# -*- coding: utf-8 -*-
# Copyright (C) 2006-2016 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# Copyright (C) 2009 by Willem Ligtenberg <W.P.A.Ligtenberg@tue.nl>
# All rights reserved.
# BSD license.
#
# Authors: Aric Hagberg (hagberg@lanl.gov)
# Willem Ligtenberg (W.P.A.Ligtenberg@tue.nl)
"""
Generators for some directed graphs, including growing network (GN) graphs and
scale-free graphs.
"""
from __future__ import division
from collections import Counter
import random
import networkx as nx
from networkx.generators.classic import empty_graph
from networkx.utils import discrete_sequence
from networkx.utils import weighted_choice
__all__ = ['gn_graph', 'gnc_graph', 'gnr_graph', 'random_k_out_graph',
'scale_free_graph']
[docs]def gn_graph(n, kernel=None, create_using=None, seed=None):
"""Return the growing network (GN) digraph with `n` nodes.
The GN graph is built by adding nodes one at a time with a link to one
previously added node. The target node for the link is chosen with
probability based on degree. The default attachment kernel is a linear
function of the degree of a node.
The graph is always a (directed) tree.
Parameters
----------
n : int
The number of nodes for the generated graph.
kernel : function
The attachment kernel.
create_using : graph, optional (default DiGraph)
Return graph of this type. The instance will be cleared.
seed : hashable object, optional
The seed for the random number generator.
Examples
--------
To create the undirected GN graph, use the :meth:`~DiGraph.to_directed`
method::
>>> D = nx.gn_graph(10) # the GN graph
>>> G = D.to_undirected() # the undirected version
To specify an attachment kernel, use the `kernel` keyword argument::
>>> D = nx.gn_graph(10, kernel=lambda x: x ** 1.5) # A_k = k^1.5
References
----------
.. [1] P. L. Krapivsky and S. Redner,
Organization of Growing Random Networks,
Phys. Rev. E, 63, 066123, 2001.
"""
if create_using is None:
create_using = nx.DiGraph()
elif not create_using.is_directed():
raise nx.NetworkXError("Directed Graph required in create_using")
if kernel is None:
kernel = lambda x: x
if seed is not None:
random.seed(seed)
G = empty_graph(1, create_using)
G.name = "gn_graph({})".format(n)
if n == 1:
return G
G.add_edge(1, 0) # get started
ds = [1, 1] # degree sequence
for source in range(2, n):
# compute distribution from kernel and degree
dist = [kernel(d) for d in ds]
# choose target from discrete distribution
target = discrete_sequence(1, distribution=dist)[0]
G.add_edge(source, target)
ds.append(1) # the source has only one link (degree one)
ds[target] += 1 # add one to the target link degree
return G
[docs]def gnr_graph(n, p, create_using=None, seed=None):
"""Return the growing network with redirection (GNR) digraph with `n`
nodes and redirection probability `p`.
The GNR graph is built by adding nodes one at a time with a link to one
previously added node. The previous target node is chosen uniformly at
random. With probabiliy `p` the link is instead "redirected" to the
successor node of the target.
The graph is always a (directed) tree.
Parameters
----------
n : int
The number of nodes for the generated graph.
p : float
The redirection probability.
create_using : graph, optional (default DiGraph)
Return graph of this type. The instance will be cleared.
seed : hashable object, optional
The seed for the random number generator.
Examples
--------
To create the undirected GNR graph, use the :meth:`~DiGraph.to_directed`
method::
>>> D = nx.gnr_graph(10, 0.5) # the GNR graph
>>> G = D.to_undirected() # the undirected version
References
----------
.. [1] P. L. Krapivsky and S. Redner,
Organization of Growing Random Networks,
Phys. Rev. E, 63, 066123, 2001.
"""
if create_using is None:
create_using = nx.DiGraph()
elif not create_using.is_directed():
raise nx.NetworkXError("Directed Graph required in create_using")
if seed is not None:
random.seed(seed)
G = empty_graph(1, create_using)
G.name = "gnr_graph(%s,%s)" % (n, p)
if n == 1:
return G
for source in range(1, n):
target = random.randrange(0, source)
if random.random() < p and target != 0:
target = next(G.successors(target))
G.add_edge(source, target)
return G
[docs]def gnc_graph(n, create_using=None, seed=None):
"""Return the growing network with copying (GNC) digraph with `n` nodes.
The GNC graph is built by adding nodes one at a time with a link to one
previously added node (chosen uniformly at random) and to all of that
node's successors.
Parameters
----------
n : int
The number of nodes for the generated graph.
create_using : graph, optional (default DiGraph)
Return graph of this type. The instance will be cleared.
seed : hashable object, optional
The seed for the random number generator.
References
----------
.. [1] P. L. Krapivsky and S. Redner,
Network Growth by Copying,
Phys. Rev. E, 71, 036118, 2005k.},
"""
if create_using is None:
create_using = nx.DiGraph()
elif not create_using.is_directed():
raise nx.NetworkXError("Directed Graph required in create_using")
if seed is not None:
random.seed(seed)
G = empty_graph(1, create_using)
G.name = "gnc_graph(%s)" % (n)
if n == 1:
return G
for source in range(1, n):
target = random.randrange(0, source)
for succ in G.successors(target):
G.add_edge(source, succ)
G.add_edge(source, target)
return G
[docs]def scale_free_graph(n, alpha=0.41, beta=0.54, gamma=0.05, delta_in=0.2,
delta_out=0, create_using=None, seed=None):
"""Returns a scale-free directed graph.
Parameters
----------
n : integer
Number of nodes in graph
alpha : float
Probability for adding a new node connected to an existing node
chosen randomly according to the in-degree distribution.
beta : float
Probability for adding an edge between two existing nodes.
One existing node is chosen randomly according the in-degree
distribution and the other chosen randomly according to the out-degree
distribution.
gamma : float
Probability for adding a new node connected to an existing node
chosen randomly according to the out-degree distribution.
delta_in : float
Bias for choosing ndoes from in-degree distribution.
delta_out : float
Bias for choosing ndoes from out-degree distribution.
create_using : graph, optional (default MultiDiGraph)
Use this graph instance to start the process (default=3-cycle).
seed : integer, optional
Seed for random number generator
Examples
--------
Create a scale-free graph on one hundred nodes::
>>> G = nx.scale_free_graph(100)
Notes
-----
The sum of `alpha`, `beta`, and `gamma` must be 1.
References
----------
.. [1] B. Bollobás, C. Borgs, J. Chayes, and O. Riordan,
Directed scale-free graphs,
Proceedings of the fourteenth annual ACM-SIAM Symposium on
Discrete Algorithms, 132--139, 2003.
"""
def _choose_node(G, distribution, delta, psum):
cumsum = 0.0
# normalization
r = random.random()
for n, d in distribution:
cumsum += (d + delta) / psum
if r < cumsum:
break
return n
if create_using is None:
# start with 3-cycle
G = nx.MultiDiGraph()
G.add_edges_from([(0, 1), (1, 2), (2, 0)])
else:
# keep existing graph structure?
G = create_using
if not (G.is_directed() and G.is_multigraph()):
raise nx.NetworkXError("MultiDiGraph required in create_using")
if alpha <= 0:
raise ValueError('alpha must be >= 0.')
if beta <= 0:
raise ValueError('beta must be >= 0.')
if gamma <= 0:
raise ValueError('beta must be >= 0.')
if alpha + beta + gamma != 1.0:
raise ValueError('alpha+beta+gamma must equal 1.')
G.name = ("directed_scale_free_graph(%s,alpha=%s,beta=%s,gamma=%s,"
"delta_in=%s,delta_out=%s)" % (n, alpha, beta, gamma, delta_in,
delta_out))
# seed random number generated (uses None as default)
random.seed(seed)
number_of_edges = G.number_of_edges()
while len(G) < n:
psum_in = number_of_edges + delta_in * len(G)
psum_out = number_of_edges + delta_out * len(G)
r = random.random()
# random choice in alpha,beta,gamma ranges
if r < alpha:
# alpha
# add new node v
v = len(G)
# choose w according to in-degree and delta_in
w = _choose_node(G, G.in_degree(), delta_in, psum_in)
elif r < alpha+beta:
# beta
# choose v according to out-degree and delta_out
v = _choose_node(G, G.out_degree(), delta_out, psum_out)
# choose w according to in-degree and delta_in
w = _choose_node(G, G.in_degree(), delta_in, psum_in)
else:
# gamma
# choose v according to out-degree and delta_out
v = _choose_node(G, G.out_degree(), delta_out, psum_out)
# add new node w
w = len(G)
G.add_edge(v, w)
number_of_edges += 1
return G
def random_uniform_k_out_graph(n, k, self_loops=True, with_replacement=True,
seed=None):
"""Returns a random `k`-out graph with uniform attachment.
A random `k`-out graph with uniform attachment is a multidigraph
generated by the following algorithm. For each node *u*, choose
`k` nodes *v* uniformly at random (with replacement). Add a
directed edge joining *u* to *v*.
Parameters
----------
n : int
The number of nodes in the returned graph.
k : int
The out-degree of each node in the returned graph.
self_loops : bool
If True, self-loops are allowed when generating the graph.
with_replacement : bool
If True, neighbors are chosen with replacement and the
returned graph will be a directed multigraph. Otherwise,
neighbors are chosen without replacement and the returned graph
will be a directed graph.
seed: int
If provided, this is used as the seed for the random number
generator.
Returns
-------
NetworkX graph
A `k`-out-regular directed graph generated according to the
above algorithm. It will be a multigraph if and only if
`with_replacement` is True.
Raises
------
ValueError
If `with_replacement` is False and `k` is greater than
`n`.
See also
--------
random_k_out_graph
Notes
-----
The return digraph or multidigraph may not be strongly connected, or
even weakly connected.
If `with_replacement` is True, this function is similar to
:func:`random_k_out_graph`, if that function had parameter `alpha`
set to positive infinity.
"""
random.seed(seed)
if with_replacement:
create_using = nx.MultiDiGraph()
def sample(v, nodes):
if not self_loops:
nodes = nodes - {v}
return (random.choice(list(nodes)) for i in range(k))
else:
create_using = nx.DiGraph()
def sample(v, nodes):
if not self_loops:
nodes = nodes - {v}
return random.sample(nodes, k)
G = nx.empty_graph(n, create_using=create_using)
nodes = set(G)
for u in G:
G.add_edges_from((u, v) for v in sample(u, nodes))
G.name = 'random_uniform_k_out_graph({}, {})'.format(n, k)
return G
[docs]def random_k_out_graph(n, k, alpha, self_loops=True, seed=None):
"""Returns a random `k`-out graph with preferential attachment.
A random `k`-out graph with preferential attachment is a
multidigraph generated by the following algorithm.
1. Begin with an empty digraph, and initially set each node to have
weight `alpha`.
2. Choose a node `u` with out-degree less than `k` uniformly at
random.
3. Choose a node `v` from with probability proportional to its
weight.
4. Add a directed edge from `u` to `v`, and increase the weight
of `v` by one.
5. If each node has out-degree `k`, halt, otherwise repeat from
step 2.
For more information on this model of random graph, see [1].
Parameters
----------
n : int
The number of nodes in the returned graph.
k : int
The out-degree of each node in the returned graph.
alpha : float
A positive :class:`float` representing the initial weight of
each vertex. A higher number means that in step 3 above, nodes
will be chosen more like a true uniformly random sample, and a
lower number means that nodes are more likely to be chosen as
their in-degree increases. If this parameter is not positive, a
:exc:`ValueError` is raised.
self_loops : bool
If True, self-loops are allowed when generating the graph.
seed: int
If provided, this is used as the seed for the random number
generator.
Returns
-------
:class:`~networkx.classes.MultiDiGraph`
A `k`-out-regular multidigraph generated according to the above
algorithm.
Raises
------
ValueError
If `alpha` is not positive.
Notes
-----
The returned multidigraph may not be strongly connected, or even
weakly connected.
References
----------
[1]: Peterson, Nicholas R., and Boris Pittel.
"Distance between two random `k`-out digraphs, with and without
preferential attachment."
arXiv preprint arXiv:1311.5961 (2013).
<http://arxiv.org/abs/1311.5961>
"""
if alpha < 0:
raise ValueError('alpha must be positive')
random.seed(seed)
G = nx.empty_graph(n, create_using=nx.MultiDiGraph())
weights = Counter({v: alpha for v in G})
for i in range(k * n):
u = random.choice([v for v, d in G.out_degree() if d < k])
# If self-loops are not allowed, make the source node `u` have
# weight zero.
if not self_loops:
adjustment = Counter({u: weights[u]})
else:
adjustment = Counter()
v = weighted_choice(weights - adjustment)
G.add_edge(u, v)
weights[v] += 1
G.name = 'random_k_out_graph({0}, {1}, {2})'.format(n, k, alpha)
return G