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jakobrunge · Nov 28, 2019 · 19305e3 · 19305e3
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diff --git a/docs/Makefile b/docs/Makefile
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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = Tigramite
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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+# 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: 43e03fac560e16bfeebe8fc7915cb678
+tags: 645f666f9bcd5a90fca523b33c5a78b7
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diff --git a/docs/_build/html/_modules/abc.html b/docs/_build/html/_modules/abc.html
diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html
@@ -0,0 +1,81 @@
+
+<!DOCTYPE html>
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta charset="utf-8" />
+    <title>Overview: module code &#8212; Tigramite 4.0 documentation</title>
+    <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
+    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+    <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
+    <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 type="text/javascript" src="../_static/language_data.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" /> 
+  </head><body>
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../index.html">Tigramite 4.0 documentation</a> &#187;</li> 
+      </ul>
+    </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<div id="searchbox" style="display: none" role="search">
+  <h3 id="searchlabel">Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="../search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" />
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="abc.html">abc</a></li>
+<li><a href="tigramite/data_processing.html">tigramite.data_processing</a></li>
+<li><a href="tigramite/independence_tests.html">tigramite.independence_tests</a></li>
+<li><a href="tigramite/models.html">tigramite.models</a></li>
+<li><a href="tigramite/pcmci.html">tigramite.pcmci</a></li>
+<li><a href="tigramite/plotting.html">tigramite.plotting</a></li>
+</ul>
+
+          </div>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../index.html">Tigramite 4.0 documentation</a> &#187;</li> 
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+        &#169; Copyright 2018, Jakob Runge.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 2.1.2.
+    </div>
+  </body>
+</html>
diff --git a/docs/_build/html/_modules/tigramite/data_processing.html b/docs/_build/html/_modules/tigramite/data_processing.html
diff --git a/docs/_build/html/_modules/tigramite/independence_tests.html b/docs/_build/html/_modules/tigramite/independence_tests.html
diff --git a/docs/_build/html/_modules/tigramite/models.html b/docs/_build/html/_modules/tigramite/models.html
diff --git a/docs/_build/html/_modules/tigramite/pcmci.html b/docs/_build/html/_modules/tigramite/pcmci.html
diff --git a/docs/_build/html/_modules/tigramite/plotting.html b/docs/_build/html/_modules/tigramite/plotting.html
diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt
@@ -0,0 +1,123 @@
+.. Tigramite documentation master file, created by
+   sphinx-quickstart on Thu May 11 18:32:05 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+TIGRAMITE
+=========
+
+`Github repo <https://github.com/jakobrunge/tigramite/>`_
+
+Tigramite is a causal time series analysis python package. It allows to efficiently reconstruct causal graphs from high-dimensional time series datasets and model the obtained causal dependencies for causal mediation and prediction analyses. Causal discovery is based on linear as well as non-parametric conditional independence tests applicable to discrete or continuously-valued time series. Also includes functions for high-quality plots of the results. Please cite the following papers depending on which method you use:
+
+
+0. J. Runge et al. (2019): Inferring causation from time series in Earth system sciences.
+   Nature Communications, 10(1):2553.
+   https://www.nature.com/articles/s41467-019-10105-3
+
+1. J. Runge, P. Nowack, M. Kretschmer, S. Flaxman, D. Sejdinovic (2019): Detecting and quantifying causal associations in large nonlinear time series datasets.
+   Sci. Adv. 5, eaau4996.
+   https://advances.sciencemag.org/content/5/11/eaau4996
+
+2. J. Runge et al. (2015): Identifying causal gateways and mediators in complex spatio-temporal systems. 
+   Nature Communications, 6, 8502. 
+   http://doi.org/10.1038/ncomms9502
+
+3. J. Runge (2015): Quantifying information transfer and mediation along causal pathways in complex systems. 
+   Phys. Rev. E, 92(6), 62829. 
+   http://doi.org/10.1103/PhysRevE.92.062829
+
+4. J. Runge (2018): Conditional Independence Testing Based on a Nearest-Neighbor Estimator of Conditional Mutual Information.
+   In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics.
+   http://proceedings.mlr.press/v84/runge18a.html
+
+5. J. Runge (2018): Causal Network Reconstruction from Time Series: From Theoretical Assumptions to Practical Estimation.
+   Chaos: An Interdisciplinary Journal of Nonlinear Science 28 (7): 075310.   
+   https://aip.scitation.org/doi/10.1063/1.5025050
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+.. autosummary::
+
+   tigramite.pcmci.PCMCI
+   tigramite.independence_tests.CondIndTest
+   tigramite.independence_tests.ParCorr
+   tigramite.independence_tests.GPDC
+   tigramite.independence_tests.CMIknn
+   tigramite.independence_tests.CMIsymb  
+   tigramite.independence_tests.RCOT  
+   tigramite.data_processing
+   tigramite.models.Models
+   tigramite.models.LinearMediation
+   tigramite.models.Prediction
+   tigramite.plotting
+
+
+:mod:`tigramite.pcmci`: PCMCI
+===========================================
+
+.. autoclass:: tigramite.pcmci.PCMCI
+   :members:
+
+:mod:`tigramite.independence_tests`: Conditional independence tests
+=================================================================================
+
+Base class:
+
+.. autoclass:: tigramite.independence_tests.CondIndTest
+   :members:
+
+Test statistics:
+
+.. autoclass:: tigramite.independence_tests.ParCorr
+   :members:
+
+.. autoclass:: tigramite.independence_tests.GPDC
+   :members:
+
+.. autoclass:: tigramite.independence_tests.CMIknn
+   :members:
+
+.. autoclass:: tigramite.independence_tests.CMIsymb
+   :members:
+
+.. autoclass:: tigramite.independence_tests.RCOT
+   :members:
+
+:mod:`tigramite.data_processing`: Data processing functions
+===========================================================
+
+.. automodule:: tigramite.data_processing
+   :members:
+
+:mod:`tigramite.models`: Time series modeling, mediation, and prediction
+========================================================================
+
+Base class:
+
+.. autoclass:: tigramite.models.Models
+   :members:
+
+Derived classes:
+
+.. autoclass:: tigramite.models.LinearMediation
+   :members:
+
+.. autoclass:: tigramite.models.Prediction
+   :members:
+
+:mod:`tigramite.plotting`: Plotting functions
+=============================================
+
+.. automodule:: tigramite.plotting
+   :members:
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
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