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gagolews · Oct 29, 2023 · 4dbacfd · 4dbacfd
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diff --git a/.devel/sphinx/conf.py b/.devel/sphinx/conf.py
@@ -6,6 +6,9 @@
 
 import clustbench
 
+
+
+
 pkg_name = "clustbench"
 pkg_title = "Clustering Benchmarks"
 pkg_version = clustbench.__version__
@@ -36,6 +39,20 @@
 highlight_language = "python"
 html_last_updated_fmt = today_fmt
 
+plot_include_source = True
+plot_html_show_source_link = False
+plot_pre_code = """
+import numpy as np
+import clustbench
+import matplotlib.pyplot as plt
+np.random.seed(123)
+"""
+doctest_global_setup = plot_pre_code
+numpydoc_use_plots = True
+# https://www.sphinx-doc.org/en/master/usage/extensions/autosummary.html
+autosummary_imported_members = True
+autosummary_generate = True
+
 extensions = [
     'myst_parser',
     'sphinx.ext.mathjax',
@@ -80,24 +97,6 @@
 }
 numfig_secnum_depth = 0
 
-plot_include_source = True
-plot_html_show_source_link = False
-plot_pre_code = """
-import numpy as np
-import clustbench
-import matplotlib.pyplot as plt
-np.random.seed(123)
-"""
-
-doctest_global_setup = plot_pre_code
-
-numpydoc_use_plots = True
-
-# https://www.sphinx-doc.org/en/master/usage/extensions/autosummary.html
-autosummary_imported_members = True
-autosummary_generate = True
-
-
 html_theme = 'furo'
 
 html_show_sourcelink = True

diff --git a/.devel/sphinx/fix-code-blocks.sh b/.devel/sphinx/fix-code-blocks.sh
diff --git a/.devel/sphinx/fix-html.sh b/.devel/sphinx/fix-html.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com>
+# Copyright (C) 2020-2023, Marek Gagolewski <https://www.gagolewski.com/>
 
 set -e
 

diff --git a/.devel/sphinx/weave/external-validity-measures-figures/partition-similarity-example-4-1.pdf b/.devel/sphinx/weave/external-validity-measures-figures/partition-similarity-example-4-1.pdf
diff --git a/...x/weave/external-validity-measures-figures/partition-similarity-example-4-1.png b/...x/weave/external-validity-measures-figures/partition-similarity-example-4-1.png
diff --git a/.devel/sphinx/weave/external-validity-measures.md b/.devel/sphinx/weave/external-validity-measures.md
@@ -477,8 +477,3 @@ Unfortunately,
 particular values of the score are rather difficult to interpret.
 
 *Implementation: [`genieclust`](https://genieclust.gagolewski.com/)`.compare_partitions.normalized_mi_score`*.
-
-In {cite}`infmeasures`, also different adjusted versions of the above are
-considered. However, in {cite}`psi`, it is noted
-that, amongst others, $\mathrm{AMI}_\mathrm{sum}$ is strongly correlated with
-$\mathrm{NMI}_\mathrm{sum}$.
diff --git a/docs/_images/partition-similarity-example-4-1.png b/docs/_images/partition-similarity-example-4-1.png
diff --git a/docs/clustbench-documentation.html b/docs/clustbench-documentation.html
@@ -840,7 +840,7 @@ <h1>Documentation<a class="headerlink" href="#documentation" title="Link to this
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -395,7 +395,7 @@ <h2>T</h2>
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/index.html b/docs/index.html
@@ -457,7 +457,7 @@ <h1>A Framework for Benchmarking Clustering Algorithms<a class="headerlink" href
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/news.html b/docs/news.html
@@ -336,7 +336,7 @@ <h2>0.0.0 (2015-12-29)<a class="headerlink" href="#id5" title="Link to this head
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/py-modindex.html b/docs/py-modindex.html
@@ -277,7 +277,7 @@ <h1>Python Module Index</h1>
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/search.html b/docs/search.html
@@ -268,7 +268,7 @@
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/searchindex.js b/docs/searchindex.js
diff --git a/docs/weave/clustbench-usage.html b/docs/weave/clustbench-usage.html
@@ -480,7 +480,7 @@ <h2>Applying Clustering Methods Manually<a class="headerlink" href="#applying-cl
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/weave/colouriser.html b/docs/weave/colouriser.html
@@ -312,7 +312,7 @@
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/weave/contributing.html b/docs/weave/contributing.html
@@ -301,7 +301,7 @@
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/weave/data-v1.html b/docs/weave/data-v1.html
@@ -480,7 +480,7 @@
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/weave/external-validity-measures.html b/docs/weave/external-validity-measures.html
@@ -321,10 +321,10 @@ <h2>Illustration<a class="headerlink" href="#illustration" title="Link to this h
 <code class="docutils literal notranslate"><span class="pre">wut/x2</span></code> <a class="reference internal" href="suite-v1.html#sec-suite-v1"><span class="std std-ref">dataset</span></a>
 are displayed below. We also report the confusion matrices and the
 values of the validity measures discussed in the sequel.</p>
-<figure class="align-default" id="id20">
+<figure class="align-default" id="id18">
 <span id="fig-partition-similarity-example-4"></span><img alt="../_images/partition-similarity-example-4-1.png" src="../_images/partition-similarity-example-4-1.png" />
 <figcaption>
-<p><span class="caption-number">Figure 10:  </span><span class="caption-text">The reference (ground truth) partition and a few predicted clusterings that we relate to it (wut/x2 dataset). Confusion matrices and the values of a few external cluster validity measures are also reported.</span><a class="headerlink" href="#id20" title="Link to this image">#</a></p>
+<p><span class="caption-number">Figure 10:  </span><span class="caption-text">The reference (ground truth) partition and a few predicted clusterings that we relate to it (wut/x2 dataset). Confusion matrices and the values of a few external cluster validity measures are also reported.</span><a class="headerlink" href="#id18" title="Link to this image">#</a></p>
 </figcaption>
 </figure>
 <p>Actually, both Genie and the k-means method output some quite reasonable
@@ -647,10 +647,6 @@ <h2>Information-Theoretic Measures<a class="headerlink" href="#information-theor
 <p>Unfortunately,
 particular values of the score are rather difficult to interpret.</p>
 <p><em>Implementation: <a class="reference external" href="https://genieclust.gagolewski.com/"><code class="docutils literal notranslate"><span class="pre">genieclust</span></code></a><code class="docutils literal notranslate"><span class="pre">.compare_partitions.normalized_mi_score</span></code></em>.</p>
-<p>In <span id="id18">[<a class="reference internal" href="../z_bibliography.html#id20" title="Vinh, N.X., Epps, J., and Bailey, J. (2010).  Information theoretic measures for clusterings comparison: Variants, properties, normalization and correction for chance. Journal of Machine Learning Research, 11(95):2837–2854. URL: http://jmlr.org/papers/v11/vinh10a.html.">57</a>]</span>, also different adjusted versions of the above are
-considered. However, in <span id="id19">[<a class="reference internal" href="../z_bibliography.html#id18" title="Rezaei, M. and Fränti, P. (2016).  Set matching measures for external cluster validity. IEEE Transactions on Knowledge and Data Engineering, 28(8):2173–2186. DOI: 10.1109/TKDE.2016.2551240.">47</a>]</span>, it is noted
-that, amongst others, <span class="math notranslate nohighlight">\(\mathrm{AMI}_\mathrm{sum}\)</span> is strongly correlated with
-<span class="math notranslate nohighlight">\(\mathrm{NMI}_\mathrm{sum}\)</span>.</p>
 <hr class="footnotes docutils" />
 <aside class="footnote-list brackets">
 <aside class="footnote brackets" id="footnoise" role="doc-footnote">
@@ -698,7 +694,7 @@ <h2>Information-Theoretic Measures<a class="headerlink" href="#information-theor
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/weave/file-format.html b/docs/weave/file-format.html
@@ -369,7 +369,7 @@ <h2>Clustering Results<a class="headerlink" href="#clustering-results" title="Li
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/weave/how-to-access.html b/docs/weave/how-to-access.html
@@ -386,7 +386,7 @@ <h2>MATLAB<a class="headerlink" href="#matlab" title="Link to this heading">#</a
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/weave/internal-validity-measures.html b/docs/weave/internal-validity-measures.html
@@ -522,7 +522,7 @@ <h2>Generalised Dunn Indices<a class="headerlink" href="#generalised-dunn-indice
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/weave/many-partitions.html b/docs/weave/many-partitions.html
@@ -384,7 +384,7 @@ <h2>Predicted vs Best-Matching Reference Labelling<a class="headerlink" href="#p
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/weave/noise-points.html b/docs/weave/noise-points.html
@@ -421,7 +421,7 @@ <h2>Evaluating Similarity<a class="headerlink" href="#evaluating-similarity" tit
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/weave/results-v1.html b/docs/weave/results-v1.html
@@ -362,7 +362,7 @@ <h2>Feature Engineering<a class="headerlink" href="#feature-engineering" title="
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/weave/suite-v1.html b/docs/weave/suite-v1.html
@@ -4156,7 +4156,7 @@
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/weave/true-vs-predicted.html b/docs/weave/true-vs-predicted.html
@@ -531,7 +531,7 @@ <h2>External Cluster Validity Measures<a class="headerlink" href="#external-clus
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>

diff --git a/docs/z_bibliography.html b/docs/z_bibliography.html
@@ -558,7 +558,7 @@ <h2>Bibliography<a class="headerlink" href="#bibliography" title="Link to this h
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2023-10-26T14:38:08+1100.
+              Last updated on 2023-10-29T14:39:43+1100.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>