TInt num_seeds;

TInt seed_bias;

TInt mode;

TInt burn;

TInt branch;

char * input_name;

runArgs (TInt ns, TInt sb, TInt md, TInt bn, TInt br, char * in) :

num_seeds (ns), seed_bias (sb), mode (md), burn (bn), branch (br), input_name (in) {}

public:

TInt id;

VisitedNode * previous;

TInt depth;

VisitedNode () : id (0), previous (NULL), depth (0) {}

VisitedNode (TInt id, VisitedNode * previous = NULL) : id (id),

previous (previous) {

if (previous != NULL) depth = previous->depth + 1;

else depth = 0;

}

TStr to_string () {

if (previous == NULL) return id.GetStr() + ", NULL, " + depth.GetStr ();

else return id.GetStr() + ", " + previous->id.GetStr() + ", "

+ depth.GetStr ();

}

if (lower == upper) return lower;

TInt mid = (lower + upper) / 2;

TInt val = choices[mid];

if (choice < val) return find (choice, choices, lower, mid);

else if (choice > val) return find (choice, choices, mid + 1, upper);

else return mid;

TVec<TInt> v;

double tot_lengths = 0.0;

for (TUNGraph::TNodeI n = p->BegNI(); n != p->EndNI(); n++) {

v = v + n.GetId();

}

// cerr << "vlen: " << v.Len() << endl;

TBreathFS<PUNGraph> b(p);

double tot_pairs = 0.0;

while (v.Len () > 0) {

TInt last = v[v.Len()-1];

b.DoBfs (last, true, true);

for (TVec<TInt>::TIter i = v.BegI(); (*i) != last; i++) {

int length;

length = b.GetHops (last, (*i));

if (length == length) {

tot_lengths += length;

tot_pairs += 1;

}

}

// cerr << "tps: " << tot_pairs << ", last: " << last << ", beg: " << v[*(v.BegI())] << endl;

v.Del(v.Len()-1);

}

// cerr << "paths: " << tot_lengths << " " << tot_pairs << " " << (tot_lengths/tot_pairs) << endl;

return tot_lengths / tot_pairs;

for (VisitedNode * node = current_node -> previous; node != NULL; node = node -> previous)

if (node -> id == neighbor) return true;

return false;

PUNGraph g = PUNGraph::New ();

for (int i = 1; i<= nodes; i++) {

g->AddNode(i);

}

for (int i =0; i < nval; i++) {

g->AddEdge(m[i], m[nval + i]);

}

return g;

const int nodes = *h;

const int nval = (*n)/2;

PUNGraph g = get_PUNGraph (m, nval, nodes);

TSnap::GetClustCf(g, -1);

const int nodes = *h;

const int nval = (*n)/2;

int num_seeds = *ns;

int infect_type = *in;

int mode = *mde;

int burnin = *bi;

int branch = *br;

PUNGraph g = get_PUNGraph (m, nval, nodes);

THash<TInt, TInt> * visited = choose_seeds (g, num_seeds, infection_state, infect_type);

TVec <VisitedNode *> queue;

TIntV qids;

for (THash<TInt, TInt>::TIter n = visited->BegI(); n != visited->EndI(); n++) {

queue = queue + new VisitedNode (n->Key);

qids = qids + n->Key;

//cerr << "enqueued " << n->Key << endl;

}

TInt counted = 0;

TInt first_unprocessed = 0;

TFlt infected_mass = 0.0;

TFlt total_mass = 0.0;

TFlt revisits = 0.0;

TFlt trehits = 0.0;

//cerr << "nodeId\tneigh\tnbh_size\tinfected?\tinfected_mass\ttotal_mass" << endl;

while (counted < 500 && first_unprocessed < queue.Len()) {

VisitedNode * current_node = queue [first_unprocessed];

first_unprocessed++;

TUNGraph::TNodeI NI = g->GetNI (current_node->id);

TInt neighborhood_size = NI.GetDeg();

// cerr << counted << " " << current_node->id << endl;

if (counted >= burnin) {

if (infection_state[(current_node->id) - 1] == 1)

infected_mass += 1.0/TFlt(neighborhood_size);

total_mass += 1.0/TFlt(neighborhood_size);

}

//cerr << current_node->id << "\t" << neighborhood_size << "\t" << (1.0/TFlt(neighborhood_size))

// << "\t" << infection_state[(current_node->id) - 1] << "\t" << infected_mass << "\t" << total_mass << endl;

// build list of unvisited neighbors

TVec<TInt> neighbors;

for (int i = 0; i < neighborhood_size; i++) {

TInt neighbor = NI.GetNbrNId(i);

if (mode == 0 && visited->IsKey(neighbor)) continue;

else if (mode == 2 && isChild (current_node, neighbor)) continue;

else if (mode == 3 && current_node-> previous != NULL && current_node->previous->id == neighbor) continue;

else neighbors = neighbors + neighbor;

}

TInt num_legal_neighbors = neighbors.Len();

TInt sample_size = TMath::Mn<TInt> (branch, num_legal_neighbors);

THash <TInt, TInt> * choices = choose (num_legal_neighbors, sample_size);

for (THash<TInt, TInt>::TIter n = choices->BegI(); n != choices->EndI(); n++) {

if (queue.Len() >= 500) break;

queue = queue + new VisitedNode (neighbors[n->Key], current_node);

if (visited->IsKey(neighbors[n->Key])) revisits++;

if (isChild(current_node, neighbors[n->Key])) trehits++;

if (!visited->IsKey(neighbors[n->Key])) qids = qids + neighbors[n->Key];

visited->AddDat(neighbors[n->Key], 1);

}

counted++;

}

// cout << (infected_mass / total_mass) << endl;

delete (visited);

result[0] = (infected_mass / total_mass);

result[1] = revisits;

result[2] = trehits;

result[3] = counted;

//PUNGraph p (&g);

PUNGraph p = TSnap:: GetSubGraph (g, qids, false);

TCnComV convec;

result[4] = TSnap::GetClustCf(p, -1);

TSnap::GetWccs(p, convec);

result[5] = convec.Len();

result[6] = ave_path_length (p);

for (int i = 0; i < numedges; i++) {

file >> edges[i] >> edges[i+numedges];

}

for (int j = 0; j < numnodes; j++) {

file >> inf[j];

}

ifstream file (input_name);

string s;

int numedges, numnodes;

file >> s >> numedges;

cerr << s << "\t" << numedges << endl;

while (numedges > 0) {

int edges [2*numedges];

get_edges (file, edges, numedges);

file >> s >> numnodes;

int inf[numnodes];

get_nodes (file, inf, numnodes);

double output[7];

int total_deg = 2 * numedges;

sample (edges, &total_deg, &numnodes, (int *) &num_seeds, (int *)&seed_bias, inf, (int *) &mode, (int *) &burn, (int *) &branch, output);

outfile << graph_num << " " << output[0] << " " << output[1] << " " << output[2] << " " << output[3] << " " << output[4] << " " << output[5] << " " << output[6] << " " << numnodes << endl;

graph_num ++;

file >> s >> numedges;

}

char line[1024];

sprintf (line, "g-%s-s%d-%s-bu%d-%s-%d.out", input_name, (int) num_seeds, biasNames[seed_bias].c_str(), (int) burn, modeNames[mode].c_str(), (int) branch);

ofstream outfile (line);

outfile << "id est revisit intree samplesize netsize subclustercf subapl subccs" << endl;

// cerr << line << endl;

sprintf( line, "%s.graph", input_name);

process_file (num_seeds, seed_bias, mode, burn, branch, line, outfile);

TInt branch, const char * input_name) {

char line[1024];

sprintf (line, "g-%s-s%d-%s-bu%d-%s-%d.out", input_name, (int) num_seeds, biasNames[seed_bias].c_str(), (int) burn, modeNames[mode].c_str(), (int) branch);

ofstream outfile (line);

cout << "outfile: " << line << endl;

outfile << "id est revisit intree samplesize subclustercf subccs subapl netsize" << endl;

int sizes [] = {1000, 715, 525};

for (int i = 0; i < 3; i++) {

sprintf( line, "g-%d-%s.graph", sizes[i], input_name);

process_file (num_seeds, seed_bias, mode, burn, branch, line, outfile);

}

char line[1024];

sprintf (line, "g-%s.out", input_name);

ofstream outfile (line);

cout << "outfile: " << line << endl;

outfile << "id clustercf comps apl netsize" << endl;

int sizes [] = {1000, 715, 525};

for (int i = 0; i < 6; i++) {

sprintf( line, "g-%d-%s.graph", sizes[i], input_name);

ifstream file (line);

cerr << "infile: " << line << endl;

string s;

int numedges, numnodes;

file >> s >> numedges;

cerr << s << "\t" << numedges << endl;

while (numedges > 0) {

int edges [2*numedges];

get_edges (file, edges, numedges);

file >> s >> numnodes;

int inf[numnodes];

get_nodes (file, inf, numnodes);

PUNGraph g = get_PUNGraph (edges, numedges, numnodes);

TCnComV convec;

TSnap::GetWccs(g, convec);

outfile << graph_num << " " << TSnap::GetClustCf(g, -1) << " " << convec.Len() << " " << " " << ave_path_length (g) << " " << numnodes << endl;

graph_num ++;

file >> s >> numedges;

}

}

TCon console;

Env = TEnv(argc, argv, TNotify::StdNotify);

//Env.PrepArgs(TStr(), 1, true);

const TInt num_seeds = Env.GetIfArgPrefixInt

("-seeds:", 6, "Number of seeds");

const TInt seed_bias = Env.GetIfArgPrefixInt

("-sbias:", 2, "Seed bias: 0=all infected, 1=all noninfected, 2=all");

const TInt mode = Env.GetIfArgPrefixInt

("-mode:", 0, "Sample mode: 0=RDS,1=with replacement, 2=DAG");

const TInt burn = Env.GetIfArgPrefixFlt

("-burn:", 0, "No. of nodes to drop for burn in.");

const TInt branch = Env.GetIfArgPrefixInt

("-branch:", 2,"Number of recruits each respondent gets");

const TInt graphstats = Env.GetIfArgPrefixInt

("-graphstats:", 0,"Just run graph stats?");

const TStr input_name = Env.GetIfArgPrefixStr

("-file:", "", "Input graph filename, without .graph extension");

if (graphstats == 0) {

run_long (num_seeds, seed_bias, mode, burn, branch, input_name());

}

else if (graphstats == 1) {

run_short (num_seeds, seed_bias, mode, burn, branch, input_name());

}

else if (graphstats == 2) {

run_graph_long (input_name());

}