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Tiago Peixoto
graph-tool
Commits
70bf7408
Commit
70bf7408
authored
Jul 18, 2016
by
Tiago Peixoto
Browse files
Fix doctests
parent
31a16689
Pipeline
#203
failed with stage
in 4047 minutes and 50 seconds
Changes
3
Pipelines
1
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doc/Makefile
View file @
70bf7408
...
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@@ -5,7 +5,7 @@ latex:
sphinx-build
-E
-b
latex
.
build
test
:
OMP_NUM_THREADS
=
1
sphinx-build
-b
doctest
.
build
sphinx-build
-b
doctest
.
build
clean
:
rm
-rf
build
...
...
doc/conf.py
View file @
70bf7408
...
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@@ -196,11 +196,11 @@ latex_elements = {
'fontpkg'
:
r
"\usepackage{bookman}"
}
# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping
=
{
'python'
:
(
'http://docs.python.org/3'
,
None
),
intersphinx_mapping
=
{
'python'
:
(
'http
s
://docs.python.org/3'
,
None
),
'numpy'
:
(
'http://docs.scipy.org/doc/numpy'
,
None
),
'scipy'
:
(
'http://docs.scipy.org/doc/scipy/reference'
,
None
),
'matplotlib'
:
(
'http://matplotlib.
sourceforge.net
'
,
None
),
'cairo'
:
(
'http://www.cairographics.org/documentation/pycairo/3
/
'
,
None
),
'matplotlib'
:
(
'http://matplotlib.
org
'
,
None
),
'cairo'
:
(
'http
s
://www.cairographics.org/documentation/pycairo/3'
,
None
),
'ipython'
:
(
'http://ipython.org/ipython-doc/stable/'
,
None
),
'panda'
:
(
'http://pandas.pydata.org/pandas-docs/stable/'
,
None
)}
...
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doc/demos/inference/inference.rst
View file @
70bf7408
...
...
@@ -506,9 +506,9 @@ example, for the American football network above, we have:
.. testoutput:: model-selection
:options: +NORMALIZE_WHITESPACE
Non-degree-corrected DL: 17
25.78502074
Degree-corrected DL: 178
4.77629595
ln Λ: -
58.9912752096
Non-degree-corrected DL: 17
38.00660528
Degree-corrected DL: 178
0.01146484
ln Λ: -
42.0048595573
Hence, with a posterior odds ratio of :math:`\Lambda \sim e^{-59} \sim
10^{-25}` in favor of the non-degree-corrected model, it seems like the
...
...
@@ -826,10 +826,9 @@ work, and we can now obtain vertex marginals on all hierarchical levels:
Marginal probabilities of group memberships of the network of
characters in the novel Les Misérables, according to the nested
degree-corrected SBM. The `pie fractions
<https://en.wikipedia.org/wiki/Pie_chart>`_ on the nodes correspond
to the probability of being in group associated with the respective
color.
degree-corrected SBM. The `pie fractions <https://en.wikipedia.org/wiki/Pie_chart>`_
on the nodes correspond to the probability of being in group
associated with the respective color.
We can also obtain a marginal probability of the number of groups
itself, as follows.
...
...
@@ -1068,7 +1067,7 @@ evidence efficiently, as we show below, using
.. testoutput:: model-evidence
Model evidence for deg_corr = True: -622.794364945 (mean field), -707.484453595 (Bethe)
Model evidence for deg_corr = False: -6
33.276625201
(mean field), -6
70.113442151
(Bethe)
Model evidence for deg_corr = False: -6
24.357861783
(mean field), -6
57.164066465
(Bethe)
Despite the (expected) discrepancy between both approximations, the
outcome shows a clear preference for the non-degree-corrected model.
...
...
@@ -1132,8 +1131,8 @@ approach for the same network, using the nested model.
.. testoutput:: model-evidence
Model evidence for deg_corr = True: -5
30.057076507
(mean field), -
702.858734133
(Bethe)
Model evidence for deg_corr = False: -5
55.073189798
(mean field), -6
49.484851667
(Bethe)
Model evidence for deg_corr = True: -5
49.845093934
(mean field), -
688.382102062
(Bethe)
Model evidence for deg_corr = False: -5
93.581546241
(mean field), -6
21.257816805
(Bethe)
The results are interesting: Not only we observe a better evidence for
the nested models themselves, when comparing to the evidences for the
...
...
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