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Tiago Peixoto
graph-tool
Commits
5955ae7f
Commit
5955ae7f
authored
Jan 01, 2017
by
Tiago Peixoto
Browse files
Fix doctests
parent
81eb2b81
Pipeline
#238
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in 285 minutes and 34 seconds
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src/graph_tool/generation/__init__.py
src/graph_tool/generation/__init__.py
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src/graph_tool/generation/__init__.py
View file @
5955ae7f
...
...
@@ -597,13 +597,13 @@ def random_rewire(g, model="configuration", n_iter=1, edge_sweep=True,
desired. If degree probabilistic correlations are provided, the mixing
time tends to be larger.
If ``model`` is either "probabilistic
" or "blockmodel", the Markov chain
still needs to be mixed, even if parallel edges and self-loops are
allowed. In this case the Markov chain
is implemented using the
Metropolis-Hastings [metropolis-equations-1953]_
[
hastings-monte-carlo-1970]_ acceptance/rejection algorithm. It will
eventually converge to the desired probabilities for sufficiently larg
e
values of ``n_iter``.
If ``model`` is either "probabilistic
-configuration", "blockmodel" or
"blockmodel-degree", the Markov chain still needs to be mixed, even if
parallel edges and self-loops are
allowed. In this case the Markov chain
is implemented using the Metropolis-Hastings
[
metropolis-equations-1953]_ [hastings-monte-carlo-1970]_
acceptance/rejection algorithm. It will eventually converge to th
e
desired probabilities for sufficiently large
values of ``n_iter``.
Each edge is tentatively swapped once per iteration, so the overall
...
...
@@ -892,16 +892,33 @@ def generate_sbm(b, probs, out_degs=None, in_degs=None, directed=False):
.. math::
\sum_i\theta_i\delta_{b_i,r} = 1
.
\sum_i\theta_i\delta_{b_i,r} = 1
,
For directed graphs, the probability is analogous:
such that the value :math:`\lambda_{rs}` will correspond to the average
number of edges between groups :math:`r` and :math:`s` (or twice that if
:math:`r = s`). If the supplied values of :math:`\theta_i` are not
normalized as above, they will be normalized prior to the generation of the
graph.
For directed graphs, the probability is analogous, with :math:`\lambda_{rs}`
being in general asymmetric:
.. math::
P({\boldsymbol A}|{\boldsymbol \lambda},{\boldsymbol \theta},{\boldsymbol b})
= \prod_{ij}\frac{e^{-\lambda_{b_ib_j}\theta^+_i\theta^-_j}(\lambda_{b_ib_j}\theta^+_i\theta^-_j)^{A_{ij}}}{A_{ij}!}.
The graph is generated in time :math:`O(V + E)`.
Again, the same normalization is assumed:
.. math::
\sum_i\theta_i^+\delta_{b_i,r} = \sum_i\theta_i^-\delta_{b_i,r} = 1,
such that the value :math:`\lambda_{rs}` will correspond to the average
number of directed edges between groups :math:`r` and :math:`s`.
The graph is generated in time :math:`O(V + E + B)`, where :math:`B` is the
number of groups.
Examples
--------
...
...
@@ -910,7 +927,8 @@ def generate_sbm(b, probs, out_degs=None, in_degs=None, directed=False):
>>> g = gt.GraphView(g, vfilt=gt.label_largest_component(g))
>>> g = gt.Graph(g, prune=True)
>>> state = gt.minimize_blockmodel_dl(g)
>>> u = gt.generate_sbm(state.b.a, gt.adjacency(state.bg, state.mrs),
>>> u = gt.generate_sbm(state.b.a, gt.adjacency(state.get_bg(),
... state.get_ers()),
... g.degree_property_map("out").a,
... g.degree_property_map("in").a, directed=True)
>>> gt.graph_draw(g, g.vp.pos, output="polblogs-sbm.png")
...
...
@@ -958,7 +976,7 @@ def generate_sbm(b, probs, out_degs=None, in_degs=None, directed=False):
idx
=
r
<=
s
r
=
r
[
idx
]
s
=
s
[
idx
]
p
=
numpy
.
squeeze
(
probs
[
r
,
s
])
p
=
numpy
.
squeeze
(
numpy
.
array
(
probs
[
r
,
s
])
)
g
.
set_directed
(
directed
)
...
...
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