Update from scikit-bio/scikit-bio@40f8f3c

Author: qiyunzhu

docs/dev/_sources/generated/skbio.diversity.alpha.inv_simpson.rst.txt

@@ -0,0 +1,6 @@
+skbio.diversity.alpha.inv\_simpson
+==================================
+
+.. currentmodule:: skbio.diversity.alpha
+
+.. autofunction:: inv_simpson

docs/dev/_sources/generated/skbio.diversity.alpha.simpson_d.rst.txt

@@ -0,0 +1,6 @@
+skbio.diversity.alpha.simpson\_d
+================================
+
+.. currentmodule:: skbio.diversity.alpha
+
+.. autofunction:: simpson_d

docs/dev/generated/skbio.diversity.alpha.ace.html

@@ -70,7 +70,7 @@
     <link rel="icon" href="../_static/favicon.ico"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="skbio.diversity.alpha.berger_parker_d" href="skbio.diversity.alpha.berger_parker_d.html" />
+    <link rel="next" title="skbio.diversity.alpha.chao1" href="skbio.diversity.alpha.chao1.html" />
     <link rel="prev" title="Alpha diversity measures (skbio.diversity.alpha)" href="skbio.diversity.alpha.html" />
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@@ -624,39 +624,41 @@
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="skbio.diversity.alpha.html">Alpha diversity measures (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.diversity.alpha</span></code>)</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
 <li class="toctree-l2 current active"><a class="current reference internal" href="#">skbio.diversity.alpha.ace</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.berger_parker_d.html">skbio.diversity.alpha.berger_parker_d</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.brillouin_d.html">skbio.diversity.alpha.brillouin_d</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.chao1.html">skbio.diversity.alpha.chao1</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.chao1_ci.html">skbio.diversity.alpha.chao1_ci</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.dominance.html">skbio.diversity.alpha.dominance</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.doubles.html">skbio.diversity.alpha.doubles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.enspie.html">skbio.diversity.alpha.enspie</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.esty_ci.html">skbio.diversity.alpha.esty_ci</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.faith_pd.html">skbio.diversity.alpha.faith_pd</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.fisher_alpha.html">skbio.diversity.alpha.fisher_alpha</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.gini_index.html">skbio.diversity.alpha.gini_index</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.goods_coverage.html">skbio.diversity.alpha.goods_coverage</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.heip_e.html">skbio.diversity.alpha.heip_e</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.kempton_taylor_q.html">skbio.diversity.alpha.kempton_taylor_q</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.lladser_ci.html">skbio.diversity.alpha.lladser_ci</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.lladser_pe.html">skbio.diversity.alpha.lladser_pe</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.margalef.html">skbio.diversity.alpha.margalef</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.mcintosh_d.html">skbio.diversity.alpha.mcintosh_d</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.mcintosh_e.html">skbio.diversity.alpha.mcintosh_e</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.menhinick.html">skbio.diversity.alpha.menhinick</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.michaelis_menten_fit.html">skbio.diversity.alpha.michaelis_menten_fit</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.observed_features.html">skbio.diversity.alpha.observed_features</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.observed_otus.html">skbio.diversity.alpha.observed_otus</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.osd.html">skbio.diversity.alpha.osd</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.singles.html">skbio.diversity.alpha.singles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.sobs.html">skbio.diversity.alpha.sobs</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.brillouin_d.html">skbio.diversity.alpha.brillouin_d</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.enspie.html">skbio.diversity.alpha.enspie</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.fisher_alpha.html">skbio.diversity.alpha.fisher_alpha</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.inv_simpson.html">skbio.diversity.alpha.inv_simpson</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.kempton_taylor_q.html">skbio.diversity.alpha.kempton_taylor_q</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.phydiv.html">skbio.diversity.alpha.phydiv</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.pielou_e.html">skbio.diversity.alpha.pielou_e</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.robbins.html">skbio.diversity.alpha.robbins</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.shannon.html">skbio.diversity.alpha.shannon</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.simpson.html">skbio.diversity.alpha.simpson</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.heip_e.html">skbio.diversity.alpha.heip_e</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.mcintosh_e.html">skbio.diversity.alpha.mcintosh_e</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.pielou_e.html">skbio.diversity.alpha.pielou_e</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.simpson_e.html">skbio.diversity.alpha.simpson_e</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.singles.html">skbio.diversity.alpha.singles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.sobs.html">skbio.diversity.alpha.sobs</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.berger_parker_d.html">skbio.diversity.alpha.berger_parker_d</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.dominance.html">skbio.diversity.alpha.dominance</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.gini_index.html">skbio.diversity.alpha.gini_index</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.mcintosh_d.html">skbio.diversity.alpha.mcintosh_d</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.simpson_d.html">skbio.diversity.alpha.simpson_d</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.strong.html">skbio.diversity.alpha.strong</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.esty_ci.html">skbio.diversity.alpha.esty_ci</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.goods_coverage.html">skbio.diversity.alpha.goods_coverage</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.lladser_ci.html">skbio.diversity.alpha.lladser_ci</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.lladser_pe.html">skbio.diversity.alpha.lladser_pe</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.diversity.alpha.robbins.html">skbio.diversity.alpha.robbins</a></li>
 </ul>
 </details></li>
 <li class="toctree-l1"><a class="reference internal" href="skbio.diversity.get_alpha_diversity_metrics.html">skbio.diversity.get_alpha_diversity_metrics</a></li>
@@ -743,14 +745,14 @@ <h1>skbio.diversity.alpha.ace<a class="headerlink" href="#skbio-diversity-alpha-
 \[S_{ace}=S_{abund}+\frac{S_{rare}}{C_{ace}}+
 \frac{F_1}{C_{ace}}\gamma^2_{ace}\]</div>
 <p>where <span class="math notranslate nohighlight">\(S_{abund}\)</span> is the number of abundant taxa (with more than
-<cite>rare_threshold</cite>  individuals) when all samples are pooled,
+<code class="docutils literal notranslate"><span class="pre">rare_threshold</span></code> individuals) when all samples are pooled,
 <span class="math notranslate nohighlight">\(S_{rare}\)</span> is the number of rare taxa (with less than or equal to
-<cite>rare_threshold</cite> individuals) when all samples are pooled, <span class="math notranslate nohighlight">\(C_{ace}\)</span>
-is the sample abundance coverage estimator, <span class="math notranslate nohighlight">\(F_1\)</span> is the frequency of
-singletons, and <span class="math notranslate nohighlight">\(\gamma^2_{ace}\)</span> is the estimated coefficient of
-variation for rare taxa.</p>
+<code class="docutils literal notranslate"><span class="pre">rare_threshold</span></code> individuals) when all samples are pooled,
+<span class="math notranslate nohighlight">\(C_{ace}\)</span> is the sample abundance coverage estimator, <span class="math notranslate nohighlight">\(F_1\)</span> is
+the frequency of singletons, and <span class="math notranslate nohighlight">\(\gamma^2_{ace}\)</span> is the estimated
+coefficient of variation for rare taxa.</p>
 <p>The estimated coefficient of variation is defined as (assuming
-<cite>rare_threshold</cite> is 10, the default):</p>
+<code class="docutils literal notranslate"><span class="pre">rare_threshold</span></code> is 10, the default):</p>
 <div class="math notranslate nohighlight">
 \[\gamma^2_{ace}=max\left[\frac{S_{rare}}{C_{ace}}
 \frac{\sum^{10}_{i=1}{{i\left(i-1\right)}}F_i}
@@ -783,9 +785,9 @@ <h1>skbio.diversity.alpha.ace<a class="headerlink" href="#skbio-diversity-alpha-
 on the description given in the EstimateS manual <a class="reference internal" href="#r34b5d5ddea45-3" id="id3">[3]</a>.</p>
 <p>If no rare taxa exist, returns the number of abundant taxa. The default
 value of 10 for <cite>rare_threshold</cite> is based on <a class="reference internal" href="#r34b5d5ddea45-4" id="id4">[4]</a>.</p>
-<p>If <cite>counts</cite> contains zeros, indicating taxa which are known to exist in the
-environment but did not appear in the sample, they will be ignored for the
-purpose of calculating the number of rare taxa.</p>
+<p>If <code class="docutils literal notranslate"><span class="pre">counts</span></code> contains zeros, indicating taxa which are known to exist in
+the environment but did not appear in the sample, they will be ignored for
+the purpose of calculating the number of rare taxa.</p>
 <p class="rubric">References</p>
 <div role="list" class="citation-list">
 <div class="citation" id="r34b5d5ddea45-1" role="doc-biblioentry">
@@ -835,11 +837,11 @@ <h1>skbio.diversity.alpha.ace<a class="headerlink" href="#skbio-diversity-alpha-
       </div>
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-       href="skbio.diversity.alpha.berger_parker_d.html"
+       href="skbio.diversity.alpha.chao1.html"
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         <p class="prev-next-subtitle">next</p>
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