Update from scikit-bio/scikit-bio@c989edd

scikit-bio · Jan 12, 2025 · a9dfd27 · a9dfd27
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diff --git a/docs/dev/_sources/generated/skbio.diversity.vectorize_counts_and_tree.rst.txt b/docs/dev/_sources/generated/skbio.diversity.vectorize_counts_and_tree.rst.txt
@@ -0,0 +1,6 @@
+skbio.diversity.vectorize\_counts\_and\_tree
+============================================
+
+.. currentmodule:: skbio.diversity
+
+.. autofunction:: vectorize_counts_and_tree
diff --git a/docs/dev/diversity.html b/docs/dev/diversity.html
@@ -613,6 +613,9 @@
 <li class="toctree-l1"><a class="reference internal" href="generated/skbio.diversity.partial_beta_diversity.html">skbio.diversity.partial_beta_diversity</a></li>
 <li class="toctree-l1"><a class="reference internal" href="generated/skbio.diversity.block_beta_diversity.html">skbio.diversity.block_beta_diversity</a></li>
 </ul>
+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="generated/skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
+</ul>
 </div>
 </nav></div>
     </div>
@@ -733,6 +736,17 @@ <h2>Beta diversity<a class="headerlink" href="#beta-diversity" title="Link to th
 </table>
 </div>
 </section>
+<section id="utility-functions">
+<h2>Utility functions<a class="headerlink" href="#utility-functions" title="Link to this heading">#</a></h2>
+<div class="pst-scrollable-table-container"><table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/skbio.diversity.vectorize_counts_and_tree.html#skbio.diversity.vectorize_counts_and_tree" title="skbio.diversity.vectorize_counts_and_tree"><code class="xref py py-obj docutils literal notranslate"><span class="pre">vectorize_counts_and_tree</span></code></a>(counts, taxa, tree)</p></td>
+<td><p>Index tree and convert counts to np.array in corresponding order.</p></td>
+</tr>
+</tbody>
+</table>
+</div>
+</section>
 <section id="introduction">
 <h2>Introduction<a class="headerlink" href="#introduction" title="Link to this heading">#</a></h2>
 <p>A community (i.e., sample) is represented by a vector of frequencies of taxa
@@ -1155,6 +1169,7 @@ <h2>Tutorial<a class="headerlink" href="#tutorial" title="Link to this heading">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#beta-diversity">Beta diversity</a><ul class="nav section-nav flex-column">
 </ul>
 </li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#utility-functions">Utility functions</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#introduction">Introduction</a><ul class="nav section-nav flex-column">
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#input-validation">Input validation</a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#count-vectors">Count vectors</a></li>

diff --git a/docs/dev/generated/skbio.diversity.alpha.ace.html b/docs/dev/generated/skbio.diversity.alpha.ace.html
@@ -653,6 +653,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.berger_parker_d.html b/docs/dev/generated/skbio.diversity.alpha.berger_parker_d.html
@@ -653,6 +653,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.brillouin_d.html b/docs/dev/generated/skbio.diversity.alpha.brillouin_d.html
@@ -653,6 +653,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
+</ul>
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     </div>

diff --git a/docs/dev/generated/skbio.diversity.alpha.chao1.html b/docs/dev/generated/skbio.diversity.alpha.chao1.html
@@ -653,6 +653,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.chao1_ci.html b/docs/dev/generated/skbio.diversity.alpha.chao1_ci.html
@@ -652,6 +652,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.dominance.html b/docs/dev/generated/skbio.diversity.alpha.dominance.html
@@ -653,6 +653,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
+</ul>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.doubles.html b/docs/dev/generated/skbio.diversity.alpha.doubles.html
@@ -652,6 +652,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
+</ul>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.enspie.html b/docs/dev/generated/skbio.diversity.alpha.enspie.html
@@ -653,6 +653,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
+</ul>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.esty_ci.html b/docs/dev/generated/skbio.diversity.alpha.esty_ci.html
@@ -653,6 +653,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
+</ul>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.faith_pd.html b/docs/dev/generated/skbio.diversity.alpha.faith_pd.html
@@ -653,6 +653,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
+</ul>
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     </div>

diff --git a/docs/dev/generated/skbio.diversity.alpha.fisher_alpha.html b/docs/dev/generated/skbio.diversity.alpha.fisher_alpha.html
@@ -653,6 +653,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
+</ul>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.gini_index.html b/docs/dev/generated/skbio.diversity.alpha.gini_index.html
@@ -653,6 +653,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
+</ul>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.goods_coverage.html b/docs/dev/generated/skbio.diversity.alpha.goods_coverage.html
@@ -653,6 +653,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
+</ul>
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     </div>

diff --git a/docs/dev/generated/skbio.diversity.alpha.heip_e.html b/docs/dev/generated/skbio.diversity.alpha.heip_e.html
@@ -653,6 +653,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
+</ul>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.hill.html b/docs/dev/generated/skbio.diversity.alpha.hill.html
@@ -653,6 +653,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
+</ul>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.html b/docs/dev/generated/skbio.diversity.alpha.html
@@ -652,6 +652,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
+</ul>
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     </div>

diff --git a/docs/dev/generated/skbio.diversity.alpha.inv_simpson.html b/docs/dev/generated/skbio.diversity.alpha.inv_simpson.html
@@ -653,6 +653,9 @@
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+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
+</ul>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.kempton_taylor_q.html b/docs/dev/generated/skbio.diversity.alpha.kempton_taylor_q.html
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+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.lladser_ci.html b/docs/dev/generated/skbio.diversity.alpha.lladser_ci.html
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diff --git a/docs/dev/generated/skbio.diversity.alpha.lladser_pe.html b/docs/dev/generated/skbio.diversity.alpha.lladser_pe.html
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diff --git a/docs/dev/generated/skbio.diversity.alpha.margalef.html b/docs/dev/generated/skbio.diversity.alpha.margalef.html
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diff --git a/docs/dev/generated/skbio.diversity.alpha.mcintosh_d.html b/docs/dev/generated/skbio.diversity.alpha.mcintosh_d.html
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diff --git a/docs/dev/generated/skbio.diversity.alpha.mcintosh_e.html b/docs/dev/generated/skbio.diversity.alpha.mcintosh_e.html
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diff --git a/docs/dev/generated/skbio.diversity.alpha.menhinick.html b/docs/dev/generated/skbio.diversity.alpha.menhinick.html
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diff --git a/docs/dev/generated/skbio.diversity.alpha.michaelis_menten_fit.html b/docs/dev/generated/skbio.diversity.alpha.michaelis_menten_fit.html
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diff --git a/docs/dev/generated/skbio.diversity.alpha.osd.html b/docs/dev/generated/skbio.diversity.alpha.osd.html
@@ -652,6 +652,9 @@
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diff --git a/docs/dev/generated/skbio.diversity.alpha.phydiv.html b/docs/dev/generated/skbio.diversity.alpha.phydiv.html
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+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.pielou_e.html b/docs/dev/generated/skbio.diversity.alpha.pielou_e.html
@@ -653,6 +653,9 @@
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+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.renyi.html b/docs/dev/generated/skbio.diversity.alpha.renyi.html
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+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
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diff --git a/docs/dev/generated/skbio.diversity.alpha.robbins.html b/docs/dev/generated/skbio.diversity.alpha.robbins.html
@@ -653,6 +653,9 @@
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+<li class="toctree-l1"><a class="reference internal" href="skbio.diversity.vectorize_counts_and_tree.html">skbio.diversity.vectorize_counts_and_tree</a></li>
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