Merge pull request #41 from pnnl/develop

Develop

README.md

@@ -33,23 +33,20 @@ Tutorials may be run in your browser using Google Colab
 <a href="https://colab.research.google.com/github/pnnl/HyperNetX/blob/master/tutorials/Tutorial%202%20-%20Visualization%20Methods.ipynb" target="_blank">
 
 
-
   <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
 	<span style={'margin-left':5px}>Tutorial 2 - Visualization Methods</span>
 </a>
 </br>
 <a href="https://colab.research.google.com/github/pnnl/HyperNetX/blob/master/tutorials/Tutorial%203%20-%20LesMis%20Case%20Study.ipynb" target="_blank">
 
 
-
   <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
 	<span style={'margin-left':5px}>Tutorial 3 - LesMis Case Study</span>
 </a>
 </br>
 <a href="https://colab.research.google.com/github/pnnl/HyperNetX/blob/master/tutorials/Tutorial%204%20-%20LesMis%20Visualizations-BookTour.ipynb" target="_blank">
 
 
-
   <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
 	<span style={'margin-left':5px}>Tutorial 4 - LesMis Visualizations-Book Tour</span>
 </a>

docs/build/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 100d5f0571659fa080bb0f6ef7eebc72
+config: 12513d66143dfa27e7a4e78bbb5b3696
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/_modules/algorithms/homology_mod2.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>algorithms.homology_mod2 &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>algorithms.homology_mod2 &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/_modules/algorithms/s_centrality_measures.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>algorithms.s_centrality_measures &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>algorithms.s_centrality_measures &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 
@@ -161,7 +161,22 @@
   <h1>Source code for algorithms.s_centrality_measures</h1><div class="highlight"><pre>
 <span></span><span class="c1"># Copyright © 2018 Battelle Memorial Institute</span>
 <span class="c1"># All rights reserved.</span>
-<span class="c1"># This module developed for PNNL&#39;s hyperbio LDRD project summer 2019</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="sd">S-Centrality Measures</span>
+<span class="sd">=====================</span>
+<span class="sd">We generalize graph metrics to s-metrics for a hypergraph by using its s-connected</span>
+<span class="sd">components. This is accomplished by computing the s edge-adjacency matrix and</span>
+<span class="sd">constructing the corresponding graph of the matrix. We then use existing graph metrics</span>
+<span class="sd">on this representation of the hypergraph. In essence we construct an *s*-line graph</span>
+<span class="sd">corresponding to the hypergraph on which to apply our methods.</span>
+
+<span class="sd">S-Metrics for hypergraphs are discussed in depth in:        </span>
+<span class="sd">*Aksoy, S.G., Joslyn, C., Ortiz Marrero, C. et al. Hypernetwork science via high-order hypergraph walks.</span>
+<span class="sd">EPJ Data Sci. 9, 16 (2020). https://doi.org/10.1140/epjds/s13688-020-00231-0*</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">from</span> <span class="nn">collections</span> <span class="k">import</span> <span class="n">defaultdict</span>
@@ -193,10 +208,12 @@ <h1>Source code for algorithms.s_centrality_measures</h1><div class="highlight">
 <span class="sd">        A dictionary of s-betweenness centrality value of the edges.</span>
 
 <span class="sd">    &#39;&#39;&#39;</span>
+
     <span class="c1"># Confirm there is at least 1 s edge for which we can compute the centrality</span>
     <span class="c1"># Find all s-edges</span>
     <span class="c1">#M,rdict,_ = H.incidence_matrix(index=True)</span>
     <span class="c1">#A = M.transpose().dot(M)</span>
+
     <span class="n">A</span><span class="p">,</span> <span class="n">coldict</span> <span class="o">=</span> <span class="n">H</span><span class="o">.</span><span class="n">edge_adjacency_matrix</span><span class="p">(</span><span class="n">s</span><span class="o">=</span><span class="n">s</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
     <span class="n">A</span><span class="o">.</span><span class="n">setdiag</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
     <span class="n">A</span> <span class="o">=</span> <span class="p">(</span><span class="n">A</span> <span class="o">&gt;=</span> <span class="n">s</span><span class="p">)</span> <span class="o">*</span> <span class="mi">1</span>
@@ -227,8 +244,10 @@ <h1>Source code for algorithms.s_centrality_measures</h1><div class="highlight">
 <span class="sd">        If edge then a single value is returned.</span>
 
 <span class="sd">    &#39;&#39;&#39;</span>
+
     <span class="c1"># Confirm there is at least 1 s edge for which we can compute the centrality</span>
     <span class="c1"># Find all s-edges</span>
+
     <span class="k">if</span> <span class="n">edge</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">H</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="n">edge</span><span class="p">])</span> <span class="o">&lt;</span> <span class="n">s</span><span class="p">:</span>
         <span class="k">return</span> <span class="mi">0</span>
 
@@ -250,6 +269,7 @@ <h1>Source code for algorithms.s_centrality_measures</h1><div class="highlight">
 
     <span class="c1"># confirm there are at least 2 s-edges</span>
     <span class="c1"># we follow the NX convention that the s-closeness centrality of a single edge Hypergraph is 0</span>
+
     <span class="n">output</span> <span class="o">=</span> <span class="p">{}</span>
     <span class="k">if</span> <span class="ow">not</span> <span class="nb">bool</span><span class="p">(</span><span class="n">Es</span><span class="p">)</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="n">Es</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
         <span class="n">output</span> <span class="o">=</span> <span class="p">{</span><span class="n">e</span><span class="p">:</span> <span class="mi">0</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">edges</span><span class="p">}</span>
@@ -280,7 +300,11 @@ <h1>Source code for algorithms.s_centrality_measures</h1><div class="highlight">
 <span class="sd">        eccentricity[f] : float</span>
 <span class="sd">    else:</span>
 <span class="sd">        eccentricity_dict : dict</span>
-<span class="sd">        </span>
+<span class="sd">     : dict or float</span>
+<span class="sd">        returns the s-eccentricity value of the edges, a floating point number</span>
+<span class="sd">        If edge=None a dictionary of values for each s-edge in H is returned.</span>
+<span class="sd">        If edge then a single value is returned.</span>
+
 <span class="sd">    &#39;&#39;&#39;</span>
     <span class="k">if</span> <span class="n">f</span><span class="p">:</span>
         <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">Entity</span><span class="p">):</span>

docs/build/_modules/classes/entity.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>classes.entity &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>classes.entity &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/_modules/classes/hypergraph.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>classes.hypergraph &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>classes.hypergraph &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/_modules/drawing/rubber_band.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>drawing.rubber_band &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>drawing.rubber_band &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/_modules/drawing/two_column.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>drawing.two_column &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>drawing.two_column &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/_modules/drawing/util.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>drawing.util &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>drawing.util &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/_modules/index.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Overview: module code &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>Overview: module code &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/_modules/reports/descriptive_stats.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>reports.descriptive_stats &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>reports.descriptive_stats &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.3.4',
+    VERSION: '0.3.5',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

docs/build/algorithms/algorithms.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>algorithms package &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>algorithms package &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 
@@ -101,7 +101,10 @@
 <li class="toctree-l4"><a class="reference internal" href="#homology-and-smith-normal-form">Homology and Smith Normal Form</a></li>
 </ul>
 </li>
-<li class="toctree-l3"><a class="reference internal" href="#module-algorithms.s_centrality_measures">algorithms.s_centrality_measures module</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#module-algorithms.s_centrality_measures">algorithms.s_centrality_measures module</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#s-centrality-measures">S-Centrality Measures</a></li>
+</ul>
+</li>
 <li class="toctree-l3"><a class="reference internal" href="#module-algorithms">Module contents</a></li>
 </ul>
 </li>
@@ -599,6 +602,16 @@ <h4>Homology Mod2<a class="headerlink" href="#homology-mod2" title="Permalink to
 </div>
 <div class="section" id="module-algorithms.s_centrality_measures">
 <span id="algorithms-s-centrality-measures-module"></span><h2>algorithms.s_centrality_measures module<a class="headerlink" href="#module-algorithms.s_centrality_measures" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="s-centrality-measures">
+<h3>S-Centrality Measures<a class="headerlink" href="#s-centrality-measures" title="Permalink to this headline">¶</a></h3>
+<p>We generalize graph metrics to s-metrics for a hypergraph by using its s-connected
+components. This is accomplished by computing the s edge-adjacency matrix and
+constructing the corresponding graph of the matrix. We then use existing graph metrics
+on this representation of the hypergraph. In essence we construct an <em>s</em>-line graph
+corresponding to the hypergraph on which to apply our methods.</p>
+<p>S-Metrics for hypergraphs are discussed in depth in:
+<em>Aksoy, S.G., Joslyn, C., Ortiz Marrero, C. et al. Hypernetwork science via high-order hypergraph walks.
+EPJ Data Sci. 9, 16 (2020). https://doi.org/10.1140/epjds/s13688-020-00231-0</em></p>
 <dl class="function">
 <dt id="algorithms.s_centrality_measures.s_betweenness_centrality">
 <code class="sig-prename descclassname">algorithms.s_centrality_measures.</code><code class="sig-name descname">s_betweenness_centrality</code><span class="sig-paren">(</span><em class="sig-param">H</em>, <em class="sig-param">s=1</em>, <em class="sig-param">normalized=True</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/algorithms/s_centrality_measures.html#s_betweenness_centrality"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#algorithms.s_centrality_measures.s_betweenness_centrality" title="Permalink to this definition">¶</a></dt>
@@ -630,10 +643,18 @@ <h4>Homology Mod2<a class="headerlink" href="#homology-mod2" title="Permalink to
 <p>H : Hypergraph
 f : Entity or str
 s : int</p>
-<dl class="simple">
+<dl>
 <dt>if f:</dt><dd><p>eccentricity[f] : float</p>
 </dd>
-<dt>else:</dt><dd><p>eccentricity_dict : dict</p>
+<dt>else:</dt><dd><blockquote>
+<div><p>eccentricity_dict : dict</p>
+</div></blockquote>
+<dl class="simple">
+<dt>: dict or float</dt><dd><p>returns the s-eccentricity value of the edges, a floating point number
+If edge=None a dictionary of values for each s-edge in H is returned.
+If edge then a single value is returned.</p>
+</dd>
+</dl>
 </dd>
 </dl>
 </dd></dl>
@@ -664,6 +685,7 @@ <h4>Homology Mod2<a class="headerlink" href="#homology-mod2" title="Permalink to
 </div></blockquote>
 </dd></dl>
 
+</div>
 </div>
 <div class="section" id="module-algorithms">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-algorithms" title="Permalink to this headline">¶</a></h2>

docs/build/algorithms/modules.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>algorithms &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>algorithms &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 
@@ -178,7 +178,10 @@ <h1>algorithms<a class="headerlink" href="#algorithms" title="Permalink to this
 </li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="algorithms.html#module-algorithms.s_centrality_measures">algorithms.s_centrality_measures module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="algorithms.html#module-algorithms.s_centrality_measures">algorithms.s_centrality_measures module</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="algorithms.html#s-centrality-measures">S-Centrality Measures</a></li>
+</ul>
+</li>
 <li class="toctree-l2"><a class="reference internal" href="algorithms.html#module-algorithms">Module contents</a></li>
 </ul>
 </li>

docs/build/classes/classes.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>classes package &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>classes package &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/classes/modules.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>classes &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>classes &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/drawing/drawing.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>drawing package &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>drawing package &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/drawing/modules.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>drawing &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>drawing &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/genindex.html

@@ -9,7 +9,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Index &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>Index &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/glossary.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Glossary of HNX terms &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>Glossary of HNX terms &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/index.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>HyperNetX (HNX) &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>HyperNetX (HNX) &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/install.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Installing HyperNetX &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>Installing HyperNetX &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/license.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>License &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>License &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/overview/index.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Overview &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>Overview &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/py-modindex.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Python Module Index &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>Python Module Index &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/reports/modules.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>reports &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>reports &mdash; HyperNetX 0.3.5 documentation</title>
 
 
 

docs/build/reports/reports.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>reports package &mdash; HyperNetX 0.3.4 documentation</title>
+  <title>reports package &mdash; HyperNetX 0.3.5 documentation</title>