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Original file line number Diff line number Diff line change
Expand Up @@ -144,7 +144,7 @@ To check if the constructed PAG is a valid one in pywhy-graphs, we can simply do
.. code-block:: none
ConditioningSetSelection.PDS
Context(observed_variables={'G', 'I', 'S', 'PSH', 'L'}, latent_variables=set(), state_variables={}, init_graph=<networkx.classes.graph.Graph object at 0x7c0ef50d2a90>, included_edges=<networkx.classes.graph.Graph object at 0x7c0ef50d3190>, excluded_edges=<networkx.classes.graph.Graph object at 0x7c0ef50d35d0>, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
Context(observed_variables={'PSH', 'S', 'L', 'G', 'I'}, latent_variables=set(), state_variables={}, init_graph=<networkx.classes.graph.Graph object at 0x7367d9cd2d90>, included_edges=<networkx.classes.graph.Graph object at 0x7367d9cd3490>, excluded_edges=<networkx.classes.graph.Graph object at 0x7367d9cd38d0>, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
True
Expand Down Expand Up @@ -180,7 +180,7 @@ relationship. As such, the resulting graph is no longer a valid PAG.
.. code-block:: none
ConditioningSetSelection.PDS
Context(observed_variables={'G', 'I', 'S', 'PSH', 'L'}, latent_variables=set(), state_variables={}, init_graph=<networkx.classes.graph.Graph object at 0x7c0ef50e6bd0>, included_edges=<networkx.classes.graph.Graph object at 0x7c0ef50e72d0>, excluded_edges=<networkx.classes.graph.Graph object at 0x7c0ef50e7710>, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
Context(observed_variables={'PSH', 'S', 'L', 'G', 'I'}, latent_variables=set(), state_variables={}, init_graph=<networkx.classes.graph.Graph object at 0x7367d9ce6fd0>, included_edges=<networkx.classes.graph.Graph object at 0x7367d9ce76d0>, excluded_edges=<networkx.classes.graph.Graph object at 0x7367d9ce7b10>, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
False
Expand All @@ -195,9 +195,9 @@ References

.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 1.112 seconds)
**Total running time of the script:** (0 minutes 1.025 seconds)

**Estimated memory usage:** 166 MB
**Estimated memory usage:** 163 MB


.. _sphx_glr_download_auto_examples_intro_checking_validity_of_a_pag.py:
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4 changes: 2 additions & 2 deletions dev/_sources/auto_examples/intro/inducing_path.rst.txt
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Expand Up @@ -241,9 +241,9 @@ References

.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 1.120 seconds)
**Total running time of the script:** (0 minutes 1.030 seconds)

**Estimated memory usage:** 165 MB
**Estimated memory usage:** 161 MB


.. _sphx_glr_download_auto_examples_intro_inducing_path.py:
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10 changes: 5 additions & 5 deletions dev/_sources/auto_examples/intro/intro_causal_graphs.rst.txt
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Expand Up @@ -169,7 +169,7 @@ Here, we will simulate some data to understand causal graphs in the context of S

.. code-block:: none
Fitting causal models: 0%| | 0/5 [00:00<?, ?it/s] Fitting causal mechanism of node x: 0%| | 0/5 [00:00<?, ?it/s] Fitting causal mechanism of node y: 0%| | 0/5 [00:00<?, ?it/s] Fitting causal mechanism of node z: 0%| | 0/5 [00:00<?, ?it/s] Fitting causal mechanism of node w: 0%| | 0/5 [00:00<?, ?it/s] Fitting causal mechanism of node xy: 0%| | 0/5 [00:00<?, ?it/s] Fitting causal mechanism of node xy: 100%|██████████| 5/5 [00:00<00:00, 952.51it/s]
Fitting causal models: 0%| | 0/5 [00:00<?, ?it/s] Fitting causal mechanism of node x: 0%| | 0/5 [00:00<?, ?it/s] Fitting causal mechanism of node y: 0%| | 0/5 [00:00<?, ?it/s] Fitting causal mechanism of node z: 0%| | 0/5 [00:00<?, ?it/s] Fitting causal mechanism of node w: 0%| | 0/5 [00:00<?, ?it/s] Fitting causal mechanism of node xy: 0%| | 0/5 [00:00<?, ?it/s] Fitting causal mechanism of node xy: 100%|██████████| 5/5 [00:00<00:00, 871.09it/s]
z xy w x y
0 1 1 1 1 1
1 1 1 2 2 3
Expand All @@ -183,7 +183,7 @@ Here, we will simulate some data to understand causal graphs in the context of S
y [1, 3, 2, 0]
dtype: object

<graphviz.graphs.Digraph object at 0x7c0ef531f2d0>
<graphviz.graphs.Digraph object at 0x736717ff0c10>



Expand Down Expand Up @@ -307,7 +307,7 @@ in the graph. These unobserved confounders are graphically depicted with a bidir

.. code-block:: none
['x', 'z']
['z', 'x']
The ADMG has confounded-components: [{'y', 'x'}, {'z'}, {'w'}]
'z' is d-separated from 'x': True
'z' is d-separated from 'x' given 'y': False
Expand Down Expand Up @@ -427,9 +427,9 @@ References

.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 2.221 seconds)
**Total running time of the script:** (0 minutes 2.142 seconds)

**Estimated memory usage:** 248 MB
**Estimated memory usage:** 247 MB


.. _sphx_glr_download_auto_examples_intro_intro_causal_graphs.py:
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14 changes: 7 additions & 7 deletions dev/_sources/auto_examples/intro/sg_execution_times.rst.txt
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Expand Up @@ -6,7 +6,7 @@

Computation times
=================
**00:04.453** total execution time for 3 files **from auto_examples/intro**:
**00:04.197** total execution time for 3 files **from auto_examples/intro**:

.. container::

Expand All @@ -33,11 +33,11 @@ Computation times
- Time
- Mem (MB)
* - :ref:`sphx_glr_auto_examples_intro_intro_causal_graphs.py` (``intro_causal_graphs.py``)
- 00:02.221
- 248.2
- 00:02.142
- 246.6
* - :ref:`sphx_glr_auto_examples_intro_inducing_path.py` (``inducing_path.py``)
- 00:01.120
- 164.6
- 00:01.030
- 161.5
* - :ref:`sphx_glr_auto_examples_intro_checking_validity_of_a_pag.py` (``checking_validity_of_a_pag.py``)
- 00:01.112
- 166.0
- 00:01.025
- 162.9
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Expand Up @@ -154,7 +154,7 @@ Mixed Edge Graph Properties
MixedEdgeGraph named 'IV Graph' with 3 nodes and 3 edges and 2 edge types is directed: False because there are directed edges.
False
['directed', 'bidirected']
{'directed': <networkx.classes.digraph.DiGraph object at 0x7c0e30173d50>, 'bidirected': <networkx.classes.graph.Graph object at 0x7c0ef474ab90>}
{'directed': <networkx.classes.digraph.DiGraph object at 0x73670ea12590>, 'bidirected': <networkx.classes.graph.Graph object at 0x73671a403350>}
Expand Down Expand Up @@ -312,9 +312,9 @@ class properties. Moreover, one can specify the edge type.
.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 1.370 seconds)
**Total running time of the script:** (0 minutes 1.247 seconds)

**Estimated memory usage:** 171 MB
**Estimated memory usage:** 168 MB


.. _sphx_glr_download_auto_examples_mixededge_plot_mixed_edge_graph.py:
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Expand Up @@ -6,7 +6,7 @@

Computation times
=================
**00:01.370** total execution time for 1 file **from auto_examples/mixededge**:
**00:01.247** total execution time for 1 file **from auto_examples/mixededge**:

.. container::

Expand All @@ -33,5 +33,5 @@ Computation times
- Time
- Mem (MB)
* - :ref:`sphx_glr_auto_examples_mixededge_plot_mixed_edge_graph.py` (``plot_mixed_edge_graph.py``)
- 00:01.370
- 170.6
- 00:01.247
- 167.7
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Expand Up @@ -139,9 +139,9 @@ such as `Dagitty <http://dagitty.net>`_.
.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 0.410 seconds)
**Total running time of the script:** (0 minutes 0.395 seconds)

**Estimated memory usage:** 165 MB
**Estimated memory usage:** 161 MB


.. _sphx_glr_download_auto_examples_visualization_draw_and_compare_graphs_with_same_layout.py:
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Expand Up @@ -136,9 +136,9 @@ which creates a nice default layout for time-series graphs.
.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 1.018 seconds)
**Total running time of the script:** (0 minutes 1.008 seconds)

**Estimated memory usage:** 165 MB
**Estimated memory usage:** 161 MB


.. _sphx_glr_download_auto_examples_visualization_plot_timeseries_graphs.py:
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Expand Up @@ -6,7 +6,7 @@

Computation times
=================
**00:01.428** total execution time for 2 files **from auto_examples/visualization**:
**00:01.403** total execution time for 2 files **from auto_examples/visualization**:

.. container::

Expand All @@ -33,8 +33,8 @@ Computation times
- Time
- Mem (MB)
* - :ref:`sphx_glr_auto_examples_visualization_plot_timeseries_graphs.py` (``plot_timeseries_graphs.py``)
- 00:01.018
- 164.6
- 00:01.008
- 161.5
* - :ref:`sphx_glr_auto_examples_visualization_draw_and_compare_graphs_with_same_layout.py` (``draw_and_compare_graphs_with_same_layout.py``)
- 00:00.410
- 164.6
- 00:00.395
- 161.5
26 changes: 13 additions & 13 deletions dev/_sources/sg_execution_times.rst.txt
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Expand Up @@ -6,7 +6,7 @@

Computation times
=================
**00:07.251** total execution time for 6 files **from all galleries**:
**00:06.846** total execution time for 6 files **from all galleries**:

.. container::

Expand All @@ -33,20 +33,20 @@ Computation times
- Time
- Mem (MB)
* - :ref:`sphx_glr_auto_examples_intro_intro_causal_graphs.py` (``../examples/intro/intro_causal_graphs.py``)
- 00:02.221
- 248.2
- 00:02.142
- 246.6
* - :ref:`sphx_glr_auto_examples_mixededge_plot_mixed_edge_graph.py` (``../examples/mixededge/plot_mixed_edge_graph.py``)
- 00:01.370
- 170.6
- 00:01.247
- 167.7
* - :ref:`sphx_glr_auto_examples_intro_inducing_path.py` (``../examples/intro/inducing_path.py``)
- 00:01.120
- 164.6
- 00:01.030
- 161.5
* - :ref:`sphx_glr_auto_examples_intro_checking_validity_of_a_pag.py` (``../examples/intro/checking_validity_of_a_pag.py``)
- 00:01.112
- 166.0
- 00:01.025
- 162.9
* - :ref:`sphx_glr_auto_examples_visualization_plot_timeseries_graphs.py` (``../examples/visualization/plot_timeseries_graphs.py``)
- 00:01.018
- 164.6
- 00:01.008
- 161.5
* - :ref:`sphx_glr_auto_examples_visualization_draw_and_compare_graphs_with_same_layout.py` (``../examples/visualization/draw_and_compare_graphs_with_same_layout.py``)
- 00:00.410
- 164.6
- 00:00.395
- 161.5
8 changes: 4 additions & 4 deletions dev/auto_examples/intro/checking_validity_of_a_pag.html
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Expand Up @@ -539,7 +539,7 @@ <h2>Validity of a PAG<a class="headerlink" href="#validity-of-a-pag" title="Link
</pre></div>
</div>
<div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>ConditioningSetSelection.PDS
Context(observed_variables={&#39;G&#39;, &#39;I&#39;, &#39;S&#39;, &#39;PSH&#39;, &#39;L&#39;}, latent_variables=set(), state_variables={}, init_graph=&lt;networkx.classes.graph.Graph object at 0x7c0ef50d2a90&gt;, included_edges=&lt;networkx.classes.graph.Graph object at 0x7c0ef50d3190&gt;, excluded_edges=&lt;networkx.classes.graph.Graph object at 0x7c0ef50d35d0&gt;, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
Context(observed_variables={&#39;PSH&#39;, &#39;S&#39;, &#39;L&#39;, &#39;G&#39;, &#39;I&#39;}, latent_variables=set(), state_variables={}, init_graph=&lt;networkx.classes.graph.Graph object at 0x7367d9cd2d90&gt;, included_edges=&lt;networkx.classes.graph.Graph object at 0x7367d9cd3490&gt;, excluded_edges=&lt;networkx.classes.graph.Graph object at 0x7367d9cd38d0&gt;, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
True
</pre></div>
</div>
Expand All @@ -558,7 +558,7 @@ <h2>Validity of a PAG<a class="headerlink" href="#validity-of-a-pag" title="Link
</pre></div>
</div>
<div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>ConditioningSetSelection.PDS
Context(observed_variables={&#39;G&#39;, &#39;I&#39;, &#39;S&#39;, &#39;PSH&#39;, &#39;L&#39;}, latent_variables=set(), state_variables={}, init_graph=&lt;networkx.classes.graph.Graph object at 0x7c0ef50e6bd0&gt;, included_edges=&lt;networkx.classes.graph.Graph object at 0x7c0ef50e72d0&gt;, excluded_edges=&lt;networkx.classes.graph.Graph object at 0x7c0ef50e7710&gt;, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
Context(observed_variables={&#39;PSH&#39;, &#39;S&#39;, &#39;L&#39;, &#39;G&#39;, &#39;I&#39;}, latent_variables=set(), state_variables={}, init_graph=&lt;networkx.classes.graph.Graph object at 0x7367d9ce6fd0&gt;, included_edges=&lt;networkx.classes.graph.Graph object at 0x7367d9ce76d0&gt;, excluded_edges=&lt;networkx.classes.graph.Graph object at 0x7367d9ce7b10&gt;, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
False
</pre></div>
</div>
Expand All @@ -574,8 +574,8 @@ <h2>References<a class="headerlink" href="#references" title="Link to this headi
</aside>
</aside>
</div>
<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.112 seconds)</p>
<p><strong>Estimated memory usage:</strong> 166 MB</p>
<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.025 seconds)</p>
<p><strong>Estimated memory usage:</strong> 163 MB</p>
<div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-intro-checking-validity-of-a-pag-py">
<div class="sphx-glr-download sphx-glr-download-jupyter docutils container">
<p><a class="reference download internal" download="" href="../../_downloads/5f927be0252fc0d8c3167ec4c832cbc7/checking_validity_of_a_pag.ipynb"><code class="xref download docutils literal notranslate"><span class="pre">Download</span> <span class="pre">Jupyter</span> <span class="pre">notebook:</span> <span class="pre">checking_validity_of_a_pag.ipynb</span></code></a></p>
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4 changes: 2 additions & 2 deletions dev/auto_examples/intro/inducing_path.html
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Expand Up @@ -610,8 +610,8 @@ <h2>References<a class="headerlink" href="#references" title="Link to this headi
</aside>
</aside>
</div>
<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.120 seconds)</p>
<p><strong>Estimated memory usage:</strong> 165 MB</p>
<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.030 seconds)</p>
<p><strong>Estimated memory usage:</strong> 161 MB</p>
<div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-intro-inducing-path-py">
<div class="sphx-glr-download sphx-glr-download-jupyter docutils container">
<p><a class="reference download internal" download="" href="../../_downloads/8259499c2b052354bd5dc54791c0d957/inducing_path.ipynb"><code class="xref download docutils literal notranslate"><span class="pre">Download</span> <span class="pre">Jupyter</span> <span class="pre">notebook:</span> <span class="pre">inducing_path.ipynb</span></code></a></p>
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10 changes: 5 additions & 5 deletions dev/auto_examples/intro/intro_causal_graphs.html
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Expand Up @@ -591,7 +591,7 @@ <h2>Structural Causal Models: Simulating some data<a class="headerlink" href="#s
Fitting causal mechanism of node z: 0%| | 0/5 [00:00&lt;?, ?it/s]
Fitting causal mechanism of node w: 0%| | 0/5 [00:00&lt;?, ?it/s]
Fitting causal mechanism of node xy: 0%| | 0/5 [00:00&lt;?, ?it/s]
Fitting causal mechanism of node xy: 100%|██████████| 5/5 [00:00&lt;00:00, 952.51it/s]
Fitting causal mechanism of node xy: 100%|██████████| 5/5 [00:00&lt;00:00, 871.09it/s]
z xy w x y
0 1 1 1 1 1
1 1 1 2 2 3
Expand All @@ -605,7 +605,7 @@ <h2>Structural Causal Models: Simulating some data<a class="headerlink" href="#s
y [1, 3, 2, 0]
dtype: object

&lt;graphviz.graphs.Digraph object at 0x7c0ef531f2d0&gt;
&lt;graphviz.graphs.Digraph object at 0x736717ff0c10&gt;
</pre></div>
</div>
</section>
Expand Down Expand Up @@ -692,7 +692,7 @@ <h2>Acyclic Directed Mixed Graphs (ADMG)<a class="headerlink" href="#acyclic-dir
<span class="c1"># details on causal discovery (i.e. structure learning algorithms), please see that repo.</span>
</pre></div>
</div>
<img src="../../_images/sphx_glr_intro_causal_graphs_002.png" srcset="../../_images/sphx_glr_intro_causal_graphs_002.png" alt="intro causal graphs" class = "sphx-glr-single-img"/><div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>[&#39;x&#39;, &#39;z&#39;]
<img src="../../_images/sphx_glr_intro_causal_graphs_002.png" srcset="../../_images/sphx_glr_intro_causal_graphs_002.png" alt="intro causal graphs" class = "sphx-glr-single-img"/><div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>[&#39;z&#39;, &#39;x&#39;]
The ADMG has confounded-components: [{&#39;y&#39;, &#39;x&#39;}, {&#39;z&#39;}, {&#39;w&#39;}]
&#39;z&#39; is d-separated from &#39;x&#39;: True
&#39;z&#39; is d-separated from &#39;x&#39; given &#39;y&#39;: False
Expand Down Expand Up @@ -774,8 +774,8 @@ <h3>References<a class="headerlink" href="#references" title="Link to this headi
</aside>
</aside>
</div>
<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 2.221 seconds)</p>
<p><strong>Estimated memory usage:</strong> 248 MB</p>
<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 2.142 seconds)</p>
<p><strong>Estimated memory usage:</strong> 247 MB</p>
<div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-intro-intro-causal-graphs-py">
<div class="sphx-glr-download sphx-glr-download-jupyter docutils container">
<p><a class="reference download internal" download="" href="../../_downloads/e92c7413422dfa4591a10ac31b2b0f4d/intro_causal_graphs.ipynb"><code class="xref download docutils literal notranslate"><span class="pre">Download</span> <span class="pre">Jupyter</span> <span class="pre">notebook:</span> <span class="pre">intro_causal_graphs.ipynb</span></code></a></p>
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14 changes: 7 additions & 7 deletions dev/auto_examples/intro/sg_execution_times.html
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Expand Up @@ -435,7 +435,7 @@

<section id="computation-times">
<span id="sphx-glr-auto-examples-intro-sg-execution-times"></span><h1>Computation times<a class="headerlink" href="#computation-times" title="Link to this heading">#</a></h1>
<p><strong>00:04.453</strong> total execution time for 3 files <strong>from auto_examples/intro</strong>:</p>
<p><strong>00:04.197</strong> total execution time for 3 files <strong>from auto_examples/intro</strong>:</p>
<div class="docutils container">
<style scoped>
<link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
Expand All @@ -457,16 +457,16 @@
</thead>
<tbody>
<tr class="row-even"><td><p><a class="reference internal" href="intro_causal_graphs.html#sphx-glr-auto-examples-intro-intro-causal-graphs-py"><span class="std std-ref">An introduction to causal graphs and how to use them</span></a> (<code class="docutils literal notranslate"><span class="pre">intro_causal_graphs.py</span></code>)</p></td>
<td><p>00:02.221</p></td>
<td><p>248.2</p></td>
<td><p>00:02.142</p></td>
<td><p>246.6</p></td>
</tr>
<tr class="row-odd"><td><p><a class="reference internal" href="inducing_path.html#sphx-glr-auto-examples-intro-inducing-path-py"><span class="std std-ref">An introduction to Inducing Paths and how to find them</span></a> (<code class="docutils literal notranslate"><span class="pre">inducing_path.py</span></code>)</p></td>
<td><p>00:01.120</p></td>
<td><p>164.6</p></td>
<td><p>00:01.030</p></td>
<td><p>161.5</p></td>
</tr>
<tr class="row-even"><td><p><a class="reference internal" href="checking_validity_of_a_pag.html#sphx-glr-auto-examples-intro-checking-validity-of-a-pag-py"><span class="std std-ref">On PAGs and their validity</span></a> (<code class="docutils literal notranslate"><span class="pre">checking_validity_of_a_pag.py</span></code>)</p></td>
<td><p>00:01.112</p></td>
<td><p>166.0</p></td>
<td><p>00:01.025</p></td>
<td><p>162.9</p></td>
</tr>
</tbody>
</table>
Expand Down
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