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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={'L', 'S', 'PSH', 'G', 'I'}, latent_variables=set(), state_variables={}, init_graph=<networkx.classes.graph.Graph object at 0x7379de5e5d10>, included_edges=<networkx.classes.graph.Graph object at 0x7379de5e6410>, excluded_edges=<networkx.classes.graph.Graph object at 0x7379de5e6850>, 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={'L', 'I', 'S', 'PSH', 'G'}, latent_variables=set(), state_variables={}, init_graph=<networkx.classes.graph.Graph object at 0x7c2cc2231490>, included_edges=<networkx.classes.graph.Graph object at 0x7c2cc2231b90>, excluded_edges=<networkx.classes.graph.Graph object at 0x7c2cc2231fd0>, 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={'L', 'S', 'PSH', 'G', 'I'}, latent_variables=set(), state_variables={}, init_graph=<networkx.classes.graph.Graph object at 0x7379de5fa090>, included_edges=<networkx.classes.graph.Graph object at 0x7379de5fa790>, excluded_edges=<networkx.classes.graph.Graph object at 0x7379de5fabd0>, 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={'L', 'I', 'S', 'PSH', 'G'}, latent_variables=set(), state_variables={}, init_graph=<networkx.classes.graph.Graph object at 0x7c2cc2241910>, included_edges=<networkx.classes.graph.Graph object at 0x7c2cc2242010>, excluded_edges=<networkx.classes.graph.Graph object at 0x7c2cc2242450>, 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 @@ -195,7 +195,7 @@ References

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

**Total running time of the script:** (0 minutes 1.111 seconds)
**Total running time of the script:** (0 minutes 1.000 seconds)

**Estimated memory usage:** 166 MB

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2 changes: 1 addition & 1 deletion dev/_sources/auto_examples/intro/inducing_path.rst.txt
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Expand Up @@ -241,7 +241,7 @@ References

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

**Total running time of the script:** (0 minutes 1.156 seconds)
**Total running time of the script:** (0 minutes 1.199 seconds)

**Estimated memory usage:** 164 MB

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8 changes: 4 additions & 4 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, 821.99it/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, 900.65it/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 0x737919161f90>
<graphviz.graphs.Digraph object at 0x7c2bf7ec6110>



Expand Down Expand Up @@ -427,9 +427,9 @@ References

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

**Total running time of the script:** (0 minutes 2.267 seconds)
**Total running time of the script:** (0 minutes 2.316 seconds)

**Estimated memory usage:** 249 MB
**Estimated memory usage:** 248 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
=================
**00:04.533** total execution time for 3 files **from auto_examples/intro**:
**00:04.515** 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``)
- 00:02.267
- 249.1
- 00:02.316
- 248.2
* - :ref:`sphx_glr_auto_examples_intro_inducing_path.py` (``inducing_path.py``)
- 00:01.156
- 164.3
- 00:01.199
- 164.1
* - :ref:`sphx_glr_auto_examples_intro_checking_validity_of_a_pag.py` (``checking_validity_of_a_pag.py``)
- 00:01.111
- 166.0
- 00:01.000
- 165.8
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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 0x7379dd8f27d0>, 'bidirected': <networkx.classes.graph.Graph object at 0x7379dda2cbd0>}
{'directed': <networkx.classes.digraph.DiGraph object at 0x7c2c441b5210>, 'bidirected': <networkx.classes.graph.Graph object at 0x7c2cc1846ed0>}
Expand Down Expand Up @@ -194,7 +194,7 @@ Mixed Edge Graph Operations on Nodes

.. code-block:: none
MixedEdgeGraph named 'IV Graph' with 3 nodes and 3 edges and 2 edge types has nodes: ['X', 'Y', 'Z']
MixedEdgeGraph named 'IV Graph' with 3 nodes and 3 edges and 2 edge types has nodes: ['Z', 'Y', 'X']
Graph has node A: False
Now graph has node A: True
Graph has node A: False
Expand Down Expand Up @@ -312,7 +312,7 @@ class properties. Moreover, one can specify the edge type.
.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 1.364 seconds)
**Total running time of the script:** (0 minutes 1.232 seconds)

**Estimated memory usage:** 170 MB

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Expand Up @@ -6,7 +6,7 @@

Computation times
=================
**00:01.364** total execution time for 1 file **from auto_examples/mixededge**:
**00:01.232** 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``)
- 00:01.364
- 170.2
- 00:01.232
- 170.4
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Expand Up @@ -139,7 +139,7 @@ such as `Dagitty <http://dagitty.net>`_.
.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 0.409 seconds)
**Total running time of the script:** (0 minutes 0.415 seconds)

**Estimated memory usage:** 164 MB

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Expand Up @@ -136,7 +136,7 @@ which creates a nice default layout for time-series graphs.
.. rst-class:: sphx-glr-timing

**Total running time of the script:** (0 minutes 1.050 seconds)
**Total running time of the script:** (0 minutes 0.960 seconds)

**Estimated memory usage:** 164 MB

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Expand Up @@ -6,7 +6,7 @@

Computation times
=================
**00:01.459** total execution time for 2 files **from auto_examples/visualization**:
**00:01.375** 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``)
- 00:01.050
- 164.3
- 00:00.960
- 164.1
* - :ref:`sphx_glr_auto_examples_visualization_draw_and_compare_graphs_with_same_layout.py` (``draw_and_compare_graphs_with_same_layout.py``)
- 00:00.409
- 164.3
- 00:00.415
- 164.1
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
=================
**00:07.357** total execution time for 6 files **from all galleries**:
**00:07.123** 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``)
- 00:02.267
- 249.1
- 00:02.316
- 248.2
* - :ref:`sphx_glr_auto_examples_mixededge_plot_mixed_edge_graph.py` (``../examples/mixededge/plot_mixed_edge_graph.py``)
- 00:01.364
- 170.2
- 00:01.232
- 170.4
* - :ref:`sphx_glr_auto_examples_intro_inducing_path.py` (``../examples/intro/inducing_path.py``)
- 00:01.156
- 164.3
- 00:01.199
- 164.1
* - :ref:`sphx_glr_auto_examples_intro_checking_validity_of_a_pag.py` (``../examples/intro/checking_validity_of_a_pag.py``)
- 00:01.111
- 166.0
- 00:01.000
- 165.8
* - :ref:`sphx_glr_auto_examples_visualization_plot_timeseries_graphs.py` (``../examples/visualization/plot_timeseries_graphs.py``)
- 00:01.050
- 164.3
- 00:00.960
- 164.1
* - :ref:`sphx_glr_auto_examples_visualization_draw_and_compare_graphs_with_same_layout.py` (``../examples/visualization/draw_and_compare_graphs_with_same_layout.py``)
- 00:00.409
- 164.3
- 00:00.415
- 164.1
6 changes: 3 additions & 3 deletions dev/auto_examples/intro/checking_validity_of_a_pag.html
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Expand Up @@ -533,7 +533,7 @@ <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;L&#39;, &#39;S&#39;, &#39;PSH&#39;, &#39;G&#39;, &#39;I&#39;}, latent_variables=set(), state_variables={}, init_graph=&lt;networkx.classes.graph.Graph object at 0x7379de5e5d10&gt;, included_edges=&lt;networkx.classes.graph.Graph object at 0x7379de5e6410&gt;, excluded_edges=&lt;networkx.classes.graph.Graph object at 0x7379de5e6850&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;L&#39;, &#39;I&#39;, &#39;S&#39;, &#39;PSH&#39;, &#39;G&#39;}, latent_variables=set(), state_variables={}, init_graph=&lt;networkx.classes.graph.Graph object at 0x7c2cc2231490&gt;, included_edges=&lt;networkx.classes.graph.Graph object at 0x7c2cc2231b90&gt;, excluded_edges=&lt;networkx.classes.graph.Graph object at 0x7c2cc2231fd0&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 @@ -552,7 +552,7 @@ <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;L&#39;, &#39;S&#39;, &#39;PSH&#39;, &#39;G&#39;, &#39;I&#39;}, latent_variables=set(), state_variables={}, init_graph=&lt;networkx.classes.graph.Graph object at 0x7379de5fa090&gt;, included_edges=&lt;networkx.classes.graph.Graph object at 0x7379de5fa790&gt;, excluded_edges=&lt;networkx.classes.graph.Graph object at 0x7379de5fabd0&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;L&#39;, &#39;I&#39;, &#39;S&#39;, &#39;PSH&#39;, &#39;G&#39;}, latent_variables=set(), state_variables={}, init_graph=&lt;networkx.classes.graph.Graph object at 0x7c2cc2241910&gt;, included_edges=&lt;networkx.classes.graph.Graph object at 0x7c2cc2242010&gt;, excluded_edges=&lt;networkx.classes.graph.Graph object at 0x7c2cc2242450&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 @@ -568,7 +568,7 @@ <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 1.111 seconds)</p>
<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.000 seconds)</p>
<p><strong>Estimated memory usage:</strong> 166 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">
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2 changes: 1 addition & 1 deletion dev/auto_examples/intro/inducing_path.html
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Expand Up @@ -604,7 +604,7 @@ <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 1.156 seconds)</p>
<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.199 seconds)</p>
<p><strong>Estimated memory usage:</strong> 164 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">
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8 changes: 4 additions & 4 deletions dev/auto_examples/intro/intro_causal_graphs.html
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Expand Up @@ -585,7 +585,7 @@ <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, 821.99it/s]
Fitting causal mechanism of node xy: 100%|██████████| 5/5 [00:00&lt;00:00, 900.65it/s]
z xy w x y
0 1 1 1 1 1
1 1 1 2 2 3
Expand All @@ -599,7 +599,7 @@ <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 0x737919161f90&gt;
&lt;graphviz.graphs.Digraph object at 0x7c2bf7ec6110&gt;
</pre></div>
</div>
</section>
Expand Down Expand Up @@ -768,8 +768,8 @@ <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 2.267 seconds)</p>
<p><strong>Estimated memory usage:</strong> 249 MB</p>
<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 2.316 seconds)</p>
<p><strong>Estimated memory usage:</strong> 248 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 @@ -429,7 +429,7 @@

<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>00:04.533</strong> total execution time for 3 files <strong>from auto_examples/intro</strong>:</p>
<p><strong>00:04.515</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 @@ -451,16 +451,16 @@
</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>00:02.267</p></td>
<td><p>249.1</p></td>
<td><p>00:02.316</p></td>
<td><p>248.2</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>00:01.156</p></td>
<td><p>164.3</p></td>
<td><p>00:01.199</p></td>
<td><p>164.1</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>00:01.111</p></td>
<td><p>166.0</p></td>
<td><p>00:01.000</p></td>
<td><p>165.8</p></td>
</tr>
</tbody>
</table>
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6 changes: 3 additions & 3 deletions dev/auto_examples/mixededge/plot_mixed_edge_graph.html
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Expand Up @@ -553,7 +553,7 @@ <h2>Mixed Edge Graph Properties<a class="headerlink" href="#mixed-edge-graph-pro
MixedEdgeGraph named &#39;IV Graph&#39; with 3 nodes and 3 edges and 2 edge types is directed: False because there are directed edges.
False
[&#39;directed&#39;, &#39;bidirected&#39;]
{&#39;directed&#39;: &lt;networkx.classes.digraph.DiGraph object at 0x7379dd8f27d0&gt;, &#39;bidirected&#39;: &lt;networkx.classes.graph.Graph object at 0x7379dda2cbd0&gt;}
{&#39;directed&#39;: &lt;networkx.classes.digraph.DiGraph object at 0x7c2c441b5210&gt;, &#39;bidirected&#39;: &lt;networkx.classes.graph.Graph object at 0x7c2cc1846ed0&gt;}
</pre></div>
</div>
</section>
Expand All @@ -577,7 +577,7 @@ <h2>Mixed Edge Graph Operations on Nodes<a class="headerlink" href="#mixed-edge-
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Graph has node A: </span><span class="si">{</span><a href="../../generated/pywhy_graphs.networkx.MixedEdgeGraph.html#pywhy_graphs.networkx.MixedEdgeGraph.has_node" title="pywhy_graphs.networkx.MixedEdgeGraph.has_node" class="sphx-glr-backref-module-pywhy_graphs-networkx sphx-glr-backref-type-py-method"><span class="n">G</span><span class="o">.</span><span class="n">has_node</span></a><span class="p">(</span><span class="s1">&#39;A&#39;</span><span class="p">)</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
</pre></div>
</div>
<div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>MixedEdgeGraph named &#39;IV Graph&#39; with 3 nodes and 3 edges and 2 edge types has nodes: [&#39;X&#39;, &#39;Y&#39;, &#39;Z&#39;]
<div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>MixedEdgeGraph named &#39;IV Graph&#39; with 3 nodes and 3 edges and 2 edge types has nodes: [&#39;Z&#39;, &#39;Y&#39;, &#39;X&#39;]
Graph has node A: False
Now graph has node A: True
Graph has node A: False
Expand Down Expand Up @@ -659,7 +659,7 @@ <h2>Mixed Edge Graph Key Differences<a class="headerlink" href="#mixed-edge-grap
bidirected with degree: [(&#39;X&#39;, 1), (&#39;Y&#39;, 1), (&#39;Z&#39;, 0)]
</pre></div>
</div>
<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.364 seconds)</p>
<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.232 seconds)</p>
<p><strong>Estimated memory usage:</strong> 170 MB</p>
<div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-mixededge-plot-mixed-edge-graph-py">
<div class="sphx-glr-download sphx-glr-download-jupyter docutils container">
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