// Computes GINI coefficient of egonet as a subset of the parent graph (edges into and out of the egonet ARE considered) double TSnap::GetGiniCoefficient(const TIntFltH DegH, const TIntV NIdV) { typename TIntV::TIter VI; typename TFltV::TIter DI; TFltV DegV; const int n = NIdV.Len(); // DegV.Gen(n); // NOTE: don't use Gen() and Sort() on the same object (!) for (VI = NIdV.BegI(); VI < NIdV.EndI(); VI++) { DegV.Add(DegH.GetDat(VI->Val)); // might need to change this (in / out / undirected) } DegV.Sort(); int i = 0; double numerator = 0.0, denominator = 0.0; for (DI = DegV.BegI(); DI < DegV.EndI(); DI++, i++) { numerator += (i + 1)*DegV[i]; denominator += DegV[i]; } return(double(2*numerator) / double(n*denominator) - double(n + 1) / double(n)); }
int main(int argc, char* argv[]) { setbuf(stdout, NULL); // disables the buffer so that print statements are not buffered and display immediately (?) Env = TEnv(argc, argv, TNotify::StdNotify); Env.PrepArgs(TStr::Fmt("Vespignani backbone method. build: %s, %s. Time: %s", __TIME__, __DATE__, TExeTm::GetCurTm())); TExeTm ExeTm; Try const TStr InFNm = Env.GetIfArgPrefixStr("-i:", "", "input network"); const TStr OutFNm = Env.GetIfArgPrefixStr("-o:", "", "output prefix (alpha value and filename extensions added)"); double alpha = Env.GetIfArgPrefixFlt("-a:", 0.01, "alpha significance level threshold"); const TStr AlphaVFNm = Env.GetIfArgPrefixStr("--alphav:", "", "vector of alpha significance level threshold (overrides -a)"); const bool verbose = Env.GetIfArgPrefixBool("--verbose:", true, "verbose output for each step of the Vespignani method"); const bool bootstrap = Env.GetIfArgPrefixBool("--bootstrap:", false, "bootstrap Vespignani method to retain --ratio of total weight W"); const double ratio = Env.GetIfArgPrefixFlt("--ratio:", 0.50, "bootstrap target ratio of total weight W"); const double lowerBound = Env.GetIfArgPrefixFlt("--lowerbound:", 0.0, "lower bound for alpha (binary search)"); const double upperBound = Env.GetIfArgPrefixFlt("--upperbound:", 1.0, "upper bound for alpha (binary search)"); const double tol = Env.GetIfArgPrefixFlt("--tolerance:", 5.0e-3, "tolerance for alpha (binary search)"); const double spread = Env.GetIfArgPrefixFlt("--spread:", 2.0, "spread for bootstrapped alpha benchmark (binary search)"); // Load graph and create directed and undirected graphs (pointer to the same memory) printf("\nLoading %s...", InFNm.CStr()); const PFltWNGraph WGraph = TSnap::LoadFltWEdgeList<TWNGraph>(InFNm); printf(" DONE (time elapsed: %s (%s))\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr()); TSnap::printFltWGraphSummary(WGraph, true, "\nWGraph\n------"); // Variables PFltWNGraph WGraphCopy; TFltV AlphaV; TFltV::TIter VI; if (!AlphaVFNm.Empty()) { AlphaV = TSnap::LoadTxtFltV(AlphaVFNm); } else { if (bootstrap) { printf("\n"); alpha = TSnap::FindVespignaniThreshold<TFlt, TWNGraph>(WGraph, ratio, tol, lowerBound, upperBound); AlphaV.Add(alpha / spread); AlphaV.Add(alpha); AlphaV.Add(alpha * spread); } else { AlphaV.Add(alpha); } } // VESPIGNANI METHOD Progress progress(ExeTm, AlphaV.Len(), 5, "Computing Vespignani method", !verbose); progress.start(); if (verbose) { printf("\n"); } int i = 0; for (VI = AlphaV.BegI(); VI < AlphaV.EndI(); VI++) { const double& alpha = VI->Val; // Compute method and save filtered printf("Computing Vespignani method (alpha: %e)\n\n", alpha); WGraphCopy = TSnap::FilterEdgesVespignani<TFlt, TWNGraph>(WGraph, alpha); TSnap::RemoveIsolated(WGraphCopy); TSnap::SaveFltWEdgeList(WGraphCopy, TStr::Fmt("%s-%9e.snap", OutFNm.CStr(), alpha), TStr::Fmt("Vespignani backbone with alpha: %e", alpha)); // Save bootstrapped if (bootstrap && i == 1) { TSnap::SaveFltWEdgeList(WGraphCopy, TStr::Fmt("%s-bootstrapped.snap", OutFNm.CStr()), TStr::Fmt("Vespignani backbone with alpha: %e", alpha)); } // Verbose summary if (verbose) { TSnap::printFltWGraphSummary(WGraphCopy, true, TStr::Fmt("WGraphCopy (alpha: %e)\n------", alpha)); printf("\n"); } i++; progress++; } Catch printf("\nrun time: %s (%s)\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr()); return 0; }
int main(int argc, char* argv[]) { setbuf(stdout, NULL); // disables the buffer so that print statements are not buffered and display immediately (?) Env = TEnv(argc, argv, TNotify::StdNotify); Env.PrepArgs(TStr::Fmt("Node centrality. build: %s, %s. Time: %s", __TIME__, __DATE__, TExeTm::GetCurTm())); TExeTm ExeTm; Try const TStr InFNm = Env.GetIfArgPrefixStr("-i:", "", "input network"); const TStr OutFNm = Env.GetIfArgPrefixStr("-o:", "", "output prefix (filename extensions added)"); const TStr BseFNm = OutFNm.RightOfLast('/'); const int k = Env.GetIfArgPrefixInt("-k:", 1, "depth of weighted degree distributions (1 / 2 / ...)"); const bool c = Env.GetIfArgPrefixBool("-c:", false, "collate centralities into matrix (T / F)"); // Load graph and create directed and undirected graphs (pointer to the same memory) printf("\nLoading %s...", InFNm.CStr()); PFltWNGraph WGraph = TSnap::LoadFltWEdgeList<TWNGraph>(InFNm); printf(" DONE\n"); printf(" nodes: %d\n", WGraph->GetNodes()); printf(" edges: %d\n", WGraph->GetEdges()); printf(" time elapsed: %s (%s)\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr()); // Declare variables TIntFltVH FirstWDegVH; TIntFltVH kWInDegVH, kWOutDegVH, kWDegVH; TIntFltVH WDegCentrVH, WEigCentrVH; TFltV WEigDiffV; TIntFltH WPgRH; double WPgRDiff; TFltWNGraph::TNodeI NI; TFltV::TIter VI; // CENTRALITY (computations) // Weighted first degree distributions printf("\nComputing weighted degree distributions..."); TSnap::GetWDegVH(WGraph, FirstWDegVH); printf(" DONE (time elapsed: %s (%s))\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr()); // 1:k degree distributions printf("Computing egonet degrees for k = 1 to %d (in / out / undirected)\n", k); TSnap::TFixedMemorykWDeg<TFlt, TWNGraph> FixedMemorykWDeg(WGraph, k); printf(" ..."); FixedMemorykWDeg.GetkWInDegSeqH(kWInDegVH); printf(" DONE (time elapsed: %s (%s))\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr()); printf(" ..."); FixedMemorykWDeg.GetkWOutDegSeqH(kWOutDegVH); printf(" DONE (time elapsed: %s (%s))\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr()); printf(" ..."); FixedMemorykWDeg.GetkWDegSeqH(kWDegVH); printf(" DONE (time elapsed: %s (%s))\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr()); // Centrality measures printf("Computing weighted degree centrality..."); TSnap::GetWDegreeCentrVH(WGraph, WDegCentrVH, 0.5); printf(" DONE (time elapsed: %s (%s))\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr()); printf("Computing weighted eigenvector centrality..."); WEigDiffV = TSnap::GetWEigenVectorCentrVH<TFlt>(WGraph, WEigCentrVH, 1e-4, 1000); printf(" DONE (time elapsed: %s (%s))\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr()); printf(" convergence differences (in / out / undirected)\n"); printf(" %f\n", double(WEigDiffV[0])); printf(" %f\n", double(WEigDiffV[1])); printf(" %f\n", double(WEigDiffV[2])); printf("Computing weighted PageRank centrality..."); WPgRDiff = TSnap::GetWPageRank<TFlt>(WGraph, WPgRH, 0.85, 1e-4, 1000); printf(" DONE (time elapsed: %s (%s))\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr()); printf(" convergence difference: %f\n", double(WPgRDiff)); // OUTPUTTING (mostly verbose printing statements, don't get scared) if (c) { printf("\nSaving %s.wcentr...", BseFNm.CStr()); const TStr AggFNm = TStr::Fmt("%s.wcentr", OutFNm.CStr()); FILE *F = fopen(AggFNm.CStr(), "wt"); fprintf(F,"# Node centrality distributions on the directed / undirected graph (as applicable)\n"); fprintf(F,"# Nodes: %d\tEdges: %d\n", WGraph->GetNodes(), WGraph->GetEdges()); fprintf(F,"# NodeId\tWInDegCentr\tWOutDegCentr\tWDegCentr\tWInEigCentr\tWOutEigCentr\tWEigCentr\tWPgRCentr\n"); for (NI = WGraph->BegNI(); NI < WGraph->EndNI(); NI++) { const int NId = NI.GetId(); fprintf(F, "%d", NId); const TFltV WDegCentrV = WDegCentrVH.GetDat(NId); for (VI = WDegCentrV.BegI(); VI < WDegCentrV.EndI(); VI++) { fprintf(F, "\t%f", VI->Val); } const TFltV WEigCentrV = WEigCentrVH.GetDat(NId); for (VI = WEigCentrV.BegI(); VI < WEigCentrV.EndI(); VI++) { fprintf(F, "\t%f", VI->Val); } const double WPgRCentr = WPgRH.GetDat(NId); fprintf(F, "\t%f", WPgRCentr); fprintf(F, "\n"); } printf(" DONE\n"); } else { printf("\nSaving %s.wdeg.centr...", BseFNm.CStr()); TSnap::SaveTxt(WDegCentrVH, TStr::Fmt("%s.wdeg.centr", OutFNm.CStr()), "Weighted degree centrality (in / out / undirected)", "NodeId", "WInDegCentr\tWOutDegCentr\tWDegCentr"); printf(" DONE\n"); printf("Saving %s.weig...", BseFNm.CStr()); TSnap::SaveTxt(WEigCentrVH, TStr::Fmt("%s.weig", OutFNm.CStr()), "Weighted eigenvector centrality (in / out / undirected)", "NodeId", "WInEigCentr\tWOutEigCentr\tWEigCentr"); printf(" DONE\n"); printf("Saving %s.wpgr...", BseFNm.CStr()); TSnap::SaveTxt(WPgRH, TStr::Fmt("%s.wpgr", OutFNm.CStr()), "Weighted PageRank centrality (wpgr)", "NodeId", "WPageRank"); printf(" DONE\n"); } printf("Saving %s.wdeg...", BseFNm.CStr()); TSnap::SaveTxt(FirstWDegVH, TStr::Fmt("%s.wdeg", OutFNm.CStr()), "Weighted degree distributions (in / out / undirected)", "NodeId", "WInDeg\tWOutDeg\tWDeg"); printf(" DONE\n"); printf("Saving %s.kwdeg.IN...", BseFNm.CStr()); TSnap::SaveTxt(kWInDegVH, TStr::Fmt("%s.kwdeg.IN", OutFNm.CStr()), TStr::Fmt("1 to %d weighted in degree distributions (kdeg.IN)", k), "NodeId", "kWInDegH"); printf(" DONE\n"); printf("Saving %s.kwdeg.OUT...", BseFNm.CStr()); TSnap::SaveTxt(kWOutDegVH, TStr::Fmt("%s.kwdeg.OUT", OutFNm.CStr()), TStr::Fmt("1 to %d weighted out degree distributions (kdeg.OUT)", k), "NodeId", "kWOutDegH"); printf(" DONE\n"); printf("Saving %s.kwdeg...", BseFNm.CStr()); TSnap::SaveTxt(kWDegVH, TStr::Fmt("%s.kwdeg", OutFNm.CStr()), TStr::Fmt("1 to %d weighted degree distributions (kdeg)", k), "NodeId", "kWDegH"); printf(" DONE\n"); Catch printf("\nrun time: %s (%s)\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr()); return 0; }