Update from scikit-bio/scikit-bio@dae9a25

Author: mortonjt

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

@@ -724,7 +724,7 @@
 <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#L657"><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#L659"><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_inv.html

@@ -724,7 +724,7 @@
 <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#L716"><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#L718"><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.ancom.html

@@ -724,7 +724,7 @@
 <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">significance_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">(0.0,</span> <span class="pre">25.0,</span> <span class="pre">50.0,</span> <span class="pre">75.0,</span> <span class="pre">100.0)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">multiple_comparisons_correction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'holm-bonferroni'</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#L1200"><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">significance_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">(0.0,</span> <span class="pre">25.0,</span> <span class="pre">50.0,</span> <span class="pre">75.0,</span> <span class="pre">100.0)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">multiple_comparisons_correction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'holm-bonferroni'</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#L1202"><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 a 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

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

@@ -723,7 +723,7 @@
 <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#L784"><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#L786"><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>

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

@@ -723,7 +723,7 @@
 <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#L100"><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#L102"><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.clr.html

@@ -724,7 +724,7 @@
 <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#L429"><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#L431"><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

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

@@ -724,7 +724,7 @@
 <h1>skbio.stats.composition.clr_inv<a class="headerlink" href="#skbio-stats-composition-clr-inv" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.stats.composition.clr_inv">
-<span class="sig-prename descclassname"><span class="pre">skbio.stats.composition.</span></span><span class="sig-name descname"><span class="pre">clr_inv</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#L475"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.clr_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">clr_inv</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#L477"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.clr_inv" title="Link to this definition">#</a></dt>
 <dd><p>Perform inverse centre log ratio transformation.</p>
 <p>This function transforms compositions from the real space to Aitchison
 geometry. The <span class="math notranslate nohighlight">\(clr^{-1}\)</span> transform is both an isometry, and an

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

@@ -723,7 +723,7 @@
 <h1>skbio.stats.composition.dirmult_ttest<a class="headerlink" href="#skbio-stats-composition-dirmult-ttest" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.stats.composition.dirmult_ttest">
-<span class="sig-prename descclassname"><span class="pre">skbio.stats.composition.</span></span><span class="sig-name descname"><span class="pre">dirmult_ttest</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">treatment</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reference</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pseudocount</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">draws</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">128</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">seed</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#L1810"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.dirmult_ttest" 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">dirmult_ttest</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">treatment</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reference</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pseudocount</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">draws</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">128</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">seed</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#L1826"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.composition.dirmult_ttest" title="Link to this definition">#</a></dt>
 <dd><p><em>T</em>-test using Dirichlet-multinomial distribution.</p>
 <p>The Dirichlet-multinomial distribution is a compound distribution that
 combines a Dirichlet distribution over the probabilities of a multinomial