Merge pull request #331 from jakobrunge/developer

Developer
jakobrunge · Jun 27, 2023 · 5a87687 · 5a87687
2 parents 343ae39 + 690f9de
commit 5a87687
Show file tree

Hide file tree

Showing 258 changed files with 84,241 additions and 48,554 deletions.
diff --git a/README.md b/README.md
@@ -42,6 +42,8 @@ Further, Tigramite provides several causal discovery methods that can be used un
 
 Tigramite is a causal inference for time series python package. It allows to efficiently estimate causal graphs from high-dimensional time series datasets (causal discovery) and to use graphs for robust forecasting and the estimation and prediction of direct, total, and mediated effects. 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:
 
+- Overview: Runge, J., Gerhardus, A., Varando, G. et al. Causal inference for time series. Nat Rev Earth Environ (2023). https://doi.org/10.1038/s43017-023-00431-y
+
 - PCMCI: J. Runge, P. Nowack, M. Kretschmer, S. Flaxman, D. Sejdinovic, Detecting and quantifying causal associations in large nonlinear time series datasets. Sci. Adv. 5, eaau4996 (2019). https://advances.sciencemag.org/content/5/11/eaau4996
 - PCMCI+: J. Runge (2020): Discovering contemporaneous and lagged causal relations in autocorrelated nonlinear time series datasets. Proceedings of the 36th Conference on Uncertainty in Artificial Intelligence, UAI 2020,Toronto, Canada, 2019, AUAI Press, 2020. http://auai.org/uai2020/proceedings/579_main_paper.pdf
 - LPCMCI: Gerhardus, A. & Runge, J. High-recall causal discovery for autocorrelated time series with latent confounders Advances in Neural Information Processing Systems, 2020, 33. https://proceedings.neurips.cc/paper/2020/hash/94e70705efae423efda1088614128d0b-Abstract.html

diff --git a/docs/Pipfile b/docs/Pipfile
@@ -0,0 +1,12 @@
+[[source]]
+url = "https://pypi.python.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+sphinx = "*"
+
+[dev-packages]
+
+[requires]
+python_version = "3.8"
diff --git a/docs/Pipfile.lock b/docs/Pipfile.lock
diff --git a/docs/_build/.buildinfo b/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: 921d6c7e445f291d7dc8f19863452108
+config: 76a64b56702803c95ff1395bf9f343be
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/.doctrees/environment.pickle b/docs/_build/.doctrees/environment.pickle
diff --git a/docs/_build/.doctrees/index.doctree b/docs/_build/.doctrees/index.doctree
diff --git a/docs/_build/_images/math/0f43f6fc8c8fa5c1bcbe7ac1e6cb52ba65f14e0a.png b/docs/_build/_images/math/0f43f6fc8c8fa5c1bcbe7ac1e6cb52ba65f14e0a.png
diff --git a/docs/_build/_images/math/23021f5b161b8c919e79247f310dde9b4ed3bb31.png b/docs/_build/_images/math/23021f5b161b8c919e79247f310dde9b4ed3bb31.png
diff --git a/docs/_build/_images/math/3ebd02270eed8e22d1d33fcc8b606dfb6a2cf77b.png b/docs/_build/_images/math/3ebd02270eed8e22d1d33fcc8b606dfb6a2cf77b.png
diff --git a/docs/_build/_images/math/7f762ad4c19826633f4d45cf2474b09d3af721ad.png b/docs/_build/_images/math/7f762ad4c19826633f4d45cf2474b09d3af721ad.png
diff --git a/docs/_build/_images/math/bbfebfb6602ca200cd0a1683a6c69ec20fde14b9.png b/docs/_build/_images/math/bbfebfb6602ca200cd0a1683a6c69ec20fde14b9.png
diff --git a/docs/_build/_images/math/dbfee27df47b7ba9492d8ee1eb592578a399e6ee.png b/docs/_build/_images/math/dbfee27df47b7ba9492d8ee1eb592578a399e6ee.png
diff --git a/docs/_build/_images/math/eb82f9af24f0851d6d6c721d6fca48286566647e.png b/docs/_build/_images/math/eb82f9af24f0851d6d6c721d6fca48286566647e.png
diff --git a/docs/_build/_images/math/efd96ac57b370ce811ab9d31f0c7f2b1efa18711.png b/docs/_build/_images/math/efd96ac57b370ce811ab9d31f0c7f2b1efa18711.png
diff --git a/docs/_build/_modules/abc.html b/docs/_build/_modules/abc.html
@@ -9,8 +9,10 @@
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../_static/alabaster.css" />
     <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
+    <script src="../_static/jquery.js"></script>
+    <script src="../_static/underscore.js"></script>
+    <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
     <script src="../_static/doctools.js"></script>
-    <script src="../_static/sphinx_highlight.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
 
@@ -72,9 +74,9 @@ <h1>Source code for abc</h1><div class="highlight"><pre>
 
     <span class="n">__isabstractmethod__</span> <span class="o">=</span> <span class="kc">True</span>
 
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">callable</span><span class="p">):</span>
-        <span class="n">callable</span><span class="o">.</span><span class="n">__isabstractmethod__</span> <span class="o">=</span> <span class="kc">True</span>
-        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">callable</span><span class="p">)</span>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">callable</span><span class="p">):</span>
+        <span class="nb">callable</span><span class="o">.</span><span class="n">__isabstractmethod__</span> <span class="o">=</span> <span class="kc">True</span>
+        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="nb">callable</span><span class="p">)</span>
 
 
 <span class="k">class</span> <span class="nc">abstractstaticmethod</span><span class="p">(</span><span class="nb">staticmethod</span><span class="p">):</span>
@@ -92,9 +94,9 @@ <h1>Source code for abc</h1><div class="highlight"><pre>
 
     <span class="n">__isabstractmethod__</span> <span class="o">=</span> <span class="kc">True</span>
 
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">callable</span><span class="p">):</span>
-        <span class="n">callable</span><span class="o">.</span><span class="n">__isabstractmethod__</span> <span class="o">=</span> <span class="kc">True</span>
-        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">callable</span><span class="p">)</span>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">callable</span><span class="p">):</span>
+        <span class="nb">callable</span><span class="o">.</span><span class="n">__isabstractmethod__</span> <span class="o">=</span> <span class="kc">True</span>
+        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="nb">callable</span><span class="p">)</span>
 
 
 <span class="k">class</span> <span class="nc">abstractproperty</span><span class="p">(</span><span class="nb">property</span><span class="p">):</span>
@@ -234,8 +236,8 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2023, Jakob Runge.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 6.1.3</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 5.0.2</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
     </div>
 

diff --git a/docs/_build/_modules/index.html b/docs/_build/_modules/index.html
@@ -9,8 +9,10 @@
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../_static/alabaster.css" />
     <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
+    <script src="../_static/jquery.js"></script>
+    <script src="../_static/underscore.js"></script>
+    <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
     <script src="../_static/doctools.js"></script>
-    <script src="../_static/sphinx_highlight.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
 
@@ -103,8 +105,8 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2023, Jakob Runge.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 6.1.3</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 5.0.2</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
     </div>