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Developer #331

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Jun 27, 2023
Merged

Developer #331

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4a4bd1b
re-wrote pcmciplus in more modular form
jakobrunge Jun 22, 2023
3f187d1
re-wrote pcmciplus in more modular form
jakobrunge Jun 23, 2023
c52f584
re-wrote pcmciplus in more modular form
jakobrunge Jun 23, 2023
bce2352
made significance=fixed_thres more coherent, now assumes pc_alpha / a…
jakobrunge Jun 27, 2023
690f9de
revised docs
jakobrunge Jun 27, 2023
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2 changes: 2 additions & 0 deletions README.md
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Expand Up @@ -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
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12 changes: 12 additions & 0 deletions docs/Pipfile
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@@ -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"
313 changes: 313 additions & 0 deletions docs/Pipfile.lock
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2 changes: 1 addition & 1 deletion docs/_build/.buildinfo
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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: 921d6c7e445f291d7dc8f19863452108
config: 76a64b56702803c95ff1395bf9f343be
tags: 645f666f9bcd5a90fca523b33c5a78b7
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20 changes: 11 additions & 9 deletions docs/_build/_modules/abc.html
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Expand Up @@ -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" />

Expand Down Expand Up @@ -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>
Expand All @@ -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>
Expand Down Expand Up @@ -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>

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8 changes: 5 additions & 3 deletions docs/_build/_modules/index.html
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Expand Up @@ -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" />

Expand Down Expand Up @@ -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>

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