updated doc to 0.1.1

KlugerLab · Aug 6, 2024 · 51251eb · 51251eb
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diff --git a/docs_html/.buildinfo b/docs_html/.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.
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+config: cb26a261997f9aa5cf562fac862fcf4b
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs_html/.doctrees/environment.pickle b/docs_html/.doctrees/environment.pickle
diff --git a/docs_html/.doctrees/index.doctree b/docs_html/.doctrees/index.doctree
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diff --git a/docs_html/.doctrees/reference/dyson_equalizer.examples.doctree b/docs_html/.doctrees/reference/dyson_equalizer.examples.doctree
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diff --git a/docs_html/.doctrees/reference/dyson_equalizer.validation.doctree b/docs_html/.doctrees/reference/dyson_equalizer.validation.doctree
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diff --git a/docs_html/_downloads/040d40c8f1a75c7ba616f303c6741e0d/dyson_equalizer-1.pdf b/docs_html/_downloads/040d40c8f1a75c7ba616f303c6741e0d/dyson_equalizer-1.pdf
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diff --git a/docs_html/_downloads/179faf11df58dc8dbf2a9aa00791e8c4/dyson_equalizer-plots-1.pdf b/docs_html/_downloads/179faf11df58dc8dbf2a9aa00791e8c4/dyson_equalizer-plots-1.pdf
diff --git a/docs_html/_downloads/1d1027295f67536b84f29d02893b6b52/dyson_equalizer-2.pdf b/docs_html/_downloads/1d1027295f67536b84f29d02893b6b52/dyson_equalizer-2.pdf
diff --git a/docs_html/_downloads/3f43ce4f187c080c6a43421015fe260c/dyson_equalizer-algorithm-1.pdf b/docs_html/_downloads/3f43ce4f187c080c6a43421015fe260c/dyson_equalizer-algorithm-1.pdf
diff --git a/docs_html/_downloads/5d36910c87e55f3fc827dd430d294b41/dyson_equalizer-2.py b/docs_html/_downloads/5d36910c87e55f3fc827dd430d294b41/dyson_equalizer-2.py
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diff --git a/docs_html/_downloads/a5c69e67e76ef2f144bc89a6dd7a27b9/dyson_equalizer-algorithm-1.py b/docs_html/_downloads/a5c69e67e76ef2f144bc89a6dd7a27b9/dyson_equalizer-algorithm-1.py
diff --git a/docs_html/_downloads/b0cb300918942c1c35d4a9bdb358a081/dyson_equalizer-3.pdf b/docs_html/_downloads/b0cb300918942c1c35d4a9bdb358a081/dyson_equalizer-3.pdf
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diff --git a/docs_html/_downloads/c3e42fed7c5fb3188b259cfa49cacb47/dyson_equalizer-3.py b/docs_html/_downloads/c3e42fed7c5fb3188b259cfa49cacb47/dyson_equalizer-3.py
diff --git a/...tml/_downloads/d0a95b0846a7db66bce8cb701c5004fc/dyson_equalizer-algorithm-1.png b/...tml/_downloads/d0a95b0846a7db66bce8cb701c5004fc/dyson_equalizer-algorithm-1.png
diff --git a/docs_html/_downloads/dc48c60a41224f72a0a8e45aacfa0d82/dyson_equalizer-plots-2.pdf b/docs_html/_downloads/dc48c60a41224f72a0a8e45aacfa0d82/dyson_equalizer-plots-2.pdf
diff --git a/docs_html/_images/dyson_equalizer-2.png b/docs_html/_images/dyson_equalizer-2.png
diff --git a/docs_html/_images/dyson_equalizer-3.png b/docs_html/_images/dyson_equalizer-3.png
diff --git a/docs_html/_images/dyson_equalizer-algorithm-1.png b/docs_html/_images/dyson_equalizer-algorithm-1.png
diff --git a/docs_html/_static/documentation_options.js b/docs_html/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.1.0',
+    VERSION: '0.1.1',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs_html/genindex.html b/docs_html/genindex.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index &#8212; Dyson Equalizer 0.1.0 documentation</title>
+    <title>Index &#8212; Dyson Equalizer 0.1.1 documentation</title>
 
 
 
@@ -35,7 +35,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=01f34227"></script>
+    <script src="_static/documentation_options.js?v=a58bc63e"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'genindex';</script>
@@ -116,7 +116,7 @@
 
 
 
-    <p class="title logo__title">Dyson Equalizer 0.1.0 documentation</p>
+    <p class="title logo__title">Dyson Equalizer 0.1.1 documentation</p>
 
 </a></div>
 

diff --git a/docs_html/index.html b/docs_html/index.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Dyson Equalizer &#8212; Dyson Equalizer 0.1.0 documentation</title>
+    <title>Dyson Equalizer &#8212; Dyson Equalizer 0.1.1 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=01f34227"></script>
+    <script src="_static/documentation_options.js?v=a58bc63e"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
@@ -119,7 +119,7 @@
 
 
 
-    <p class="title logo__title">Dyson Equalizer 0.1.0 documentation</p>
+    <p class="title logo__title">Dyson Equalizer 0.1.1 documentation</p>
 
 </a></div>
 
@@ -299,6 +299,7 @@ <h1>Dyson Equalizer<a class="headerlink" href="#dyson-equalizer" title="Link to
 <p>This package is a Python implementation of the Dyson Equalizer.
 The method is described in detail in the article <a class="reference external" href="https://doi.org/10.48550/arXiv.2306.11263">The Dyson Equalizer: Adaptive Noise Stabilization for Low-Rank Signal Detection and Recovery
 </a></p>
+<p>The documentation is available at <a class="reference external" href="https://klugerlab.github.io/DysonEqualizer">https://klugerlab.github.io/DysonEqualizer</a>.</p>
 <section id="installation">
 <h2>Installation<a class="headerlink" href="#installation" title="Link to this heading">#</a></h2>
 <p>The main version of the package can be installed as</p>

diff --git a/docs_html/objects.inv b/docs_html/objects.inv
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diff --git a/docs_html/plot_directive/reference/dyson_equalizer-2.pdf b/docs_html/plot_directive/reference/dyson_equalizer-2.pdf
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diff --git a/docs_html/plot_directive/reference/dyson_equalizer-2.py b/docs_html/plot_directive/reference/dyson_equalizer-2.py
diff --git a/docs_html/plot_directive/reference/dyson_equalizer-3.hires.png b/docs_html/plot_directive/reference/dyson_equalizer-3.hires.png
diff --git a/docs_html/plot_directive/reference/dyson_equalizer-3.pdf b/docs_html/plot_directive/reference/dyson_equalizer-3.pdf
diff --git a/docs_html/plot_directive/reference/dyson_equalizer-3.png b/docs_html/plot_directive/reference/dyson_equalizer-3.png
diff --git a/docs_html/plot_directive/reference/dyson_equalizer-3.py b/docs_html/plot_directive/reference/dyson_equalizer-3.py
diff --git a/docs_html/plot_directive/reference/dyson_equalizer-algorithm-1.hires.png b/docs_html/plot_directive/reference/dyson_equalizer-algorithm-1.hires.png
diff --git a/docs_html/plot_directive/reference/dyson_equalizer-algorithm-1.pdf b/docs_html/plot_directive/reference/dyson_equalizer-algorithm-1.pdf
diff --git a/docs_html/plot_directive/reference/dyson_equalizer-algorithm-1.png b/docs_html/plot_directive/reference/dyson_equalizer-algorithm-1.png
diff --git a/docs_html/plot_directive/reference/dyson_equalizer-algorithm-1.py b/docs_html/plot_directive/reference/dyson_equalizer-algorithm-1.py
diff --git a/docs_html/plot_directive/reference/dyson_equalizer-plots-1.pdf b/docs_html/plot_directive/reference/dyson_equalizer-plots-1.pdf
diff --git a/docs_html/plot_directive/reference/dyson_equalizer-plots-2.pdf b/docs_html/plot_directive/reference/dyson_equalizer-plots-2.pdf
diff --git a/docs_html/py-modindex.html b/docs_html/py-modindex.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Python Module Index &#8212; Dyson Equalizer 0.1.0 documentation</title>
+    <title>Python Module Index &#8212; Dyson Equalizer 0.1.1 documentation</title>
 
 
 
@@ -35,7 +35,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=01f34227"></script>
+    <script src="_static/documentation_options.js?v=a58bc63e"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'py-modindex';</script>
@@ -119,7 +119,7 @@
 
 
 
-    <p class="title logo__title">Dyson Equalizer 0.1.0 documentation</p>
+    <p class="title logo__title">Dyson Equalizer 0.1.1 documentation</p>
 
 </a></div>
 

diff --git a/docs_html/reference/dyson_equalizer.algorithm.html b/docs_html/reference/dyson_equalizer.algorithm.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>dyson_equalizer.algorithm module &#8212; Dyson Equalizer 0.1.0 documentation</title>
+    <title>dyson_equalizer.algorithm module &#8212; Dyson Equalizer 0.1.1 documentation</title>
 
 
 
@@ -29,22 +29,22 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
 
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
-    <link rel="stylesheet" type="text/css" href="../_static/plot_directive.css?v=7f9a90b1" />
+    <link rel="stylesheet" type="text/css" href="../_static/plot_directive.css" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=dfe6caa3a7d634c4db9b" />
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   <script src="../_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="../_static/documentation_options.js?v=01f34227"></script>
+    <script src="../_static/documentation_options.js?v=a58bc63e"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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     <script>DOCUMENTATION_OPTIONS.pagename = 'reference/dyson_equalizer.algorithm';</script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="dyson_equalizer.dyson_equalizer module" href="dyson_equalizer.dyson_equalizer.html" />
-    <link rel="prev" title="API and modules" href="dyson_equalizer.html" />
+    <link rel="prev" title="dyson_equalizer package" href="dyson_equalizer.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -120,7 +120,7 @@
 
 
 
-    <p class="title logo__title">Dyson Equalizer 0.1.0 documentation</p>
+    <p class="title logo__title">Dyson Equalizer 0.1.1 documentation</p>
 
 </a></div>
 
@@ -143,7 +143,7 @@
 
 <li class="nav-item current active">
   <a class="nav-link nav-internal" href="dyson_equalizer.html">
-    API and modules
+    dyson_equalizer package
   </a>
 </li>
 
@@ -240,7 +240,7 @@
 
 <li class="nav-item current active">
   <a class="nav-link nav-internal" href="dyson_equalizer.html">
-    API and modules
+    dyson_equalizer package
   </a>
 </li>
 
@@ -319,7 +319,7 @@
       </a>
     </li>
 
-    <li class="breadcrumb-item"><a href="dyson_equalizer.html" class="nav-link">API and modules</a></li>
+    <li class="breadcrumb-item"><a href="dyson_equalizer.html" class="nav-link">dyson_equalizer package</a></li>
 
     <li class="breadcrumb-item active" aria-current="page">dyson_equali...</li>
   </ul>
@@ -348,7 +348,7 @@
 <span class="sig-prename descclassname"><span class="pre">dyson_equalizer.algorithm.</span></span><span class="sig-name descname"><span class="pre">compute_low_rank_approximation_mp</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">svd</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.12)"><span class="pre">tuple</span></a><span class="p"><span class="pre">[</span></span><span class="pre">array</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#dyson_equalizer.algorithm.compute_low_rank_approximation_mp" title="Link to this definition">#</a></dt>
 <dd><p>Computes the low rank approximation by keeping all eigeinvalues above the maximum
 of the Marchenko-Pastur distribution.
-Details, derivation and convergence analysis are provided in <a href="#id3"><span class="problematic" id="id1">[1]_</span></a>, in particular Algorithms 2 and 3.</p>
+Details, derivation and convergence analysis are provided in <a class="reference internal" href="#rab46b60d179e-1" id="id1">[1]</a>, in particular Algorithms 2 and 3.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><dl class="simple">
@@ -375,6 +375,14 @@
 <p class="rubric">Notes</p>
 <p>The threshold for significance is based on the Marchenko-Pastur distribution
 and is estimated as <span class="math notranslate nohighlight">\(\sqrt{m} + \sqrt{m}\)</span>,  where <span class="math notranslate nohighlight">\(m \le n\)</span> are the matrix’s dimensions.</p>
+<p class="rubric">References</p>
+<div role="list" class="citation-list">
+<div class="citation" id="rab46b60d179e-1" role="doc-biblioentry">
+<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id1">1</a><span class="fn-bracket">]</span></span>
+<p>Landa B., Kluger Y., “The Dyson Equalizer: Adaptive Noise Stabilization for Low-Rank Signal
+Detection and Recovery,” arXiv, <a class="reference external" href="https://arxiv.org/abs/2306.11263">https://arxiv.org/abs/2306.11263</a></p>
+</div>
+</div>
 </dd></dl>
 
 <dl class="py function">
@@ -405,7 +413,7 @@
 </div>
 <p class="rubric">Notes</p>
 <p>This function computes the normalizing factors for the Dyson equalizer.
-Details, derivation and convergence analysis are provided in <a href="#id4"><span class="problematic" id="id2">[1]_</span></a>, in particular Algorithm 1.</p>
+Details, derivation and convergence analysis are provided in <a class="reference internal" href="#r493b555ec528-1" id="id3">[1]</a>, in particular Algorithm 1.</p>
 <p>First, it computes the solutions to the Dyson equation as</p>
 <div class="math notranslate nohighlight">
 \[\hat{g}_{i}^{(1)} = \sum_{k=1}^{m} \frac{\eta^2}{\sigma^2_k + \eta^2} U^2_{ik}\]</div>
@@ -427,6 +435,14 @@
 </ul>
 </dd>
 </dl>
+<p class="rubric">References</p>
+<div role="list" class="citation-list">
+<div class="citation" id="r493b555ec528-1" role="doc-biblioentry">
+<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id3">1</a><span class="fn-bracket">]</span></span>
+<p>Landa B., Kluger Y., “The Dyson Equalizer: Adaptive Noise Stabilization for Low-Rank Signal
+Detection and Recovery,” arXiv, <a class="reference external" href="https://arxiv.org/abs/2306.11263">https://arxiv.org/abs/2306.11263</a></p>
+</div>
+</div>
 </dd></dl>
 
 <dl class="py function">
@@ -510,7 +526,7 @@
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">API and modules</p>
+        <p class="prev-next-title">dyson_equalizer package</p>
       </div>
     </a>
     <a class="right-next"

diff --git a/docs_html/reference/dyson_equalizer.dyson_equalizer.html b/docs_html/reference/dyson_equalizer.dyson_equalizer.html
@@ -8,7 +8,7 @@
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     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>dyson_equalizer.dyson_equalizer module &#8212; Dyson Equalizer 0.1.0 documentation</title>
+    <title>dyson_equalizer.dyson_equalizer module &#8212; Dyson Equalizer 0.1.1 documentation</title>
 
 
 
@@ -29,14 +29,14 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
 
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
-    <link rel="stylesheet" type="text/css" href="../_static/plot_directive.css?v=7f9a90b1" />
+    <link rel="stylesheet" type="text/css" href="../_static/plot_directive.css" />
 
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-    <script src="../_static/documentation_options.js?v=01f34227"></script>
+    <script src="../_static/documentation_options.js?v=a58bc63e"></script>
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     <script>DOCUMENTATION_OPTIONS.pagename = 'reference/dyson_equalizer.dyson_equalizer';</script>
@@ -119,7 +119,7 @@
 
 
 
-    <p class="title logo__title">Dyson Equalizer 0.1.0 documentation</p>
+    <p class="title logo__title">Dyson Equalizer 0.1.1 documentation</p>
 
 </a></div>
 

diff --git a/docs_html/reference/dyson_equalizer.examples.html b/docs_html/reference/dyson_equalizer.examples.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>dyson_equalizer.examples module &#8212; Dyson Equalizer 0.1.0 documentation</title>
+    <title>dyson_equalizer.examples module &#8212; Dyson Equalizer 0.1.1 documentation</title>
 
 
 
@@ -29,14 +29,14 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
 
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
-    <link rel="stylesheet" type="text/css" href="../_static/plot_directive.css?v=7f9a90b1" />
+    <link rel="stylesheet" type="text/css" href="../_static/plot_directive.css" />
 
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   <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=dfe6caa3a7d634c4db9b" />
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   <script src="../_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="../_static/documentation_options.js?v=01f34227"></script>
+    <script src="../_static/documentation_options.js?v=a58bc63e"></script>
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     <script>DOCUMENTATION_OPTIONS.pagename = 'reference/dyson_equalizer.examples';</script>
@@ -119,7 +119,7 @@
 
 
 
-    <p class="title logo__title">Dyson Equalizer 0.1.0 documentation</p>
+    <p class="title logo__title">Dyson Equalizer 0.1.1 documentation</p>
 
 </a></div>
 
@@ -142,7 +142,7 @@
 
 <li class="nav-item current active">
   <a class="nav-link nav-internal" href="dyson_equalizer.html">
-    API and modules
+    dyson_equalizer package
   </a>
 </li>
 
@@ -239,7 +239,7 @@
 
 <li class="nav-item current active">
   <a class="nav-link nav-internal" href="dyson_equalizer.html">
-    API and modules
+    dyson_equalizer package
   </a>
 </li>
 
@@ -318,7 +318,7 @@
       </a>
     </li>
 
-    <li class="breadcrumb-item"><a href="dyson_equalizer.html" class="nav-link">API and modules</a></li>
+    <li class="breadcrumb-item"><a href="dyson_equalizer.html" class="nav-link">dyson_equalizer package</a></li>
 
     <li class="breadcrumb-item active" aria-current="page">dyson_equali...</li>
   </ul>