Update from scikit-bio/scikit-bio@9926815

Author: qiyunzhu

docs/dev/_sources/generated/skbio.stats.composition.dirmult_lme.rst.txt

@@ -607,7 +607,6 @@
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="skbio.stats.composition.html">Composition Statistics (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.stats.composition</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"><a class="reference internal" href="skbio.stats.composition.ancom.html">skbio.stats.composition.ancom</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.dirmult_ttest.html">skbio.stats.composition.dirmult_ttest</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.dirmult_lme.html">skbio.stats.composition.dirmult_lme</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.centralize.html">skbio.stats.composition.centralize</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.closure.html">skbio.stats.composition.closure</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.inner.html">skbio.stats.composition.inner</a></li>
@@ -703,7 +702,7 @@
 <h1>skbio.stats.composition.alr<a class="headerlink" href="#skbio-stats-composition-alr" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.stats.composition.alr">
-<span class="sig-prename descclassname"><span class="pre">skbio.stats.composition.</span></span><span class="sig-name descname"><span class="pre">alr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">denominator_idx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/stats/composition.py#L681"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.alr" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.stats.composition.</span></span><span class="sig-name descname"><span class="pre">alr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">denominator_idx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/stats/composition.py#L680"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.alr" title="Link to this definition">#</a></dt>
 <dd><p>Perform additive log ratio transformation.</p>
 <p>This function transforms compositions from a D-part Aitchison simplex to
 a non-isometric real space of D-1 dimensions. The argument

docs/dev/generated/skbio.stats.composition.alr.html

@@ -607,7 +607,6 @@
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="skbio.stats.composition.html">Composition Statistics (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.stats.composition</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"><a class="reference internal" href="skbio.stats.composition.ancom.html">skbio.stats.composition.ancom</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.dirmult_ttest.html">skbio.stats.composition.dirmult_ttest</a></li>
-<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.dirmult_lme.html">skbio.stats.composition.dirmult_lme</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.centralize.html">skbio.stats.composition.centralize</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.closure.html">skbio.stats.composition.closure</a></li>
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@@ -703,7 +702,7 @@
 <h1>skbio.stats.composition.alr_inv<a class="headerlink" href="#skbio-stats-composition-alr-inv" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.stats.composition.alr_inv">
-<span class="sig-prename descclassname"><span class="pre">skbio.stats.composition.</span></span><span class="sig-name descname"><span class="pre">alr_inv</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">denominator_idx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/stats/composition.py#L740"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.alr_inv" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.stats.composition.</span></span><span class="sig-name descname"><span class="pre">alr_inv</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">denominator_idx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/stats/composition.py#L739"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.alr_inv" title="Link to this definition">#</a></dt>
 <dd><p>Perform inverse additive log ratio transform.</p>
 <p>This function transforms compositions from the non-isometric real space of
 alrs to Aitchison geometry.</p>

docs/dev/generated/skbio.stats.composition.alr_inv.html

@@ -607,7 +607,6 @@
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="skbio.stats.composition.html">Composition Statistics (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.stats.composition</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.stats.composition.ancom</a></li>
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 <li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.centralize.html">skbio.stats.composition.centralize</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.closure.html">skbio.stats.composition.closure</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.inner.html">skbio.stats.composition.inner</a></li>

docs/dev/generated/skbio.stats.composition.ancom.html

@@ -75,7 +75,7 @@
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@@ -606,7 +606,6 @@
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="skbio.stats.composition.html">Composition Statistics (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.stats.composition</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">
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@@ -702,7 +701,7 @@
 <h1>skbio.stats.composition.centralize<a class="headerlink" href="#skbio-stats-composition-centralize" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.stats.composition.centralize">
-<span class="sig-prename descclassname"><span class="pre">skbio.stats.composition.</span></span><span class="sig-name descname"><span class="pre">centralize</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mat</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/stats/composition.py#L808"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.centralize" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.stats.composition.</span></span><span class="sig-name descname"><span class="pre">centralize</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mat</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/stats/composition.py#L807"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.centralize" title="Link to this definition">#</a></dt>
 <dd><p>Center data around its geometric average.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -742,12 +741,12 @@ <h1>skbio.stats.composition.centralize<a class="headerlink" href="#skbio-stats-c
 
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docs/dev/generated/skbio.stats.composition.centralize.html

@@ -606,7 +606,6 @@
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="skbio.stats.composition.html">Composition Statistics (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.stats.composition</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">
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@@ -702,7 +701,7 @@
 <h1>skbio.stats.composition.closure<a class="headerlink" href="#skbio-stats-composition-closure" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.stats.composition.closure">
-<span class="sig-prename descclassname"><span class="pre">skbio.stats.composition.</span></span><span class="sig-name descname"><span class="pre">closure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mat</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/stats/composition.py#L162"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.closure" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.stats.composition.</span></span><span class="sig-name descname"><span class="pre">closure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mat</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/stats/composition.py#L161"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.closure" title="Link to this definition">#</a></dt>
 <dd><p>Perform closure to ensure that all elements add up to 1.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/dev/generated/skbio.stats.composition.closure.html

@@ -607,7 +607,6 @@
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="skbio.stats.composition.html">Composition Statistics (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.stats.composition</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">
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@@ -703,7 +702,7 @@
 <h1>skbio.stats.composition.clr<a class="headerlink" href="#skbio-stats-composition-clr" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.stats.composition.clr">
-<span class="sig-prename descclassname"><span class="pre">skbio.stats.composition.</span></span><span class="sig-name descname"><span class="pre">clr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mat</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/stats/composition.py#L453"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.clr" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.stats.composition.</span></span><span class="sig-name descname"><span class="pre">clr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mat</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/stats/composition.py#L452"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.clr" title="Link to this definition">#</a></dt>
 <dd><p>Perform centre log ratio transformation.</p>
 <p>This function transforms compositions from Aitchison geometry to the real
 space. The <span class="math notranslate nohighlight">\(clr\)</span> transform is both an isometry and an isomorphism