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3 changes: 1 addition & 2 deletions docs/html/_modules/idtxl/active_information_storage.html
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<script type="text/javascript" src="../../_static/jquery.js"></script>
<script type="text/javascript" src="../../_static/underscore.js"></script>
<script type="text/javascript" src="../../_static/doctools.js"></script>
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Expand Down Expand Up @@ -679,7 +678,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2018, Patricia Wollstadt, Joseph T. Lizier, Raul Vicente, Conor Finn, Mario Martinez-Zarzuela, Pedro Mediano, Leonardo Novelli, Michael Wibral.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.1.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.2.
</div>
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5 changes: 2 additions & 3 deletions docs/html/_modules/idtxl/bivariate_mi.html
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<script type="text/javascript" src="../../_static/jquery.js"></script>
<script type="text/javascript" src="../../_static/underscore.js"></script>
<script type="text/javascript" src="../../_static/doctools.js"></script>
<script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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Expand Down Expand Up @@ -316,7 +315,7 @@ <h1>Source code for idtxl.bivariate_mi</h1><div class="highlight"><pre>
<span class="c1"># Main algorithm.</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">---------------------------- (1) include source candidates&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_include_source_candidates</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">---------------------------- (2) prune cadidates&#39;</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">---------------------------- (2) prune candidates&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_prune_candidates</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">---------------------------- (3) final statistics&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_test_final_conditional</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
Expand Down Expand Up @@ -389,7 +388,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2018, Patricia Wollstadt, Joseph T. Lizier, Raul Vicente, Conor Finn, Mario Martinez-Zarzuela, Pedro Mediano, Leonardo Novelli, Michael Wibral.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.1.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.2.
</div>
</body>
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5 changes: 2 additions & 3 deletions docs/html/_modules/idtxl/bivariate_te.html
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<script type="text/javascript" src="../../_static/jquery.js"></script>
<script type="text/javascript" src="../../_static/underscore.js"></script>
<script type="text/javascript" src="../../_static/doctools.js"></script>
<script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
Expand Down Expand Up @@ -321,7 +320,7 @@ <h1>Source code for idtxl.bivariate_te</h1><div class="highlight"><pre>
<span class="bp">self</span><span class="o">.</span><span class="n">_include_target_candidates</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">---------------------------- (2) include source candidates&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_include_source_candidates</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">---------------------------- (3) prune cadidates&#39;</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">---------------------------- (3) prune candidates&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_prune_candidates</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">---------------------------- (4) final statistics&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_test_final_conditional</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
Expand Down Expand Up @@ -393,7 +392,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2018, Patricia Wollstadt, Joseph T. Lizier, Raul Vicente, Conor Finn, Mario Martinez-Zarzuela, Pedro Mediano, Leonardo Novelli, Michael Wibral.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.1.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.2.
</div>
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21 changes: 15 additions & 6 deletions docs/html/_modules/idtxl/data.html
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<script type="text/javascript" src="../../_static/jquery.js"></script>
<script type="text/javascript" src="../../_static/underscore.js"></script>
<script type="text/javascript" src="../../_static/doctools.js"></script>
<script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
Expand Down Expand Up @@ -80,7 +79,7 @@ <h1>Source code for idtxl.data</h1><div class="highlight"><pre>
<span class="sd"> &gt;&gt;&gt; data_2.set_data(data_new, &#39;s&#39;)</span>

<span class="sd"> Note:</span>
<span class="sd"> Realisations are stored as attribute &#39;data&#39;. This can only be set via </span>
<span class="sd"> Realisations are stored as attribute &#39;data&#39;. This can only be set via</span>
<span class="sd"> the &#39;set_data()&#39; method.</span>

<span class="sd"> Args:</span>
Expand Down Expand Up @@ -874,16 +873,26 @@ <h1>Source code for idtxl.data</h1><div class="highlight"><pre>

<span class="sd"> Generate example data and overwrite the instance&#39;s current data. The</span>
<span class="sd"> network is used as an example the paper on the MuTE toolbox (Montalto,</span>
<span class="sd"> PLOS ONE, 2014, eq. 14). The network consists of five autoregressive</span>
<span class="sd"> (AR) processes with model orders 2 and the following (non-linear)</span>
<span class="sd"> couplings:</span>
<span class="sd"> PLOS ONE, 2014, eq. 14) and was orginially proposed by Baccala &amp;</span>
<span class="sd"> Sameshima (2001). The network consists of five autoregressive (AR)</span>
<span class="sd"> processes with model orders 2 and the following (non-linear) couplings:</span>

<span class="sd"> 0 -&gt; 1, u = 2 (non-linear)</span>
<span class="sd"> 0 -&gt; 2, u = 3</span>
<span class="sd"> 0 -&gt; 3, u = 2 (non-linear)</span>
<span class="sd"> 3 -&gt; 4, u = 1</span>
<span class="sd"> 4 -&gt; 3, u = 1</span>

<span class="sd"> References:</span>

<span class="sd"> - Montalto, A., Faes, L., &amp; Marinazzo, D. (2014) MuTE: A MATLAB toolbox</span>
<span class="sd"> to compare established and novel estimators of the multivariate</span>
<span class="sd"> transfer entropy. PLoS ONE 9(10): e109462.</span>
<span class="sd"> https://doi.org/10.1371/journal.pone.0109462</span>
<span class="sd"> - Baccala, L.A. &amp; Sameshima, K. (2001). Partial directed coherence: a</span>
<span class="sd"> new concept in neural structure determination. Biol Cybern 84:</span>
<span class="sd"> 463–474. https://doi.org/10.1007/PL00007990</span>

<span class="sd"> Args:</span>
<span class="sd"> n_samples : int</span>
<span class="sd"> number of samples simulated for each process and replication</span>
Expand Down Expand Up @@ -1115,7 +1124,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2018, Patricia Wollstadt, Joseph T. Lizier, Raul Vicente, Conor Finn, Mario Martinez-Zarzuela, Pedro Mediano, Leonardo Novelli, Michael Wibral.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.1.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.2.
</div>
</body>
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3 changes: 1 addition & 2 deletions docs/html/_modules/idtxl/estimator.html
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<script type="text/javascript" src="../../_static/jquery.js"></script>
<script type="text/javascript" src="../../_static/underscore.js"></script>
<script type="text/javascript" src="../../_static/doctools.js"></script>
<script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<link rel="index" title="Index" href="../../genindex.html" />
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<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
Expand Down Expand Up @@ -416,7 +415,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2018, Patricia Wollstadt, Joseph T. Lizier, Raul Vicente, Conor Finn, Mario Martinez-Zarzuela, Pedro Mediano, Leonardo Novelli, Michael Wibral.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.1.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.2.
</div>
</body>
</html>
3 changes: 1 addition & 2 deletions docs/html/_modules/idtxl/estimators_jidt.html
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<script type="text/javascript" src="../../_static/jquery.js"></script>
<script type="text/javascript" src="../../_static/underscore.js"></script>
<script type="text/javascript" src="../../_static/doctools.js"></script>
<script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<link rel="index" title="Index" href="../../genindex.html" />
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<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
Expand Down Expand Up @@ -1851,7 +1850,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2018, Patricia Wollstadt, Joseph T. Lizier, Raul Vicente, Conor Finn, Mario Martinez-Zarzuela, Pedro Mediano, Leonardo Novelli, Michael Wibral.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.1.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.2.
</div>
</body>
</html>
7 changes: 5 additions & 2 deletions docs/html/_modules/idtxl/estimators_opencl.html
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<script type="text/javascript" src="../../_static/jquery.js"></script>
<script type="text/javascript" src="../../_static/underscore.js"></script>
<script type="text/javascript" src="../../_static/doctools.js"></script>
<script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
Expand Down Expand Up @@ -149,6 +148,10 @@ <h1>Source code for idtxl.estimators_opencl</h1><div class="highlight"><pre>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s1">&#39;No OpenCL GPU device found.&#39;</span><span class="p">)</span>
<span class="n">my_gpu_devices</span> <span class="o">=</span> <span class="n">platform</span><span class="o">.</span><span class="n">get_devices</span><span class="p">(</span><span class="n">device_type</span><span class="o">=</span><span class="n">cl</span><span class="o">.</span><span class="n">device_type</span><span class="o">.</span><span class="n">GPU</span><span class="p">)</span>
<span class="n">context</span> <span class="o">=</span> <span class="n">cl</span><span class="o">.</span><span class="n">Context</span><span class="p">(</span><span class="n">devices</span><span class="o">=</span><span class="n">my_gpu_devices</span><span class="p">)</span>
<span class="k">if</span> <span class="n">gpuid</span> <span class="o">&gt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">my_gpu_devices</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span>
<span class="s1">&#39;No device with gpuid </span><span class="si">{0}</span><span class="s1"> (available device IDs: </span><span class="si">{1}</span><span class="s1">).&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">gpuid</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">my_gpu_devices</span><span class="p">))))</span>
<span class="n">queue</span> <span class="o">=</span> <span class="n">cl</span><span class="o">.</span><span class="n">CommandQueue</span><span class="p">(</span><span class="n">context</span><span class="p">,</span> <span class="n">my_gpu_devices</span><span class="p">[</span><span class="n">gpuid</span><span class="p">])</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;debug&#39;</span><span class="p">]:</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Selected Device: &quot;</span><span class="p">,</span> <span class="n">my_gpu_devices</span><span class="p">[</span><span class="n">gpuid</span><span class="p">]</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
Expand Down Expand Up @@ -814,7 +817,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2018, Patricia Wollstadt, Joseph T. Lizier, Raul Vicente, Conor Finn, Mario Martinez-Zarzuela, Pedro Mediano, Leonardo Novelli, Michael Wibral.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.1.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.2.
</div>
</body>
</html>
16 changes: 10 additions & 6 deletions docs/html/_modules/idtxl/estimators_pid.html
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<script type="text/javascript" src="../../_static/jquery.js"></script>
<script type="text/javascript" src="../../_static/underscore.js"></script>
<script type="text/javascript" src="../../_static/doctools.js"></script>
<script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<link rel="index" title="Index" href="../../genindex.html" />
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Expand Down Expand Up @@ -51,7 +50,6 @@ <h1>Source code for idtxl.estimators_pid</h1><div class="highlight"><pre>

<span class="sd">Bertschinger, N., Rauh, J., Olbrich, E., Jost, J., &amp; Ay, N. (2014). Quantifying</span>
<span class="sd">Unique Information. Entropy, 16(4), 2161–2183. http://doi.org/10.3390/e16042161</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">.</span> <span class="k">import</span> <span class="n">synergy_tartu</span>
Expand All @@ -63,9 +61,9 @@ <h1>Source code for idtxl.estimators_pid</h1><div class="highlight"><pre>
<div class="viewcode-block" id="SydneyPID"><a class="viewcode-back" href="../../idtxl_estimators.html#idtxl.estimators_pid.SydneyPID">[docs]</a><span class="k">class</span> <span class="nc">SydneyPID</span><span class="p">(</span><span class="n">Estimator</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Estimate partial information decomposition of discrete variables.</span>

<span class="sd"> Fast implementation of the partial information decomposition (PID)</span>
<span class="sd"> estimator for discrete data. The estimator does not require JAVA or GPU</span>
<span class="sd"> modules to run.</span>
<span class="sd"> Fast implementation of the BROJA partial information decomposition (PID)</span>
<span class="sd"> estimator for discrete data (Bertschinger, 2014). The estimator does not</span>
<span class="sd"> require JAVA or GPU modules to run.</span>

<span class="sd"> The estimator finds shared information, unique information and</span>
<span class="sd"> synergistic information between the two inputs s1 and s2 with respect to</span>
Expand All @@ -80,6 +78,12 @@ <h1>Source code for idtxl.estimators_pid</h1><div class="highlight"><pre>
<span class="sd"> CMI decreases; and an outer loop which decreases the size of the</span>
<span class="sd"> probability mass increment the virtualised swapping utilises.</span>

<span class="sd"> References</span>

<span class="sd"> - Bertschinger, N., Rauh, J., Olbrich, E., Jost, J., &amp; Ay, N. (2014).</span>
<span class="sd"> Quantifying unique information. Entropy, 16(4), 2161–2183.</span>
<span class="sd"> http://doi.org/10.3390/e16042161</span>

<span class="sd"> Args:</span>
<span class="sd"> settings : dict</span>
<span class="sd"> estimation parameters</span>
Expand Down Expand Up @@ -701,7 +705,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2018, Patricia Wollstadt, Joseph T. Lizier, Raul Vicente, Conor Finn, Mario Martinez-Zarzuela, Pedro Mediano, Leonardo Novelli, Michael Wibral.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.1.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.2.
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