def test_caveman_graph():
G = nx.caveman_graph(4,3)
assert_equal(len(G),12)
G = nx.caveman_graph(1,5)
K5 = nx.complete_graph(5)
assert_true(nx.is_isomorphic(G,K5))
def test_limited_infection_caveman_graph(self):
# A caveman graph has a bunch of cliques of the same size.
# We can only approximate the limit by the size of the cliques.
graph = nx.caveman_graph(10, 3) # 10 cliques of size 3
# 9 is multiple of 3, we can do match this limit precisely.
infected = infection.limited_infection(graph, 9)
self.assertEqual(9, len(infected))
# 10 is not a multiple of 3. We'll approximate with the next multiple of 3.
infected = infection.limited_infection(graph, 10)
self.assertEqual(12, len(infected))
def relaxed_caveman_graph(l, k, p, seed=None, directed=False):
"""Return a relaxed caveman graph.
A relaxed caveman graph starts with l cliques of size k. Edges
are then randomly rewired with probability p to link different
cliques.
Parameters
----------
l : int
Number of groups
k : int
Size of cliques
p : float
Probabilty of rewiring each edge.
seed : int,optional
Seed for random number generator(default=None)
directed : bool,optional (default=False)
If True return a directed graph
Returns
-------
G : NetworkX Graph
Relaxed Caveman Graph
Raises
------
NetworkXError:
If p is not in [0,1]
Examples
--------
>>> G = nx.relaxed_caveman_graph(2, 3, 0.1, seed=42)
References
----------
.. [1] Santo Fortunato, Community Detection in Graphs,
Physics Reports Volume 486, Issues 3-5, February 2010, Pages 75-174.
http://arxiv.org/abs/0906.0612
"""
if not seed is None:
random.seed(seed)
G = nx.caveman_graph(l, k)
nodes = G.nodes()
G.name = "relaxed_caveman_graph (%s,%s,%s)" % (l, k, p)
for (u, v) in G.edges():
if random.random() < p: # rewire the edge
x = random.choice(nodes)
if G.has_edge(u, x):
continue
G.remove_edge(u, v)
G.add_edge(u, x)
return G
def relaxed_caveman_graph(l, k, p, seed=None):
"""Returns a relaxed caveman graph.
A relaxed caveman graph starts with `l` cliques of size `k`. Edges are
then randomly rewired with probability `p` to link different cliques.
Parameters
----------
l : int
Number of groups
k : int
Size of cliques
p : float
Probabilty of rewiring each edge.
seed : integer, random_state, or None (default)
Indicator of random number generation state.
See :ref:`Randomness<randomness>`.
Returns
-------
G : NetworkX Graph
Relaxed Caveman Graph
Raises
------
NetworkXError:
If p is not in [0,1]
Examples
--------
>>> G = nx.relaxed_caveman_graph(2, 3, 0.1, seed=42)
References
----------
.. [1] Santo Fortunato, Community Detection in Graphs,
Physics Reports Volume 486, Issues 3-5, February 2010, Pages 75-174.
https://arxiv.org/abs/0906.0612
"""
G = nx.caveman_graph(l, k)
nodes = list(G)
for (u, v) in G.edges():
if seed.random() < p: # rewire the edge
x = seed.choice(nodes)
if G.has_edge(u, x):
continue
G.remove_edge(u, v)
G.add_edge(u, x)
return G
def caveman_special(c=2,k=20,p_path=0.1,p_edge=0.3):
p = p_path
path_count = max(int(np.ceil(p * k)),1)
G = nx.caveman_graph(c, k)
# remove 50% edges
p = 1-p_edge
for (u, v) in list(G.edges()):
if np.random.rand() < p and ((u < k and v < k) or (u >= k and v >= k)):
G.remove_edge(u, v)
# add path_count links
for i in range(path_count):
u = np.random.randint(0, k)
v = np.random.randint(k, k * 2)
G.add_edge(u, v)
G = max(nx.connected_component_subgraphs(G), key=len)
return G
def connected_caveman_graph(l, k):
"""Returns a connected caveman graph of n cliques of size k.
The connected caveman graph is formed by creating n cliques of size k. Then
a single node in each clique is rewired to a node in the adjacent clique.
Parameters
----------
n : int
number of cliques
k : int
size of cliques
directed : boolean optional (default=True)
if true return directed caveman graph
Returns
-------
G : NetworkX Graph
caveman graph
Notes
-----
This returns an undirected graph, it can be converted to a directed
graph using nx.to_directed(), or a multigraph using
nx.MultiGraph(nx.caveman_graph). Only the undirected version is
described in [1]_ and it is unclear which of the directed
generalizations is most useful.
Examples
--------
>>> G = nx.caveman_graph(3, 3)
Reference
---------
.. [1] Watts, D. J. 'Networks, Dynamics, and the Small-World Phenomenon.'
Amer. J. Soc. 105, 493-527, 1999.
"""
G = nx.caveman_graph(l, k)
G.name = "connected_caveman_graph(%s,%s)" % (l, k)
for start in range(0, l*k, k):
G.remove_edge(start, start+1)
G.add_edge(start, (start-1) % (l*k))
return G
def connected_caveman_graph(l, k):
"""Returns a connected caveman graph of `l` cliques of size `k`.
The connected caveman graph is formed by creating `n` cliques of size
`k`, then a single edge in each clique is rewired to a node in an
adjacent clique.
Parameters
----------
l : int
number of cliques
k : int
size of cliques
Returns
-------
G : NetworkX Graph
connected caveman graph
Notes
-----
This returns an undirected graph, it can be converted to a directed
graph using :func:`nx.to_directed`, or a multigraph using
``nx.MultiGraph(nx.caveman_graph(l, k))``. Only the undirected version is
described in [1]_ and it is unclear which of the directed
generalizations is most useful.
Examples
--------
>>> G = nx.connected_caveman_graph(3, 3)
References
----------
.. [1] Watts, D. J. 'Networks, Dynamics, and the Small-World Phenomenon.'
Amer. J. Soc. 105, 493-527, 1999.
"""
G = nx.caveman_graph(l, k)
for start in range(0, l * k, k):
G.remove_edge(start, start + 1)
G.add_edge(start, (start - 1) % (l * k))
return G
# Social Graph
path_output_data = path_input + 'social/'
makedir(path_output_data)
# Karate club graph
path_output_data_type = path_output_data + 'karate_club/'
makedir(path_output_data_type)
G = nx.karate_club_graph()
makedir(path_output_data_type + 'entity_' + str(0))
save_graph(path_output_data_type + 'entity_' + str(0) + '/' + 'J_ij.csv', G)
# Caveman Graph
path_output_data_type = path_output_data + 'caveman_graph/'
makedir(path_output_data_type)
G = nx.caveman_graph(int(default_size / 10), 10)
makedir(path_output_data_type + 'entity_' + str(0))
save_graph(path_output_data_type + 'entity_' + str(0) + '/' + 'J_ij.csv', G)
path_output_data = path_input + 'biological/'
makedir(path_output_data)
#Enzimes structure
#http://networkrepository.com/ENZYMES-g16.php
path = '/home/brainlab/Downloads/ENZYMES_g16 (1)/ENZYMES_g16.edgelist'
path_output_data_type = path_output_data + 'enzimes_g16/'
makedir(path_output_data_type)
G = nx.read_edgelist(path,
nodetype=int,
create_using=nx.DiGraph,
data=(('weight', float), ))
if __name__ == "__main__":
# random graph, relaxed caveman 100 clusters with 50 each
# Massachusetts nursing homes, 500 nursing homes, nursing home has 100 residents,
# 30 employees each, transmission rate within nursing home,
# some rate outside
# 500 tests a day, 10 of the nursing homes actually have COVID
# 30-40% in the nursing homes that have them
# start with 1, 10, 50 groups
for simulation_num in range(2, 11):
print("Creating the nursing_home_graph... ")
l = 500
k = 100
N = l * k + 15000
G = nx.caveman_graph(l, k)
nursing_homes = [set(i) for i in (nx.algorithms.find_cliques(G))]
worker_id = 50000
# frequencies = {}
print("Finding workers jobs... ")
for worker in range(50000, 50000 + 12500):
home = random.sample(nursing_homes, 1)[0]
G.add_node(worker)
# if worker in frequencies:
#
# frequencies[worker] += 1
# else:
# frequencies[worker] = 1
G.add_edge(worker, next(iter(home)))
home.add(worker)
elif (InitMatrix[i][j] == 1) and (random.random() <= beta):
break
return AdjMatrix
a = [0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1]
print
m = 30 ## dimensionality
n = 280 ## organization size
## [Code to Individual] socialization coefficient
## [Individual to Code] learning coefficient
## [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9] [0.1, 0.5, 0.9]
G = nx.caveman_graph(n, 7)
InitMatrix = [[0] * n for i in range(n)]
for i in range(0, n):
Adjs = nx.all_neighbors(G, i)
for ele in Adjs:
InitMatrix[i][ele] = 1
f = open('./Fang16.txt', 'a')
"""
for beta in numpy.arange(0,1,0.05):
for learning in [0.3]:
Equils = []
for instance in range(0, 100):
AdjMatrix = copy.deepcopy(InitMatrix)
