/usr/lib/python2.7/dist-packages/networkx/algorithms/richclub.py is in python-networkx 1.8.1-0ubuntu3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 | # -*- coding: utf-8 -*-
import networkx as nx
__author__ = """\n""".join(['Ben Edwards',
'Aric Hagberg <hagberg@lanl.gov>'])
__all__ = ['rich_club_coefficient']
def rich_club_coefficient(G, normalized=True, Q=100):
"""Return the rich-club coefficient of the graph G.
The rich-club coefficient is the ratio, for every degree k, of the
number of actual to the number of potential edges for nodes
with degree greater than k:
.. math::
\\phi(k) = \\frac{2 Ek}{Nk(Nk-1)}
where Nk is the number of nodes with degree larger than k, and Ek
be the number of edges among those nodes.
Parameters
----------
G : NetworkX graph
normalized : bool (optional)
Normalize using randomized network (see [1]_)
Q : float (optional, default=100)
If normalized=True build a random network by performing
Q*M double-edge swaps, where M is the number of edges in G,
to use as a null-model for normalization.
Returns
-------
rc : dictionary
A dictionary, keyed by degree, with rich club coefficient values.
Examples
--------
>>> G = nx.Graph([(0,1),(0,2),(1,2),(1,3),(1,4),(4,5)])
>>> rc = nx.rich_club_coefficient(G,normalized=False)
>>> rc[0] # doctest: +SKIP
0.4
Notes
------
The rich club definition and algorithm are found in [1]_. This
algorithm ignores any edge weights and is not defined for directed
graphs or graphs with parallel edges or self loops.
Estimates for appropriate values of Q are found in [2]_.
References
----------
.. [1] Julian J. McAuley, Luciano da Fontoura Costa, and Tibério S. Caetano,
"The rich-club phenomenon across complex network hierarchies",
Applied Physics Letters Vol 91 Issue 8, August 2007.
http://arxiv.org/abs/physics/0701290
.. [2] R. Milo, N. Kashtan, S. Itzkovitz, M. E. J. Newman, U. Alon,
"Uniform generation of random graphs with arbitrary degree
sequences", 2006. http://arxiv.org/abs/cond-mat/0312028
"""
if G.is_multigraph() or G.is_directed():
raise Exception('rich_club_coefficient is not implemented for ',
'directed or multiedge graphs.')
if len(G.selfloop_edges()) > 0:
raise Exception('rich_club_coefficient is not implemented for ',
'graphs with self loops.')
rc=_compute_rc(G)
if normalized:
# make R a copy of G, randomize with Q*|E| double edge swaps
# and use rich_club coefficient of R to normalize
R = G.copy()
E = R.number_of_edges()
nx.double_edge_swap(R,Q*E,max_tries=Q*E*10)
rcran=_compute_rc(R)
for d in rc:
# if rcran[d] > 0:
rc[d]/=rcran[d]
return rc
def _compute_rc(G):
# compute rich club coefficient for all k degrees in G
deghist = nx.degree_histogram(G)
total = sum(deghist)
# number of nodes with degree > k (omit last entry which is zero)
nks = [total-cs for cs in nx.utils.cumulative_sum(deghist) if total-cs > 1]
deg=G.degree()
edge_degrees=sorted(sorted((deg[u],deg[v])) for u,v in G.edges_iter())
ek=G.number_of_edges()
k1,k2=edge_degrees.pop(0)
rc={}
for d,nk in zip(range(len(nks)),nks):
while k1 <= d:
if len(edge_degrees)==0:
break
k1,k2=edge_degrees.pop(0)
ek-=1
rc[d] = 2.0*ek/(nk*(nk-1))
return rc
|