
GGEN_CHECK_IGRAPH(igraph_add_vertices(g,j,NULL));
// cannot fail
igraph_vector_resize(&edges,j*2);
for(k = 0; k < j; k++)
{
VECTOR(edges)[2*k] = i;
VECTOR(edges)[2*k+1] = vcount + k;
}
vcount+=k;
}
else //Fan-In Step
{
// register all vertices having an available outdegree
j = 0;
for (i = 0; i < vcount; i++)
if(VECTOR(available_od)[i] > 0)
VECTOR(vertices)[j++] = i;
// we can add at most id vertices
max =( j > id)? id: j;
// how many edges to add
GGEN_CHECK_GSL_DO(k = gsl_rng_uniform_int(r,max));
k = k+1;
// choose that many nodes and add edges from them to the new node
// cannot fail either
igraph_vector_resize(&choice,k);
gsl_ran_choose(r,VECTOR(choice),k,
VECTOR(vertices),j,sizeof(VECTOR(vertices)[0]));
// add a vertex to the graph
GGEN_CHECK_IGRAPH(igraph_add_vertices(g,1,NULL));
igraph_vector_resize(&edges,k*2);
// be carefull, vcount is the last ID of vertices not vcount +1
for(i = 0; i < k; i++)
{
VECTOR(edges)[2*i] = VECTOR(choice)[i];
VECTOR(edges)[2*i+1] = vcount;
}
vcount++;
}
// in all cases, edges should be added
GGEN_CHECK_IGRAPH(igraph_add_edges(g,&edges,NULL));
}
ggen_error_clean(1);
return g;
ggen_error_label:
return NULL;
}
static void
fit_rvine_trees(igraph_t **trees,
const gsl_matrix *data,
const dml_vine_weight_t weight,
const dml_vine_trunc_t trunc,
const dml_copula_indeptest_t indeptest,
const double indeptest_level,
const dml_copula_type_t *types,
const size_t types_size,
const dml_copula_select_t select,
const gsl_rng *rng)
{
size_t m, n;
igraph_t *graph;
igraph_vector_t *graph_weight;
dml_copula_t *copula;
gsl_vector *x;
igraph_integer_t e; // Edge id.
igraph_integer_t a, aa, ab, b, ba, bb; // Vertex id.
gsl_vector *u = NULL, *v = NULL;
igraph_integer_t Cea, Ceb;
gsl_vector_short *Ue, *Ua, *Ub;
size_t k;
dml_measure_t *measure;
double tree_aic, copula_aic;
gsl_permutation *perm, *rank, *u_rank = NULL, *v_rank = NULL;
igraph_i_set_attribute_table(&igraph_cattribute_table);
m = data->size1;
n = data->size2;
graph = g_malloc(sizeof(igraph_t));
graph_weight = g_malloc(sizeof(igraph_vector_t));
perm = gsl_permutation_alloc(m);
for (k = 0; k < n - 1; k++) { // Tree index.
if (k == 0) {
igraph_full(graph, n, IGRAPH_UNDIRECTED, IGRAPH_NO_LOOPS);
// Assign the observations to the nodes.
for (size_t i = 0; i < n; i++) { // Variable and node index.
x = gsl_vector_alloc(m);
gsl_matrix_get_col(x, data, i);
// Results of the h-function of the copula assigned to the
// edge that corresponds to this vertex in the previous tree.
// h for the h-function with its arguments in order and
// hrev for the h-function with its arguments reversed. In the
// first tree both are equal to the observations of the
// corresponding variable, in the rest of the trees they differ.
SETVAP(graph, "h", i, x);
SETVAP(graph, "hrev", i, x);
gsl_sort_vector_index(perm, x);
rank = gsl_permutation_alloc(m);
gsl_permutation_inverse(rank, perm);
// Ranks of the h and hrev vectors.
SETVAP(graph, "hrank", i, rank);
SETVAP(graph, "hrevrank", i, rank);
}
for (e = 0; e < igraph_ecount(graph); e++) {
igraph_edge(graph, e, &a, &b);
// Variables "connected" by this edge.
Ue = gsl_vector_short_calloc(n);
gsl_vector_short_set(Ue, a, 1);
gsl_vector_short_set(Ue, b, 1);
SETEAP(graph, "Ue", e, Ue);
// Conditioned set.
SETEAN(graph, "Cea", e, a + 1);
SETEAN(graph, "Ceb", e, b + 1);
Cea = EAN(graph, "Cea", e);
Ceb = EAN(graph, "Ceb", e);
// Calculate the weight of the edge.
u = VAP(graph, "h", a);
v = VAP(graph, "h", b);
u_rank = VAP(graph, "hrank", a);
v_rank = VAP(graph, "hrank", b);
// The conditioned set is ordered to make the order of the
// arguments in the bivariate copulas unique as suggested in
// Czado, C. (2010) Pair-Copula Constructions of Multivariate
// Copulas. In Jaworski, P. and Durante, F. and Hardle, W. K.
// and Rychlik, T. (eds.) Copula Theory and Its Applications,
// Springer-Verlag, 93-109.
if (Cea < Ceb) {
rvine_set_weight(graph, weight, e, u, v, u_rank, v_rank);
} else {
rvine_set_weight(graph, weight, e, v, u, v_rank, u_rank);
}
}
} else {
igraph_empty(graph, n - k, IGRAPH_UNDIRECTED);
// Adding all "possible" edges.
for (a = 0; a < igraph_vcount(graph) - 1; a++) {
for (b = a + 1; b < igraph_vcount(graph); b++) {
igraph_edge(trees[k - 1], a, &aa, &ab);
igraph_edge(trees[k - 1], b, &ba, &bb);
// Checking the proximity condition.
if (aa == ba || aa == bb || ab == ba || ab == bb) {
igraph_add_edge(graph, a, b);
igraph_get_eid(graph, &e, a, b, IGRAPH_UNDIRECTED, 1);
// Variables "connected" by this edge and conditioned set.
Ua = EAP(trees[k - 1], "Ue", a);
Ub = EAP(trees[k - 1], "Ue", b);
Ue = gsl_vector_short_calloc(n);
for (size_t i = 0; i < n; i++) {
gsl_vector_short_set(Ue, i,
gsl_vector_short_get(Ua, i)
| gsl_vector_short_get(Ub, i));
if (gsl_vector_short_get(Ua, i)
&& !gsl_vector_short_get(Ub, i)) {
SETEAN(graph, "Cea", e, i + 1);
}
if (gsl_vector_short_get(Ub, i)
&& !gsl_vector_short_get(Ua, i)) {
SETEAN(graph, "Ceb", e, i + 1);
}
}
SETEAP(graph, "Ue", e, Ue);
}
}
}
// Compute pseudo-observations and edge weights.
for (a = 0; a < igraph_vcount(graph); a++) {
// See the comment in the code for the first tree.
SETVAP(graph, "h", a, NULL);
SETVAP(graph, "hrev", a, NULL);
SETVAP(graph, "hrank", a, NULL);
SETVAP(graph, "hrevrank", a, NULL);
}
for (e = 0; e < igraph_ecount(graph); e++) {
igraph_edge(graph, e, &a, &b);
Cea = EAN(graph, "Cea", e);
Ceb = EAN(graph, "Ceb", e);
// Assign u and u_rank.
if ((Cea == EAN(trees[k - 1], "Cea", a)
&& (EAN(trees[k - 1], "Cea", a)
< EAN(trees[k - 1], "Ceb", a)))
|| (Cea != EAN(trees[k - 1], "Cea", a)
&& (EAN(trees[k - 1], "Cea", a)
> EAN(trees[k - 1], "Ceb", a)))) {
u = VAP(graph, "h", a);
if (u == NULL) {
copula = EAP(trees[k - 1], "copula", a);
measure = EAP(trees[k - 1], "measure", a);
u = gsl_vector_alloc(m);
dml_copula_h(copula, measure->x, measure->y, u);
SETVAP(graph, "h", a, u);
gsl_sort_vector_index(perm, u);
rank = gsl_permutation_alloc(m);
gsl_permutation_inverse(rank, perm);
SETVAP(graph, "hrank", a, rank);
}
u_rank = VAP(graph, "hrank", a);
}
if ((Cea == EAN(trees[k - 1], "Cea", a)
&& (EAN(trees[k - 1], "Cea", a)
> EAN(trees[k - 1], "Ceb", a)))
|| (Cea != EAN(trees[k - 1], "Cea", a)
&& (EAN(trees[k - 1], "Cea", a)
< EAN(trees[k - 1], "Ceb", a)))) {
u = VAP(graph, "hrev", a);
if (u == NULL) {
copula = EAP(trees[k - 1], "copula", a);
measure = EAP(trees[k - 1], "measure", a);
u = gsl_vector_alloc(m);
dml_copula_h(copula, measure->y, measure->x, u);
SETVAP(graph, "hrev", a, u);
gsl_sort_vector_index(perm, u);
rank = gsl_permutation_alloc(m);
gsl_permutation_inverse(rank, perm);
SETVAP(graph, "hrevrank", a, rank);
}
u_rank = VAP(graph, "hrevrank", a);
}
// Assign v and v_rank.
if ((Ceb == EAN(trees[k - 1], "Cea", b)
&& (EAN(trees[k - 1], "Cea", b)
< EAN(trees[k - 1], "Ceb", b)))
|| (Ceb != EAN(trees[k - 1], "Cea", b)
&& (EAN(trees[k - 1], "Cea", b)
> EAN(trees[k - 1], "Ceb", b)))) {
v = VAP(graph, "h", b);
if (v == NULL) {
copula = EAP(trees[k - 1], "copula", b);
measure = EAP(trees[k - 1], "measure", b);
v = gsl_vector_alloc(m);
dml_copula_h(copula, measure->x, measure->y, v);
SETVAP(graph, "h", b, v);
gsl_sort_vector_index(perm, v);
rank = gsl_permutation_alloc(m);
gsl_permutation_inverse(rank, perm);
SETVAP(graph, "hrank", b, rank);
}
v_rank = VAP(graph, "hrank", b);
}
if ((Ceb == EAN(trees[k - 1], "Cea", b)
&& (EAN(trees[k - 1], "Cea", b)
> EAN(trees[k - 1], "Ceb", b)))
|| (Ceb != EAN(trees[k - 1], "Cea", b)
&& (EAN(trees[k - 1], "Cea", b)
< EAN(trees[k - 1], "Ceb", b)))) {
v = VAP(graph, "hrev", b);
if (v == NULL) {
copula = EAP(trees[k - 1], "copula", b);
measure = EAP(trees[k - 1], "measure", b);
v = gsl_vector_alloc(m);
dml_copula_h(copula, measure->y, measure->x, v);
SETVAP(graph, "hrev", b, v);
gsl_sort_vector_index(perm, v);
rank = gsl_permutation_alloc(m);
gsl_permutation_inverse(rank, perm);
SETVAP(graph, "hrevrank", b, rank);
}
v_rank = VAP(graph, "hrevrank", b);
}
// Set the weight of the edge. The arguments are ordered here.
// The order determines the x and y fields of measure.
if (Cea < Ceb) {
rvine_set_weight(graph, weight, e, u, v, u_rank, v_rank);
} else {
rvine_set_weight(graph, weight, e, v, u, v_rank, u_rank);
}
}
}
// Compute the minimum weight spanning tree.
trees[k] = g_malloc(sizeof(igraph_t));
igraph_vector_init(graph_weight, igraph_ecount(graph));
EANV(graph, "weight", graph_weight);
igraph_minimum_spanning_tree_prim(graph, trees[k], graph_weight);
igraph_vector_destroy(graph_weight);
tree_aic = 0;
for (e = 0; e < igraph_ecount(trees[k]); e++) {
igraph_edge(trees[k], e, &a, &b);
Cea = EAN(trees[k], "Cea", e);
Ceb = EAN(trees[k], "Ceb", e);
measure = EAP(trees[k], "measure", e);
// Assign a bivariate copula to the edge.
if (Cea < Ceb) {
copula = dml_copula_select(measure->x, measure->y, measure,
indeptest, indeptest_level, types,
types_size, select, rng);
// Get information for the truncation of the vine.
if (trunc == DML_VINE_TRUNC_AIC) {
dml_copula_aic(copula, measure->x, measure->y, &copula_aic);
tree_aic += copula_aic;
}
} else {
copula = dml_copula_select(measure->y, measure->x, measure,
indeptest, indeptest_level, types,
types_size, select, rng);
// Get information for the truncation of the vine.
if (trunc == DML_VINE_TRUNC_AIC) {
dml_copula_aic(copula, measure->y, measure->x, &copula_aic);
tree_aic += copula_aic;
}
}
SETEAP(trees[k], "copula", e, copula);
}
igraph_destroy(graph);
// Check if the vine should be truncated.
if (trunc == DML_VINE_TRUNC_AIC && tree_aic >= 0) {
// Free the memory used for the last tree.
rvine_tree_cleanup(trees[k]);
for (e = 0; e < igraph_ecount(trees[k]); e++) {
copula = EAP(trees[k], "copula", e);
dml_copula_free(copula);
}
igraph_destroy(trees[k]);
g_free(trees[k]);
trees[k] = NULL;
break;
}
if (k > 0) rvine_tree_cleanup(trees[k - 1]);
}
// Cleanup the last tree if the vine was completely estimated.
// If the vine was truncated, the last tree will be freed in
// the function vine_fit_rvine, because the rvine_trees_to_vine
// function needs some attributes of its edges.
if (k == n - 1) {
rvine_tree_cleanup(trees[n - 2]);
}
g_free(graph_weight);
g_free(graph);
gsl_permutation_free(perm);
}