update images with the new plots

erdogant · Oct 1, 2024 · 3fe7292 · 3fe7292
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diff --git a/docs/figs/Chow1.png b/docs/figs/Chow1.png
diff --git a/docs/figs/Chow2.png b/docs/figs/Chow2.png
diff --git a/docs/figs/Hillclimbsearch1.png b/docs/figs/Hillclimbsearch1.png
diff --git a/docs/figs/Hillclimbsearch1_graphviz.png b/docs/figs/Hillclimbsearch1_graphviz.png
diff --git a/docs/figs/Hillclimbsearch2.png b/docs/figs/Hillclimbsearch2.png
diff --git a/docs/figs/Hillclimbsearch3.png b/docs/figs/Hillclimbsearch3.png
diff --git a/docs/figs/asia_graphviz.png b/docs/figs/asia_graphviz.png
diff --git a/docs/figs/asia_networkx.png b/docs/figs/asia_networkx.png
diff --git a/docs/figs/const0.png b/docs/figs/const0.png
diff --git a/docs/figs/const1.png b/docs/figs/const1.png
diff --git a/docs/figs/const2.png b/docs/figs/const2.png
diff --git a/docs/figs/edge_properties_1.png b/docs/figs/edge_properties_1.png
diff --git a/docs/figs/exhaustivesearch_example.png b/docs/figs/exhaustivesearch_example.png
diff --git a/docs/figs/fig2a_asia_groundtruth.png b/docs/figs/fig2a_asia_groundtruth.png
diff --git a/docs/figs/fig2b_asia_structurelearning.png b/docs/figs/fig2b_asia_structurelearning.png
diff --git a/docs/figs/fig2c_asia_comparion.png b/docs/figs/fig2c_asia_comparion.png
diff --git a/docs/figs/node_properties_1.png b/docs/figs/node_properties_1.png
diff --git a/docs/figs/tan0.png b/docs/figs/tan0.png
diff --git a/docs/figs/tan1.png b/docs/figs/tan1.png
diff --git a/docs/figs/tan2.png b/docs/figs/tan2.png
diff --git a/docs/figs/tan3.png b/docs/figs/tan3.png
diff --git a/docs/pages/doctrees/Continuous Data.doctree b/docs/pages/doctrees/Continuous Data.doctree
diff --git a/docs/pages/doctrees/Parameter learning.doctree b/docs/pages/doctrees/Parameter learning.doctree
diff --git a/docs/pages/doctrees/Plot.doctree b/docs/pages/doctrees/Plot.doctree
diff --git a/docs/pages/doctrees/Structure learning.doctree b/docs/pages/doctrees/Structure learning.doctree
diff --git a/docs/pages/doctrees/environment.pickle b/docs/pages/doctrees/environment.pickle
diff --git a/docs/pages/html/Continuous Data.html b/docs/pages/html/Continuous Data.html
@@ -117,7 +117,8 @@
 <p class="caption" role="heading"><span class="caption-text">Plot</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html">Interactive plot</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot">Static plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-networkx">Static plot (networkx)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-graphviz">Static plot (graphviz)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#comparison-of-two-networks">Comparison of two networks</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#node-properties">Node properties</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#edge-properties">Edge properties</a></li>
@@ -190,9 +191,9 @@
 
   <section id="working-with-continous-data">
 <h1>Working with Continous data<a class="headerlink" href="#working-with-continous-data" title="Link to this heading"></a></h1>
-<p>Learning Bayesian Networks from continuous data is an challanging task.
-There are different manner on how to work with continuous or hybrid datasets. Each manner has their own advantages and disadvantages.
-In <code class="docutils literal notranslate"><span class="pre">bnlearn</span></code> there are two automated approaches.</p>
+<p>Learning Bayesian Networks from continuous data is a challanging task.
+There are different manner on how to work with continuous and/or hybrid datasets. Each manner has their own advantages and disadvantages.</p>
+<p>In <code class="docutils literal notranslate"><span class="pre">bnlearn</span></code> the following options are available to work with continuous datasets:</p>
 <ul class="simple">
 <li><ol class="arabic simple">
 <li><p>Discretize continuous datasets manually using domain knowledge.</p></li>
@@ -499,16 +500,6 @@ <h2>LiNGAM Example<a class="headerlink" href="#lingam-example" title="Link to th
 <li><p>step 4: [x1] and [x4] are created by multiplication with values of [x0] and thus making it depended of [x0]</p></li>
 </ul>
 </div></blockquote>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span>       <span class="n">x3</span>
-      <span class="o">/</span>  \
-    <span class="mi">6</span>      <span class="mi">3</span>
-    <span class="o">/</span>       \
-  <span class="n">x2</span>         <span class="n">x0</span>
-  <span class="o">/</span> \      <span class="o">/</span>  <span class="o">|</span>  \
-<span class="o">-</span><span class="mi">1</span>   <span class="mi">2</span>    <span class="mi">8</span>   <span class="mi">3</span>    <span class="mi">4</span>
-<span class="n">x4</span>   <span class="n">etc</span>           <span class="n">x5</span>
-</pre></div>
-</div>
 <table class="docutils align-center">
 <tbody>
 <tr class="row-odd"><td><p><img alt="fig8a" src="_images/fig_lingam_example_input.png" /></p></td>
@@ -542,7 +533,7 @@ <h2>LiNGAM Example<a class="headerlink" href="#lingam-example" title="Link to th
 <span class="n">dot</span>
 </pre></div>
 </div>
-<p>To run Structure learning, we now can use the direct-lingam method for fitting.</p>
+<p>Structure learning can be applied with the direct-lingam method for fitting.</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">model</span> <span class="o">=</span> <span class="n">bn</span><span class="o">.</span><span class="n">structure_learning</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">methodtype</span><span class="o">=</span><span class="s1">&#39;direct-lingam&#39;</span><span class="p">)</span>
 
 <span class="c1"># When we no look at the output, we can see that the dependency values are very well recovered for the various variables.</span>
@@ -583,7 +574,7 @@ <h2>LiNGAM Example<a class="headerlink" href="#lingam-example" title="Link to th
 </tr>
 </tbody>
 </table>
-<p>This exmaple nicely demonstrates that we can capture the dependencies with the causal factors acurately.</p>
+<p>This example nicely demonstrates that we can capture the dependencies with the causal factors acurately.</p>
 </section>
 <section id="direct-lingam-method">
 <h2>Direct-LiNGAM method<a class="headerlink" href="#direct-lingam-method" title="Link to this heading"></a></h2>

diff --git a/docs/pages/html/Create DAG.html b/docs/pages/html/Create DAG.html
@@ -103,7 +103,8 @@
 <p class="caption" role="heading"><span class="caption-text">Plot</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html">Interactive plot</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot">Static plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-networkx">Static plot (networkx)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-graphviz">Static plot (graphviz)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#comparison-of-two-networks">Comparison of two networks</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#node-properties">Node properties</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#edge-properties">Edge properties</a></li>

diff --git a/docs/pages/html/Documentation.html b/docs/pages/html/Documentation.html
@@ -102,7 +102,8 @@
 <p class="caption" role="heading"><span class="caption-text">Plot</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html">Interactive plot</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot">Static plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-networkx">Static plot (networkx)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-graphviz">Static plot (graphviz)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#comparison-of-two-networks">Comparison of two networks</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#node-properties">Node properties</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#edge-properties">Edge properties</a></li>

diff --git a/docs/pages/html/Example Datasets.html b/docs/pages/html/Example Datasets.html
@@ -103,7 +103,8 @@
 <p class="caption" role="heading"><span class="caption-text">Plot</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html">Interactive plot</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot">Static plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-networkx">Static plot (networkx)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-graphviz">Static plot (graphviz)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#comparison-of-two-networks">Comparison of two networks</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#node-properties">Node properties</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#edge-properties">Edge properties</a></li>

diff --git a/docs/pages/html/Examples.html b/docs/pages/html/Examples.html
@@ -103,7 +103,8 @@
 <p class="caption" role="heading"><span class="caption-text">Plot</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html">Interactive plot</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot">Static plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-networkx">Static plot (networkx)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-graphviz">Static plot (graphviz)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#comparison-of-two-networks">Comparison of two networks</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#node-properties">Node properties</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#edge-properties">Edge properties</a></li>

diff --git a/docs/pages/html/Inference.html b/docs/pages/html/Inference.html
@@ -108,7 +108,8 @@
 <p class="caption" role="heading"><span class="caption-text">Plot</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html">Interactive plot</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot">Static plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-networkx">Static plot (networkx)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-graphviz">Static plot (graphviz)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#comparison-of-two-networks">Comparison of two networks</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#node-properties">Node properties</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#edge-properties">Edge properties</a></li>

diff --git a/docs/pages/html/Installation.html b/docs/pages/html/Installation.html
@@ -103,7 +103,8 @@
 <p class="caption" role="heading"><span class="caption-text">Plot</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html">Interactive plot</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot">Static plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-networkx">Static plot (networkx)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-graphviz">Static plot (graphviz)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#comparison-of-two-networks">Comparison of two networks</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#node-properties">Node properties</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#edge-properties">Edge properties</a></li>

diff --git a/docs/pages/html/Introduction.html b/docs/pages/html/Introduction.html
@@ -110,7 +110,8 @@
 <p class="caption" role="heading"><span class="caption-text">Plot</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html">Interactive plot</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot">Static plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-networkx">Static plot (networkx)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-graphviz">Static plot (graphviz)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#comparison-of-two-networks">Comparison of two networks</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#node-properties">Node properties</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#edge-properties">Edge properties</a></li>

diff --git a/docs/pages/html/Licence.html b/docs/pages/html/Licence.html
@@ -101,7 +101,8 @@
 <p class="caption" role="heading"><span class="caption-text">Plot</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html">Interactive plot</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot">Static plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-networkx">Static plot (networkx)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-graphviz">Static plot (graphviz)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#comparison-of-two-networks">Comparison of two networks</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#node-properties">Node properties</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#edge-properties">Edge properties</a></li>

diff --git a/docs/pages/html/Parameter learning.html b/docs/pages/html/Parameter learning.html
@@ -107,7 +107,8 @@
 <p class="caption" role="heading"><span class="caption-text">Plot</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html">Interactive plot</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot">Static plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-networkx">Static plot (networkx)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Plot.html#static-plot-graphviz">Static plot (graphviz)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#comparison-of-two-networks">Comparison of two networks</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#node-properties">Node properties</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Plot.html#edge-properties">Edge properties</a></li>
@@ -318,7 +319,7 @@ <h2>Example (1)<a class="headerlink" href="#example-1" title="Link to this headi
 <figure class="align-default" id="id1">
 <span id="fig-pl"></span><img alt="_images/fig_sprinkler_sl.png" src="_images/fig_sprinkler_sl.png" />
 <figcaption>
-<p><span class="caption-text">DAG of the prinkler data set.</span><a class="headerlink" href="#id1" title="Link to this image"></a></p>
+<p><span class="caption-text">DAG of the Sprinkler data set.</span><a class="headerlink" href="#id1" title="Link to this image"></a></p>
 </figcaption>
 </figure>
 <p>Suppose we observed <strong>N</strong> “cloudy” occurences among a total of “all clouds”, so we might guess that about “50%” of “cloudy” are “sprinkler” or so.