new class Graphs

jakobrunge · Oct 28, 2024 · c128bf6 · c128bf6
1 parent 7718fe1
commit c128bf6
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Showing 17 changed files with 2,077 additions and 1,412 deletions.
diff --git a/docs/_build/.doctrees/environment.pickle b/docs/_build/.doctrees/environment.pickle
diff --git a/docs/_build/.doctrees/index.doctree b/docs/_build/.doctrees/index.doctree
diff --git a/docs/_build/_modules/index.html b/docs/_build/_modules/index.html
@@ -34,9 +34,11 @@ <h1>All modules for which code is available</h1>
 <li><a href="tigramite/causal_effects.html">tigramite.causal_effects</a></li>
 <li><a href="tigramite/causal_mediation.html">tigramite.causal_mediation</a></li>
 <li><a href="tigramite/data_processing.html">tigramite.data_processing</a></li>
+<li><a href="tigramite/graphs.html">tigramite.graphs</a></li>
 <li><a href="tigramite/independence_tests/cmiknn.html">tigramite.independence_tests.cmiknn</a></li>
 <li><a href="tigramite/independence_tests/cmisymb.html">tigramite.independence_tests.cmisymb</a></li>
 <li><a href="tigramite/independence_tests/gpdc.html">tigramite.independence_tests.gpdc</a></li>
+<li><a href="tigramite/independence_tests/gpdc_torch.html">tigramite.independence_tests.gpdc_torch</a></li>
 <li><a href="tigramite/independence_tests/gsquared.html">tigramite.independence_tests.gsquared</a></li>
 <li><a href="tigramite/independence_tests/independence_tests_base.html">tigramite.independence_tests.independence_tests_base</a></li>
 <li><a href="tigramite/independence_tests/oracle_conditional_independence.html">tigramite.independence_tests.oracle_conditional_independence</a></li>

diff --git a/docs/_build/_modules/tigramite/causal_effects.html b/docs/_build/_modules/tigramite/causal_effects.html
diff --git a/docs/_build/_modules/tigramite/graphs.html b/docs/_build/_modules/tigramite/graphs.html
diff --git a/docs/_build/_modules/tigramite/independence_tests/cmiknn.html b/docs/_build/_modules/tigramite/independence_tests/cmiknn.html
@@ -338,7 +338,7 @@ <h1>Source code for tigramite.independence_tests.cmiknn</h1><div class="highligh
                       <span class="bp">self</span><span class="o">.</span><span class="n">shuffle_neighbors</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">sig_samples</span><span class="p">))</span>
 
             <span class="c1"># Get nearest neighbors around each sample point in Z</span>
-            <span class="n">z_array</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">fastCopyAndTranspose</span><span class="p">(</span><span class="n">array</span><span class="p">[</span><span class="n">z_indices</span><span class="p">,</span> <span class="p">:])</span>
+            <span class="n">z_array</span> <span class="o">=</span> <span class="n">array</span><span class="p">[</span><span class="n">z_indices</span><span class="p">,</span> <span class="p">:]</span><span class="o">.</span><span class="n">T</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
             <span class="n">tree_xyz</span> <span class="o">=</span> <span class="n">spatial</span><span class="o">.</span><span class="n">cKDTree</span><span class="p">(</span><span class="n">z_array</span><span class="p">)</span>
             <span class="n">neighbors</span> <span class="o">=</span> <span class="n">tree_xyz</span><span class="o">.</span><span class="n">query</span><span class="p">(</span><span class="n">z_array</span><span class="p">,</span>
                                        <span class="n">k</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">shuffle_neighbors</span><span class="p">,</span>
@@ -461,7 +461,7 @@ <h1>Source code for tigramite.independence_tests.cmiknn</h1><div class="highligh
             <span class="n">dim_y</span> <span class="o">=</span> <span class="mi">0</span>
 
 
-        <span class="n">x_array</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">fastCopyAndTranspose</span><span class="p">(</span><span class="n">array</span><span class="p">[</span><span class="n">x_indices</span><span class="p">,</span> <span class="p">:])</span>
+        <span class="n">x_array</span> <span class="o">=</span> <span class="n">array</span><span class="p">[</span><span class="n">x_indices</span><span class="p">,</span> <span class="p">:]</span><span class="o">.</span><span class="n">T</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
         <span class="n">tree_xyz</span> <span class="o">=</span> <span class="n">spatial</span><span class="o">.</span><span class="n">cKDTree</span><span class="p">(</span><span class="n">x_array</span><span class="p">)</span>
         <span class="n">epsarray</span> <span class="o">=</span> <span class="n">tree_xyz</span><span class="o">.</span><span class="n">query</span><span class="p">(</span><span class="n">x_array</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="p">[</span><span class="n">knn_here</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span> <span class="n">p</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">inf</span><span class="p">,</span>
                                   <span class="n">eps</span><span class="o">=</span><span class="mf">0.</span><span class="p">,</span> <span class="n">workers</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">workers</span><span class="p">)[</span><span class="mi">0</span><span class="p">][:,</span> <span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span>

diff --git a/docs/_build/_modules/tigramite/independence_tests/gpdc.html b/docs/_build/_modules/tigramite/independence_tests/gpdc.html
@@ -255,7 +255,7 @@ <h1>Source code for tigramite.independence_tests.gpdc</h1><div class="highlight"
             <span class="c1">#                      &quot;possibly constant array!&quot;)</span>
 
         <span class="n">target_series</span> <span class="o">=</span> <span class="n">array</span><span class="p">[</span><span class="n">target_var</span><span class="p">,</span> <span class="p">:]</span>
-        <span class="n">z</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">fastCopyAndTranspose</span><span class="p">(</span><span class="n">array</span><span class="p">[</span><span class="mi">2</span><span class="p">:])</span>
+        <span class="n">z</span> <span class="o">=</span> <span class="n">array</span><span class="p">[</span><span class="mi">2</span><span class="p">:]</span><span class="o">.</span><span class="n">T</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
         <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">ndim</span><span class="p">(</span><span class="n">z</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
             <span class="n">z</span> <span class="o">=</span> <span class="n">z</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>