Update from scikit-bio/scikit-bio@f863136

Author: mataton

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

@@ -0,0 +1,6 @@
+skbio.stats.composition.ancombc
+===============================
+
+.. currentmodule:: skbio.stats.composition
+
+.. autofunction:: ancombc

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

@@ -614,6 +614,7 @@
 <ul class="current nav bd-sidenav">
 <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.ancombc.html">skbio.stats.composition.ancombc</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>
@@ -711,7 +712,7 @@
 <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">ref_idx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">validate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</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#L916"><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">ref_idx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">validate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</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/_base.py#L773"><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 (ALR) 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_inv.html

@@ -614,6 +614,7 @@
 <ul class="current nav bd-sidenav">
 <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.ancombc.html">skbio.stats.composition.ancombc</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>
@@ -711,7 +712,7 @@
 <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">ref_idx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-1</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#L1025"><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">ref_idx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-1</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/_base.py#L882"><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 (ALR) 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.ancom.html

@@ -69,7 +69,7 @@
     <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.stats.composition.dirmult_ttest" href="skbio.stats.composition.dirmult_ttest.html" />
+    <link rel="next" title="skbio.stats.composition.ancombc" href="skbio.stats.composition.ancombc.html" />
     <link rel="prev" title="Composition Statistics (skbio.stats.composition)" href="skbio.stats.composition.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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@@ -614,6 +614,7 @@
 <ul class="current nav bd-sidenav">
 <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>
+<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.ancombc.html">skbio.stats.composition.ancombc</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>
@@ -711,7 +712,7 @@
 <h1>skbio.stats.composition.ancom<a class="headerlink" href="#skbio-stats-composition-ancom" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.stats.composition.ancom">
-<span class="sig-prename descclassname"><span class="pre">skbio.stats.composition.</span></span><span class="sig-name descname"><span class="pre">ancom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">table</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">grouping</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tau</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.02</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">theta</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p_adjust</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'holm'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sig_test</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'f_oneway'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">percentiles</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</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#L1771"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.ancom" 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">ancom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">table</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">grouping</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tau</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.02</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">theta</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p_adjust</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'holm'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sig_test</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'f_oneway'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">percentiles</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</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/_ancom.py#L18"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.ancom" title="Link to this definition">#</a></dt>
 <dd><p>Perform differential abundance test using ANCOM.</p>
 <p>Analysis of composition of microbiomes (ANCOM) is done by calculating
 pairwise log ratios between all features and performing a significance
@@ -813,6 +814,7 @@ <h1>skbio.stats.composition.ancom<a class="headerlink" href="#skbio-stats-compos
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
 <dl class="simple">
+<dt><a class="reference internal" href="skbio.stats.composition.ancombc.html#skbio.stats.composition.ancombc" title="skbio.stats.composition.ancombc"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ancombc</span></code></a></dt><dd></dd>
 <dt><a class="reference internal" href="skbio.stats.composition.multi_replace.html#skbio.stats.composition.multi_replace" title="skbio.stats.composition.multi_replace"><code class="xref py py-obj docutils literal notranslate"><span class="pre">multi_replace</span></code></a></dt><dd></dd>
 <dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_ind.html#scipy.stats.ttest_ind" title="(in SciPy v1.16.2)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.ttest_ind</span></code></a></dt><dd></dd>
 <dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.f_oneway.html#scipy.stats.f_oneway" title="(in SciPy v1.16.2)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.f_oneway</span></code></a></dt><dd></dd>
@@ -973,11 +975,11 @@ <h1>skbio.stats.composition.ancom<a class="headerlink" href="#skbio-stats-compos
       </div>
     </a>
     <a class="right-next"
-       href="skbio.stats.composition.dirmult_ttest.html"
+       href="skbio.stats.composition.ancombc.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">skbio.stats.composition.dirmult_ttest</p>
+        <p class="prev-next-title">skbio.stats.composition.ancombc</p>
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       <i class="fa-solid fa-angle-right"></i>
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