First commit on github -- NetBunch 1.0

3 files changed, 929 insertions, 0 deletions

diff --git a/src/hidden/Makefile.am b/src/hidden/Makefile.am
new file mode 100644
index 0000000..5751f24
--- /dev/null
+++ b/src/hidden/Makefile.am
@@ -0,0 +1,7 @@
+include ../common.mk 
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+../utils/utils.c ../utils/cum_distr.c \
+../include/utils.h ../include/cum_distr.h
+hv_net_LDADD = -lm
+
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new file mode 100644
index 0000000..fb0104b
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+	-rm -f ../utils/$(DEPDIR)/$(am__dirstamp)
+	-rm -f ../utils/$(am__dirstamp)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
+
+distclean: distclean-am
+	-rm -rf ../utils/$(DEPDIR) ./$(DEPDIR)
+	-rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+	distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am: install-binPROGRAMS
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -rf ../utils/$(DEPDIR) ./$(DEPDIR)
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-binPROGRAMS
+
+.MAKE: install-am install-strip
+
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+	clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+	distclean distclean-compile distclean-generic distclean-tags \
+	distdir dvi dvi-am html html-am info info-am install \
+	install-am install-binPROGRAMS install-data install-data-am \
+	install-dvi install-dvi-am install-exec install-exec-am \
+	install-html install-html-am install-info install-info-am \
+	install-man install-pdf install-pdf-am install-ps \
+	install-ps-am install-strip installcheck installcheck-am \
+	installdirs maintainer-clean maintainer-clean-generic \
+	mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+	ps ps-am tags tags-am uninstall uninstall-am \
+	uninstall-binPROGRAMS
+
+.PRECIOUS: Makefile
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/src/hidden/hv_net.c b/src/hidden/hv_net.c
new file mode 100644
index 0000000..cfba020
--- /dev/null
+++ b/src/hidden/hv_net.c
@@ -0,0 +1,337 @@
+/**
+ *  This program is free software: you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License as
+ *  published by the Free Software Foundation, either version 3 of the
+ *  License, or (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ *  General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see
+ *  <http://www.gnu.org/licenses/>.
+ *
+ *  (c) Vincenzo Nicosia 2009-2017 -- <v.nicosia@qmul.ac.uk>
+ * 
+ *  This file is part of NetBunch, a package for complex network
+ *  analysis and modelling. For more information please visit:
+ *
+ *             http://www.complex-networks.net/
+ *
+ *  If you use this software, please add a reference to 
+ *
+ *               V. Latora, V. Nicosia, G. Russo             
+ *   "Complex Networks: Principles, Methods and Applications"
+ *              Cambridge University Press (2017) 
+ *                ISBN: 9781107103184
+ *
+ ***********************************************************************
+ *
+ *  This in an implementation of the hidden-variable model by Bogunya'
+ *  and Pastor-Satorras. The program creates a random graph whose
+ *  joint degree distribution is identical to that of a network given
+ *  as input.
+ *
+ *  References:
+ *  
+ *  [1] M. Boguna and R. Pastor-Satorras. "Class of correlated random
+ *  networks with hidden variables". Phys. Rev. E 68 (2003), 036112.
+ *
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <time.h>
+#include <math.h>
+
+#include "utils.h"
+#include "cum_distr.h"
+
+
+void usage(char *argv[]){
+  printf("********************************************************************\n"
+         "**                                                                **\n"
+         "**                        -*-   hv_net   -*-                      **\n"
+         "**                                                                **\n"
+         "**   Create a random graph whose joint degree distribution is     **\n"
+         "**   identical to that of a network provided as input.            **\n"
+         "**                                                                **\n"
+         "**   If 'graph_in' is equal to '-' (dash), read the edge list     **\n"
+         "**   from STDIN.                                                  **\n"
+         "**                                                                **\n"
+         "**   The program prints on STDOUT the edge-list of the sampled    **\n"
+         "**   graph.                                                       **\n"
+         "**                                                                **\n"
+         "**   If 'SHOW' is specified as second parameter, the program      **\n"
+         "**   prints on STDERR the values of the hidden variable           **\n"
+         "**   associated to each node and of the actual degree they have   **\n"
+         "**   in the newly-created random graph, in the format:            **\n"
+         "**                                                                **\n"
+         "**       h_1 k_1                                                  **\n"
+         "**       h_2 k_2                                                  **\n"
+         "**       ...                                                      **\n"
+         "**       h_N k_N                                                  **\n"
+         "**                                                                **\n"
+         "********************************************************************\n"
+         " This is Free Software - You can use and distribute it under \n"
+         " the terms of the GNU General Public License, version 3 or later\n\n"
+         " (c) Vincenzo Nicosia 2009-2017 (v.nicosia@qmul.ac.uk)\n\n"
+         "********************************************************************\n\n"
+         );
+  printf("Usage: %s <graph_in> [SHOW]\n", argv[0]);
+}
+
+
+
+typedef struct{
+  unsigned int N;
+  unsigned int K;
+  unsigned int *J_slap;
+  unsigned int *r_slap;
+  unsigned int k_min;
+  unsigned int k_max;
+  double *pk; /* degree distribution -- this is equal to rho!!!! */
+  double **pkk; /* joint degree distribution */
+  double **f; /* the linking function */
+  unsigned int *h; /* The array containing hidden variables for the N nodes */
+  unsigned int *new_degs; /* the new degrees of the sampled graph */
+} params_t;
+
+
+/**
+ * 
+ * sample the hidden degrees of the nodes using the cumulative
+ * distribution P(k)
+ *
+ */
+void sample_node_variables(params_t *p, cum_distr_t *P){
+  
+  unsigned int i;
+  unsigned int k;
+  
+
+  for(i=0; i<p->N; i++){
+    k = cum_distr_sample(P);
+    p->h[i] = k;
+  }
+}
+
+/**
+ *
+ * Compute the function f(h,h') for each pair of degrees
+ *
+ */
+void compute_fhh(params_t *p){
+  
+  unsigned int k1, k2;
+  double avg_k;
+
+  avg_k = 1.0 * p->K / p->N;
+  
+  for(k1 = p->k_min; k1 <= p->k_max; k1++){
+    for(k2 = k1; k2 <= p->k_max; k2++){
+      p->f[k1][k2] = p->f[k2][k1] = avg_k * p->pkk[k1][k2] / (p->N * p->pk[k1] * p->pk[k2]);
+    }
+  }
+}
+
+
+
+/**
+ * 
+ * Sample the edges of the graph
+ *
+ */
+void sample_edges(params_t *p){
+ 
+  unsigned int i, j, ki, kj;
+  double val;
+
+  for(i=0; i<p->N; i++){
+    ki = p->h[i];
+    for (j=i+1; j<p->N; j++){
+      kj = p->h[j];
+      val = 1.0 * rand() / RAND_MAX;
+      /* we create the edge (i,j) with proability f[ki][kj]*/
+      if (val < p->f[ki][kj]){
+        printf("%d %d\n", i, j);
+        p->new_degs[i] += 1;
+        p->new_degs[j] += 1;
+      }
+    }
+  }
+}
+
+
+void init_hv_params(params_t *p){
+  
+  unsigned int  i;
+
+  p->h = malloc(p->N * sizeof(unsigned int));
+  p->f = malloc((p->k_max + 1) * sizeof(double*));
+  p->new_degs = malloc(p->N * sizeof(unsigned int));
+
+  for(i=0; i<=p->k_max; i++){
+    p->f[i] = malloc((p->k_max + 1) * sizeof(double));
+  }
+  for (i=0; i<p->N; i++){
+    p->new_degs[i] = 0;
+  }
+}
+
+
+
+void compute_distributions(params_t *g){
+  
+  unsigned int i,j, neigh, k1, k2;
+  double sumk, sumkk;
+
+  g->k_min = g->N;
+  g->k_max = 0;
+  
+  g->pk = NULL;
+
+  /* Compute (and allocate on the fly) the degree distribution */
+
+  for(i=0; i< g->N; i ++){
+    k1 = g->r_slap [i+1] - g->r_slap[i];
+    if (k1 > g->k_max){
+      g->pk = realloc(g->pk, (k1 + 1) * sizeof(double));
+      for(j=g->k_max+1; j<=k1; j++){
+        g->pk[j] = 0;
+      }
+      g->k_max = k1;
+    }
+    else if(k1 < g->k_min){
+      g->k_min = k1;
+    }
+    g->pk[k1] += 1;
+  }
+  
+  /* Allocate and initialise the joint degree distribution */
+  g->pkk = malloc((g->k_max + 1 ) * sizeof(double*));
+  for(i=0; i<=g->k_max ; i++){
+    g->pkk[i] = malloc((g->k_max + 1) * sizeof(double));
+    memset(g->pkk[i], 0, (g->k_max + 1) * sizeof(double));
+  }
+  
+  for(i=0; i<g->N; i++){
+    k1 = g->r_slap[i+1] - g->r_slap[i];
+    for(j=g->r_slap[i]; j< g->r_slap[i+1]; j++){
+      neigh = g->J_slap[j];
+      k2 = g->r_slap[neigh+1] - g->r_slap[neigh];
+      g->pkk[k1][k2] += 1;
+    }
+  }
+
+  /* Now we normalise both pk and pkk...*/
+
+  sumk = sumkk = 0.0;
+  
+  for(i=0; i<=g->k_max; i++){
+    g->pk[i] /= g->N;
+    sumk += g->pk[i];
+    g->pkk[i][i] /= (g->K);
+    sumkk += g->pkk[i][i];
+    for(j=i+1; j<=g->k_max; j++){
+      g->pkk[i][j] /= (g->K);
+      g->pkk[j][i] = g->pkk[i][j];
+      sumkk += 2* g->pkk[i][j];
+    }
+  }
+    
+}
+
+
+void compute_rho(params_t *g, cum_distr_t *P){
+  
+  unsigned int k;
+
+  for(k=g->k_min; k<= g->k_max; k++){
+
+    if(g->pk[k] > 0){
+      if (cum_distr_add(P, k, g->pk[k]) != 0){
+        fprintf(stderr, "Error in the computation of the cumulative degree distribution!!!!"
+               " Exiting!!!\n");
+        exit(3);
+      }
+    }
+  }
+}
+
+void dump_deg_h(params_t *p){
+
+  unsigned int i;
+
+  for(i=0; i<p->N; i++){
+    fprintf(stderr, "%d %d\n", p->h[i], p->new_degs[i]);
+  }
+}
+
+
+int main(int argc, char *argv[]){
+  
+  params_t p;
+  cum_distr_t *P;
+  int i;
+
+  FILE *filein;
+
+
+  if (argc < 2){
+    usage(argv);
+    exit(1);
+  }
+
+  srand(time(NULL));
+
+  if (!strcmp(argv[1], "-")){
+    /* take the input from STDIN */
+    filein = stdin;
+  }
+  else {
+    filein = openfile_or_exit(argv[1], "r", 2);
+  }
+  
+  p.J_slap = p.r_slap = NULL;
+  
+  read_slap(filein, &(p.K), &(p.N), &(p.J_slap), &(p.r_slap));
+
+  fclose(filein);
+  
+  compute_distributions(&p);
+
+  init_hv_params(&p);
+  
+  P = cum_distr_init(p.k_max + 1);
+  compute_rho(&p, P);
+  compute_fhh(&p);
+  
+  sample_node_variables(&p, P);
+  sample_edges(&p);
+  
+  /* 
+   *  If 'SHOW' is provided, print on STDERR the value of the hidden
+   *  variable of each node
+   */
+  if (argc > 2 && !my_strcasecmp(argv[2], "SHOW")){
+    dump_deg_h(&p);
+  }
+
+  cum_distr_destroy(P);
+  free(p.J_slap);
+  free(p.r_slap);
+  free(p.pk);
+  free(p.h);
+  free(p.new_degs);
+  for(i=0; i<=p.k_max ; i++){
+    free(p.pkk[i]);
+    free(p.f[i]);
+  }
+  free(p.pkk);
+  free(p.f);
+}
+