deploy: c35aced

ucl-cssb · Jul 5, 2024 · cc37e0e · cc37e0e
commit cc37e0e
Show file tree

Hide file tree

Showing 213 changed files with 42,415 additions and 0 deletions.
diff --git a/.buildinfo b/.buildinfo
@@ -0,0 +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: fa07b3c96b1e829a03f30001fa844c65
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.nojekyll b/.nojekyll
diff --git a/_images/notebooks_GP_examples-impute-GP_5_1.png b/_images/notebooks_GP_examples-impute-GP_5_1.png
diff --git a/_images/notebooks_GP_examples-impute-GP_7_1.png b/_images/notebooks_GP_examples-impute-GP_7_1.png
diff --git a/_images/notebooks_GP_examples-impute-GP_8_1.png b/_images/notebooks_GP_examples-impute-GP_8_1.png
diff --git a/_images/notebooks_GP_examples-impute-GP_Stein_10_1.png b/_images/notebooks_GP_examples-impute-GP_Stein_10_1.png
diff --git a/_images/notebooks_GP_examples-impute-GP_Stein_12_1.png b/_images/notebooks_GP_examples-impute-GP_Stein_12_1.png
diff --git a/_images/notebooks_GP_examples-impute-GP_Stein_7_1.png b/_images/notebooks_GP_examples-impute-GP_Stein_7_1.png
diff --git a/_images/notebooks_GP_examples-impute-GP_Stein_8_1.png b/_images/notebooks_GP_examples-impute-GP_Stein_8_1.png
diff --git a/_images/notebooks_GP_examples-impute-GP_Stein_9_1.png b/_images/notebooks_GP_examples-impute-GP_Stein_9_1.png
diff --git a/_images/notebooks_MVAR_examples-infer-MVAR_13_1.png b/_images/notebooks_MVAR_examples-infer-MVAR_13_1.png
diff --git a/_images/notebooks_MVAR_examples-infer-MVAR_13_2.png b/_images/notebooks_MVAR_examples-infer-MVAR_13_2.png
diff --git a/_images/notebooks_MVAR_examples-infer-MVAR_15_1.png b/_images/notebooks_MVAR_examples-infer-MVAR_15_1.png
diff --git a/_images/notebooks_MVAR_examples-infer-MVAR_15_2.png b/_images/notebooks_MVAR_examples-infer-MVAR_15_2.png
diff --git a/_images/notebooks_MVAR_examples-infer-MVAR_18_1.png b/_images/notebooks_MVAR_examples-infer-MVAR_18_1.png
diff --git a/_images/notebooks_MVAR_examples-infer-MVAR_18_2.png b/_images/notebooks_MVAR_examples-infer-MVAR_18_2.png
diff --git a/_images/notebooks_MVAR_examples-infer-MVAR_8_1.png b/_images/notebooks_MVAR_examples-infer-MVAR_8_1.png
diff --git a/_images/notebooks_MVAR_examples-sim-MVAR_10_0.png b/_images/notebooks_MVAR_examples-sim-MVAR_10_0.png
diff --git a/_images/notebooks_MVAR_examples-sim-MVAR_8_1.png b/_images/notebooks_MVAR_examples-sim-MVAR_8_1.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_10_0.png b/_images/notebooks_MultiModel_Herold_examples-Herold_10_0.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_16_1.png b/_images/notebooks_MultiModel_Herold_examples-Herold_16_1.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_20_1.png b/_images/notebooks_MultiModel_Herold_examples-Herold_20_1.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_22_1.png b/_images/notebooks_MultiModel_Herold_examples-Herold_22_1.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_25_1.png b/_images/notebooks_MultiModel_Herold_examples-Herold_25_1.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_25_11.png b/_images/notebooks_MultiModel_Herold_examples-Herold_25_11.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_25_13.png b/_images/notebooks_MultiModel_Herold_examples-Herold_25_13.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_25_15.png b/_images/notebooks_MultiModel_Herold_examples-Herold_25_15.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_25_17.png b/_images/notebooks_MultiModel_Herold_examples-Herold_25_17.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_25_19.png b/_images/notebooks_MultiModel_Herold_examples-Herold_25_19.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_25_21.png b/_images/notebooks_MultiModel_Herold_examples-Herold_25_21.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_25_23.png b/_images/notebooks_MultiModel_Herold_examples-Herold_25_23.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_25_3.png b/_images/notebooks_MultiModel_Herold_examples-Herold_25_3.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_25_5.png b/_images/notebooks_MultiModel_Herold_examples-Herold_25_5.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_25_7.png b/_images/notebooks_MultiModel_Herold_examples-Herold_25_7.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_25_9.png b/_images/notebooks_MultiModel_Herold_examples-Herold_25_9.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_28_6.png b/_images/notebooks_MultiModel_Herold_examples-Herold_28_6.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_30_5.png b/_images/notebooks_MultiModel_Herold_examples-Herold_30_5.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_33_5.png b/_images/notebooks_MultiModel_Herold_examples-Herold_33_5.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_36_4.png b/_images/notebooks_MultiModel_Herold_examples-Herold_36_4.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_38_4.png b/_images/notebooks_MultiModel_Herold_examples-Herold_38_4.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_40_4.png b/_images/notebooks_MultiModel_Herold_examples-Herold_40_4.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_41_5.png b/_images/notebooks_MultiModel_Herold_examples-Herold_41_5.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_48_5.png b/_images/notebooks_MultiModel_Herold_examples-Herold_48_5.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_54_6.png b/_images/notebooks_MultiModel_Herold_examples-Herold_54_6.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_57_5.png b/_images/notebooks_MultiModel_Herold_examples-Herold_57_5.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_58_0.png b/_images/notebooks_MultiModel_Herold_examples-Herold_58_0.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_60_2.png b/_images/notebooks_MultiModel_Herold_examples-Herold_60_2.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_65_5.png b/_images/notebooks_MultiModel_Herold_examples-Herold_65_5.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_66_1.png b/_images/notebooks_MultiModel_Herold_examples-Herold_66_1.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_66_2.png b/_images/notebooks_MultiModel_Herold_examples-Herold_66_2.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_68_5.png b/_images/notebooks_MultiModel_Herold_examples-Herold_68_5.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_69_1.png b/_images/notebooks_MultiModel_Herold_examples-Herold_69_1.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_69_2.png b/_images/notebooks_MultiModel_Herold_examples-Herold_69_2.png
diff --git a/_images/notebooks_MultiModel_Herold_examples-Herold_9_1.png b/_images/notebooks_MultiModel_Herold_examples-Herold_9_1.png
diff --git a/_images/notebooks_VAR_examples-bayes-VAR_3_1.png b/_images/notebooks_VAR_examples-bayes-VAR_3_1.png
diff --git a/_images/notebooks_VAR_examples-bayes-VAR_4_5.png b/_images/notebooks_VAR_examples-bayes-VAR_4_5.png
diff --git a/_images/notebooks_VAR_examples-bayes-VAR_7_5.png b/_images/notebooks_VAR_examples-bayes-VAR_7_5.png
diff --git a/_images/notebooks_VAR_examples-bayes-VAR_8_0.png b/_images/notebooks_VAR_examples-bayes-VAR_8_0.png
diff --git a/_images/notebooks_VAR_examples-sim-VAR_10_1.png b/_images/notebooks_VAR_examples-sim-VAR_10_1.png
diff --git a/_images/notebooks_VAR_examples-sim-VAR_15_1.png b/_images/notebooks_VAR_examples-sim-VAR_15_1.png
diff --git a/_images/notebooks_VAR_examples-sim-VAR_17_1.png b/_images/notebooks_VAR_examples-sim-VAR_17_1.png
diff --git a/_images/notebooks_VAR_examples-sim-VAR_19_0.png b/_images/notebooks_VAR_examples-sim-VAR_19_0.png
diff --git a/_images/notebooks_VAR_examples-sim-VAR_20_0.png b/_images/notebooks_VAR_examples-sim-VAR_20_0.png
diff --git a/_images/notebooks_gLV_examples-Stein_3_2.png b/_images/notebooks_gLV_examples-Stein_3_2.png
diff --git a/_images/notebooks_gLV_examples-Stein_3_3.png b/_images/notebooks_gLV_examples-Stein_3_3.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_10_0.png b/_images/notebooks_gLV_examples-bayes-gLV_10_0.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_13_6.png b/_images/notebooks_gLV_examples-bayes-gLV_13_6.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_13_7.png b/_images/notebooks_gLV_examples-bayes-gLV_13_7.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_13_8.png b/_images/notebooks_gLV_examples-bayes-gLV_13_8.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_15_1.png b/_images/notebooks_gLV_examples-bayes-gLV_15_1.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_15_2.png b/_images/notebooks_gLV_examples-bayes-gLV_15_2.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_15_3.png b/_images/notebooks_gLV_examples-bayes-gLV_15_3.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_15_4.png b/_images/notebooks_gLV_examples-bayes-gLV_15_4.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_17_1.png b/_images/notebooks_gLV_examples-bayes-gLV_17_1.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_19_5.png b/_images/notebooks_gLV_examples-bayes-gLV_19_5.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_19_6.png b/_images/notebooks_gLV_examples-bayes-gLV_19_6.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_19_7.png b/_images/notebooks_gLV_examples-bayes-gLV_19_7.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_19_8.png b/_images/notebooks_gLV_examples-bayes-gLV_19_8.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_21_1.png b/_images/notebooks_gLV_examples-bayes-gLV_21_1.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_21_2.png b/_images/notebooks_gLV_examples-bayes-gLV_21_2.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_21_3.png b/_images/notebooks_gLV_examples-bayes-gLV_21_3.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_21_4.png b/_images/notebooks_gLV_examples-bayes-gLV_21_4.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_21_5.png b/_images/notebooks_gLV_examples-bayes-gLV_21_5.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_3_1.png b/_images/notebooks_gLV_examples-bayes-gLV_3_1.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_7_5.png b/_images/notebooks_gLV_examples-bayes-gLV_7_5.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_7_6.png b/_images/notebooks_gLV_examples-bayes-gLV_7_6.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_7_7.png b/_images/notebooks_gLV_examples-bayes-gLV_7_7.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_9_1.png b/_images/notebooks_gLV_examples-bayes-gLV_9_1.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_9_2.png b/_images/notebooks_gLV_examples-bayes-gLV_9_2.png
diff --git a/_images/notebooks_gLV_examples-bayes-gLV_9_3.png b/_images/notebooks_gLV_examples-bayes-gLV_9_3.png
diff --git a/_images/notebooks_gLV_examples-lasso-gLV_3_1.png b/_images/notebooks_gLV_examples-lasso-gLV_3_1.png
diff --git a/_images/notebooks_gLV_examples-lasso-gLV_5_1.png b/_images/notebooks_gLV_examples-lasso-gLV_5_1.png
diff --git a/_images/notebooks_gLV_examples-lasso-gLV_5_2.png b/_images/notebooks_gLV_examples-lasso-gLV_5_2.png
diff --git a/_images/notebooks_gLV_examples-lasso-gLV_5_3.png b/_images/notebooks_gLV_examples-lasso-gLV_5_3.png
diff --git a/_images/notebooks_gLV_examples-lasso-gLV_7_1.png b/_images/notebooks_gLV_examples-lasso-gLV_7_1.png
diff --git a/_images/notebooks_gLV_examples-lasso-gLV_7_2.png b/_images/notebooks_gLV_examples-lasso-gLV_7_2.png
diff --git a/_images/notebooks_gLV_examples-lasso-gLV_7_3.png b/_images/notebooks_gLV_examples-lasso-gLV_7_3.png
diff --git a/_images/notebooks_gLV_examples-lasso-gLV_7_4.png b/_images/notebooks_gLV_examples-lasso-gLV_7_4.png
diff --git a/_images/notebooks_gLV_examples-ridge-gLV_3_1.png b/_images/notebooks_gLV_examples-ridge-gLV_3_1.png
diff --git a/_images/notebooks_gLV_examples-ridge-gLV_3_2.png b/_images/notebooks_gLV_examples-ridge-gLV_3_2.png
diff --git a/_images/notebooks_gLV_examples-ridge-gLV_3_3.png b/_images/notebooks_gLV_examples-ridge-gLV_3_3.png
diff --git a/_images/notebooks_gLV_examples-ridge-gLV_5_1.png b/_images/notebooks_gLV_examples-ridge-gLV_5_1.png
diff --git a/_images/notebooks_gLV_examples-ridge-gLV_5_2.png b/_images/notebooks_gLV_examples-ridge-gLV_5_2.png
diff --git a/_images/notebooks_gLV_examples-ridge-gLV_5_3.png b/_images/notebooks_gLV_examples-ridge-gLV_5_3.png
diff --git a/_images/notebooks_gLV_examples-ridge-gLV_5_4.png b/_images/notebooks_gLV_examples-ridge-gLV_5_4.png
diff --git a/_images/notebooks_gLV_examples-ridge-gLV_5_5.png b/_images/notebooks_gLV_examples-ridge-gLV_5_5.png
diff --git a/_images/notebooks_gLV_examples-ridge-gLV_7_1.png b/_images/notebooks_gLV_examples-ridge-gLV_7_1.png
diff --git a/_images/notebooks_gLV_examples-ridge-gLV_8_1.png b/_images/notebooks_gLV_examples-ridge-gLV_8_1.png
diff --git a/_images/notebooks_gLV_examples-ridge-gLV_8_2.png b/_images/notebooks_gLV_examples-ridge-gLV_8_2.png
diff --git a/_images/notebooks_gLV_examples-ridge-gLV_8_3.png b/_images/notebooks_gLV_examples-ridge-gLV_8_3.png
diff --git a/_images/notebooks_gLV_examples-ridge-gLV_8_4.png b/_images/notebooks_gLV_examples-ridge-gLV_8_4.png
diff --git a/_images/notebooks_gLV_examples-sim-gLV_3_1.png b/_images/notebooks_gLV_examples-sim-gLV_3_1.png
diff --git a/_images/notebooks_gLV_examples-sim-gLV_5_1.png b/_images/notebooks_gLV_examples-sim-gLV_5_1.png
diff --git a/_images/notebooks_gMLV_examples-ridge-lasso-gMLV_2_1.png b/_images/notebooks_gMLV_examples-ridge-lasso-gMLV_2_1.png
diff --git a/_images/notebooks_gMLV_examples-ridge-lasso-gMLV_6_1.png b/_images/notebooks_gMLV_examples-ridge-lasso-gMLV_6_1.png
diff --git a/_images/notebooks_gMLV_examples-ridge-lasso-gMLV_6_3.png b/_images/notebooks_gMLV_examples-ridge-lasso-gMLV_6_3.png
diff --git a/_images/notebooks_gMLV_examples-ridge-lasso-gMLV_6_4.png b/_images/notebooks_gMLV_examples-ridge-lasso-gMLV_6_4.png
diff --git a/_images/notebooks_gMLV_examples-ridge-lasso-gMLV_6_5.png b/_images/notebooks_gMLV_examples-ridge-lasso-gMLV_6_5.png
diff --git a/_images/notebooks_gMLV_examples-ridge-lasso-gMLV_6_6.png b/_images/notebooks_gMLV_examples-ridge-lasso-gMLV_6_6.png
diff --git a/_images/notebooks_gMLV_examples-sim-gMLV_3_1.png b/_images/notebooks_gMLV_examples-sim-gMLV_3_1.png
diff --git a/_images/notebooks_gMLV_examples-sim-gMLV_7_1.png b/_images/notebooks_gMLV_examples-sim-gMLV_7_1.png
diff --git a/_modules/index.html b/_modules/index.html
@@ -0,0 +1,108 @@
+<!DOCTYPE html>
+
+<html lang="en" data-content_root="../">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Overview: module code &#8212; MIMIC 0.1.0 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="../_static/alabaster.css?v=12dfc556" />
+    <script src="../_static/documentation_options.js?v=01f34227"></script>
+    <script src="../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
+
+  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+
+
+
+
+
+  </head><body>
+
+
+    <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="mimic/model_simulate/sim_gMLV.html">mimic.model_simulate.sim_gMLV</a></li>
+<li><a href="mimic/utilities/utilities.html">mimic.utilities.utilities</a></li>
+</ul>
+
+          </div>
+
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">MIMIC</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../readme.html">Modelling and Inference of MICrobiomes Project (MIMIC)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../usage.html">Usage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">mimic</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../authors.html">Credits</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../contributing.html">Contributing to MIMIC</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../history.html">History</a></li>
+</ul>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="../index.html">Documentation overview</a><ul>
+  </ul></li>
+</ul>
+</div>
+<search 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" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</search>
+<script>document.getElementById('searchbox').style.display = "block"</script>
+
+
+
+
+
+
+
+
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &#169;2024, Pedro Fontanarrosa.
+
+      |
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.3.7</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
+
+    </div>
+
+
+
+
+  </body>
+</html>
diff --git a/_modules/mimic/model_simulate/sim_gMLV.html b/_modules/mimic/model_simulate/sim_gMLV.html
diff --git a/_modules/mimic/utilities/utilities.html b/_modules/mimic/utilities/utilities.html
diff --git a/_sources/authors.rst.txt b/_sources/authors.rst.txt
@@ -0,0 +1 @@
+.. include:: ../../AUTHORS.rst
diff --git a/_sources/contributing.rst.txt b/_sources/contributing.rst.txt
@@ -0,0 +1 @@
+.. include:: ../../CONTRIBUTING.rst
diff --git a/_sources/examples.rst.txt b/_sources/examples.rst.txt
@@ -0,0 +1,20 @@
+Examples
+========
+
+.. toctree::
+   :maxdepth: 2
+
+   notebooks/MultiModel/Herold/examples-Herold
+   notebooks/gMLV/examples-sim-gMLV
+   notebooks/gMLV/examples-ridge-lasso-gMLV
+   notebooks/MVAR/examples-infer-MVAR
+   notebooks/MVAR/examples-sim-MVAR
+   notebooks/VAR/examples-sim-VAR
+   notebooks/VAR/examples-bayes-VAR
+   notebooks/gLV/examples-Stein
+   notebooks/gLV/examples-bayes-gLV
+   notebooks/gLV/examples-lasso-gLV
+   notebooks/gLV/examples-sim-gLV
+   notebooks/gLV/examples-ridge-gLV
+   notebooks/GP/examples-impute-GP_Stein
+   notebooks/GP/examples-impute-GP
diff --git a/_sources/history.rst.txt b/_sources/history.rst.txt
@@ -0,0 +1 @@
+.. include:: ../../HISTORY.rst
diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
@@ -0,0 +1,27 @@
+.. MIMIC documentation master file, created by
+   sphinx-quickstart on Thu Feb  8 15:13:02 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Modelling and Inference of MICrobiomes Project (MIMIC)
+======================================================
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Contents:
+
+   readme
+   installation
+   usage
+   modules
+   examples
+   authors
+   contributing
+   history
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/_sources/installation.rst.txt b/_sources/installation.rst.txt
@@ -0,0 +1,51 @@
+.. highlight:: shell
+
+============
+Installation
+============
+
+
+Stable release
+--------------
+
+To install MIMIC, run this command in your terminal:
+
+.. code-block:: console
+
+    $ pip install mimic
+
+This is the preferred method to install MIMIC, as it will always install the most recent stable release.
+
+If you don't have `pip`_ installed, this `Python installation guide`_ can guide
+you through the process.
+
+.. _pip: https://pip.pypa.io
+.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
+
+
+From sources
+------------
+
+The sources for MIMIC can be downloaded from the `Github repo`_.
+
+You can either clone the public repository:
+
+.. code-block:: console
+
+    $ git clone git://github.com/Fontanapink/mimic
+
+Or download the `tarball`_:
+
+.. code-block:: console
+
+    $ curl -OJL https://github.com/Fontanapink/mimic/tarball/master
+
+Once you have a copy of the source, you can install it with:
+
+.. code-block:: console
+
+    $ python setup.py install
+
+
+.. _Github repo: https://github.com/Fontanapink/mimic
+.. _tarball: https://github.com/Fontanapink/mimic/tarball/master
diff --git a/_sources/mimic.model_infer.rst.txt b/_sources/mimic.model_infer.rst.txt
@@ -0,0 +1,45 @@
+mimic.model\_infer package
+==========================
+
+Submodules
+----------
+
+mimic.model\_infer.cLV module
+-----------------------------
+
+.. automodule:: mimic.model_infer.cLV
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mimic.model\_infer.infer\_VAR\_bayes module
+-------------------------------------------
+
+.. automodule:: mimic.model_infer.infer_VAR_bayes
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mimic.model\_infer.infer\_gMLV\_lm module
+-----------------------------------------
+
+.. automodule:: mimic.model_infer.infer_gMLV_lm
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mimic.model\_infer.multi\_penalty\_lasso module
+-----------------------------------------------
+
+.. automodule:: mimic.model_infer.multi_penalty_lasso
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mimic.model_infer
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/_sources/mimic.model_simulate.rst.txt b/_sources/mimic.model_simulate.rst.txt
@@ -0,0 +1,37 @@
+mimic.model\_simulate package
+=============================
+
+Submodules
+----------
+
+mimic.model\_simulate.base\_model module
+----------------------------------------
+
+.. automodule:: mimic.model_simulate.base_model
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mimic.model\_simulate.sim\_VAR module
+-------------------------------------
+
+.. automodule:: mimic.model_simulate.sim_VAR
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mimic.model\_simulate.sim\_gMLV module
+--------------------------------------
+
+.. automodule:: mimic.model_simulate.sim_gMLV
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mimic.model_simulate
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/_sources/mimic.rst.txt b/_sources/mimic.rst.txt
@@ -0,0 +1,20 @@
+mimic package
+=============
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   mimic.model_infer
+   mimic.model_simulate
+   mimic.utilities
+
+Module contents
+---------------
+
+.. automodule:: mimic
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/_sources/mimic.utilities.rst.txt b/_sources/mimic.utilities.rst.txt
@@ -0,0 +1,21 @@
+mimic.utilities package
+=======================
+
+Submodules
+----------
+
+mimic.utilities.utilities module
+--------------------------------
+
+.. automodule:: mimic.utilities.utilities
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mimic.utilities
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/_sources/modules.rst.txt b/_sources/modules.rst.txt
@@ -0,0 +1,7 @@
+mimic
+=====
+
+.. toctree::
+   :maxdepth: 4
+
+   mimic