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Rebuild docs with new BoolODE documentation #35

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601 changes: 0 additions & 601 deletions Beeline.html
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450 changes: 450 additions & 0 deletions BoolODE-intro.html
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60 changes: 46 additions & 14 deletions _modules/BLEval.html
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<ul>
<li class="toctree-l1"><a class="reference internal" href="../BEELINE.html">BEELINE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../BoolODE.html">BoolODE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../BoolODE-intro.html">BoolODE</a></li>
</ul>


Expand Down Expand Up @@ -179,11 +179,12 @@ <h1>Source code for BLEval</h1><div class="highlight"><pre>
<span class="c1"># local imports</span>
<span class="kn">from</span> <span class="nn">BLEval.parseTime</span> <span class="k">import</span> <span class="n">getTime</span>
<span class="kn">from</span> <span class="nn">BLEval.computeDGAUC</span> <span class="k">import</span> <span class="n">PRROC</span>
<span class="kn">from</span> <span class="nn">BLEval.computeBorda</span> <span class="k">import</span> <span class="n">Borda</span>
<span class="kn">from</span> <span class="nn">BLEval.computeJaccard</span> <span class="k">import</span> <span class="n">Jaccard</span>
<span class="kn">from</span> <span class="nn">BLEval.computeSpearman</span> <span class="k">import</span> <span class="n">Spearman</span>
<span class="kn">from</span> <span class="nn">BLEval.computeNetMotifs</span> <span class="k">import</span> <span class="n">Motifs</span>
<span class="kn">from</span> <span class="nn">BLEval.computeEarlyPrec</span> <span class="k">import</span> <span class="n">EarlyPrec</span>
<span class="c1">#from BLEval.computePathStats import pathAnalysis</span>
<span class="kn">from</span> <span class="nn">BLEval.computePathStats</span> <span class="k">import</span> <span class="n">pathAnalysis</span>
<span class="kn">from</span> <span class="nn">BLEval.computeSignedEPrec</span> <span class="k">import</span> <span class="n">signedEPrec</span>


Expand Down Expand Up @@ -372,17 +373,17 @@ <h1>Source code for BLEval</h1><div class="highlight"><pre>
<span class="k">return</span> <span class="n">FBL</span><span class="p">,</span> <span class="n">FFL</span><span class="p">,</span> <span class="n">MI</span></div>


<span class="c1"># def computePaths(self):</span>
<span class="c1"># &#39;&#39;&#39;</span>
<span class="c1"># For each algorithm-dataset combination, this function computes path lengths</span>
<span class="c1"># through TP edges and FP edges, returns statistics on path lengths.</span>

<span class="c1"># :returns:</span>
<span class="c1"># - pathStats: A dataframe path lengths in predicted network</span>
<span class="c1"># &#39;&#39;&#39;</span>
<span class="c1"># for dataset in tqdm(self.input_settings.datasets, </span>
<span class="c1"># total = len(self.input_settings.datasets), unit = &quot; Datasets&quot;):</span>
<span class="c1"># pathAnalysis(dataset, self.input_settings)</span>
<div class="viewcode-block" id="BLEval.computePaths"><a class="viewcode-back" href="../BLEval.html#BLEval.BLEval.computePaths">[docs]</a> <span class="k">def</span> <span class="nf">computePaths</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">&#39;&#39;&#39;</span>
<span class="sd"> For each algorithm-dataset combination, this function computes path lengths</span>
<span class="sd"> through TP edges and FP edges, returns statistics on path lengths.</span>

<span class="sd"> :returns:</span>
<span class="sd"> - pathStats: A dataframe path lengths in predicted network</span>
<span class="sd"> &#39;&#39;&#39;</span>
<span class="k">for</span> <span class="n">dataset</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input_settings</span><span class="o">.</span><span class="n">datasets</span><span class="p">,</span>
<span class="n">total</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input_settings</span><span class="o">.</span><span class="n">datasets</span><span class="p">),</span> <span class="n">unit</span> <span class="o">=</span> <span class="s2">&quot; Datasets&quot;</span><span class="p">):</span>
<span class="n">pathAnalysis</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">input_settings</span><span class="p">)</span></div>


<div class="viewcode-block" id="BLEval.computeEarlyPrec"><a class="viewcode-back" href="../BLEval.html#BLEval.BLEval.computeEarlyPrec">[docs]</a> <span class="k">def</span> <span class="nf">computeEarlyPrec</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
Expand Down Expand Up @@ -428,8 +429,39 @@ <h1>Source code for BLEval</h1><div class="highlight"><pre>
<span class="n">sEPrecDF</span> <span class="o">=</span> <span class="n">signedEPrec</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">algo</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">sEPRDict</span><span class="p">[</span><span class="s1">&#39;EPrec Activation&#39;</span><span class="p">][</span><span class="n">algo</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">sEPrecDF</span><span class="p">[</span><span class="s1">&#39;+&#39;</span><span class="p">]</span>
<span class="n">sEPRDict</span><span class="p">[</span><span class="s1">&#39;EPrec Inhibition&#39;</span><span class="p">][</span><span class="n">algo</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">sEPrecDF</span><span class="p">[</span><span class="s1">&#39;-&#39;</span><span class="p">]</span>
<span class="k">return</span><span class="p">(</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">sEPRDict</span><span class="p">[</span><span class="s1">&#39;EPrec Activation&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">T</span><span class="p">,</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">sEPRDict</span><span class="p">[</span><span class="s1">&#39;EPrec Inhibition&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">T</span><span class="p">)</span></div></div>
<span class="k">return</span><span class="p">(</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">sEPRDict</span><span class="p">[</span><span class="s1">&#39;EPrec Activation&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">T</span><span class="p">,</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">sEPRDict</span><span class="p">[</span><span class="s1">&#39;EPrec Inhibition&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">T</span><span class="p">)</span></div>

<div class="viewcode-block" id="BLEval.computeBorda"><a class="viewcode-back" href="../BLEval.html#BLEval.BLEval.computeBorda">[docs]</a> <span class="k">def</span> <span class="nf">computeBorda</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">selectedAlgorithms</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">aggregationMethod</span><span class="o">=</span><span class="s2">&quot;average&quot;</span><span class="p">):</span>

<span class="sd">&#39;&#39;&#39;</span>
<span class="sd"> Computes edge ranked list using the Borda method for each dataset.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> selectedAlgorithms: [str]</span>
<span class="sd"> List of algorithm names used to run borda method on selected</span>
<span class="sd"> algorithms. If nothing is provided, the function runs borda on</span>
<span class="sd"> all available algorithms.</span>
<span class="sd"> aggregationMethod: str</span>
<span class="sd"> Method used to aggregate rank in borda method. Available options are</span>
<span class="sd"> {‘average’, ‘min’, ‘max’, ‘first’}, default ‘average’</span>
<span class="sd"> :returns:</span>
<span class="sd"> None</span>
<span class="sd"> &#39;&#39;&#39;</span>
<span class="n">feasibleAlgorithmOptions</span> <span class="o">=</span> <span class="p">[</span><span class="n">algorithmName</span> <span class="k">for</span> <span class="n">algorithmName</span><span class="p">,</span> <span class="n">_</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">input_settings</span><span class="o">.</span><span class="n">algorithms</span><span class="p">]</span>
<span class="n">feasibleaggregationMethodOptions</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;average&#39;</span><span class="p">,</span> <span class="s1">&#39;min&#39;</span><span class="p">,</span> <span class="s1">&#39;max&#39;</span><span class="p">,</span> <span class="s1">&#39;first&#39;</span><span class="p">]</span>

<span class="n">selectedAlgorithms</span> <span class="o">=</span> <span class="n">feasibleAlgorithmOptions</span> <span class="k">if</span> <span class="n">selectedAlgorithms</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">selectedAlgorithms</span>

<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">selectedAlgorithms</span><span class="p">:</span>
<span class="k">if</span> <span class="n">a</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">feasibleAlgorithmOptions</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">ERROR: No data available on algorithm </span><span class="si">%s</span><span class="s2">. Please choose an algorithm from the following options: </span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">feasibleAlgorithmOptions</span><span class="p">))</span>
<span class="k">return</span>

<span class="k">if</span> <span class="n">aggregationMethod</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">feasibleaggregationMethodOptions</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">ERROR: Please choose an aggregation method algorithm from following options: &quot;</span> <span class="o">%</span> <span class="n">feasibleaggregationMethodOptions</span><span class="p">)</span>
<span class="k">return</span>

<span class="n">Borda</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">selectedAlgorithms</span><span class="p">,</span> <span class="n">aggregationMethod</span><span class="p">)</span></div></div>

<div class="viewcode-block" id="ConfigParser"><a class="viewcode-back" href="../BLEval.html#BLEval.ConfigParser">[docs]</a><span class="k">class</span> <span class="nc">ConfigParser</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">&#39;&#39;&#39;</span>
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<ul>
<li class="toctree-l1"><a class="reference internal" href="../../BEELINE.html">BEELINE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../BoolODE.html">BoolODE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../BoolODE-intro.html">BoolODE</a></li>
</ul>


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<ul>
<li class="toctree-l1"><a class="reference internal" href="../../BEELINE.html">BEELINE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../BoolODE.html">BoolODE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../BoolODE-intro.html">BoolODE</a></li>
</ul>


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<ul>
<li class="toctree-l1"><a class="reference internal" href="../../BEELINE.html">BEELINE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../BoolODE.html">BoolODE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../BoolODE-intro.html">BoolODE</a></li>
</ul>


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<ul>
<li class="toctree-l1"><a class="reference internal" href="../../BEELINE.html">BEELINE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../BoolODE.html">BoolODE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../BoolODE-intro.html">BoolODE</a></li>
</ul>


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<ul>
<li class="toctree-l1"><a class="reference internal" href="../../BEELINE.html">BEELINE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../BoolODE.html">BoolODE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../BoolODE-intro.html">BoolODE</a></li>
</ul>


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<ul>
<li class="toctree-l1"><a class="reference internal" href="../../BEELINE.html">BEELINE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../BoolODE.html">BoolODE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../BoolODE-intro.html">BoolODE</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../BoolODE.html">BoolODE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../BoolODE-intro.html">BoolODE</a></li>
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