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

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skbio.stats.composition.struc\_zero
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===================================
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.. currentmodule:: skbio.stats.composition
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.. autofunction:: struc_zero

‎docs/dev/generated/skbio.sequence.SubstitutionMatrix.html‎

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<td><p>List names of pre-defined substitution matrices.</p></td>
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</tr>
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<tr class="row-odd"><td><p><a class="reference internal" href="skbio.sequence.SubstitutionMatrix.identity.html#skbio.sequence.SubstitutionMatrix.identity" title="skbio.sequence.SubstitutionMatrix.identity"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identity</span></code></a>(alphabet, match, mismatch[, dtype])</p></td>
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<td><p></p></td>
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<td><p>Create an identity substitution matrix.</p></td>
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</tr>
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<tr class="row-even"><td><p><a class="reference internal" href="skbio.sequence.SubstitutionMatrix.to_dict.html#skbio.sequence.SubstitutionMatrix.to_dict" title="skbio.sequence.SubstitutionMatrix.to_dict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_dict</span></code></a>()</p></td>
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<td><p>Create a 2D dictionary from the substitution matrix.</p></td>

‎docs/dev/generated/skbio.sequence.SubstitutionMatrix.identity.html‎

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<head>
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<meta charset="utf-8" />
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<meta name="description" content="Create an identity substitution matrix." />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>skbio.sequence.SubstitutionMatrix.identity &#8212; scikit-bio 0.7.1-dev documentation</title>
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<dl class="py method">
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<dt class="sig sig-object py" id="skbio.sequence.SubstitutionMatrix.identity">
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<em class="property"><span class="k"><span class="pre">classmethod</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">SubstitutionMatrix.</span></span><span class="sig-name descname"><span class="pre">identity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">alphabet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">match</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mismatch</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dtype</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'float32'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/sequence/_substitution.py#L337"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.sequence.SubstitutionMatrix.identity" title="Link to this definition">#</a></dt>
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<dd></dd></dl>
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<dd><p>Create an identity substitution matrix.</p>
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<p>All matches and mismatches will have the identical scores,
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respectively, regardless of the character.</p>
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<dl class="field-list simple">
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<dt class="field-odd">Parameters<span class="colon">:</span></dt>
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<dd class="field-odd"><dl class="simple">
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<dt><strong>alphabet</strong><span class="classifier">iterable</span></dt><dd><p>Characters that constitute the alphabet.</p>
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</dd>
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<dt><strong>match</strong><span class="classifier">int or float</span></dt><dd><p>Score assigned to all matches.</p>
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</dd>
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<dt><strong>mismatch</strong><span class="classifier">int or float</span></dt><dd><p>Score assigned to all mismatches.</p>
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</dd>
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<dt><strong>dtype</strong><span class="classifier">{“float32”, “float64”}, optional</span></dt><dd><p>Floating-point data type of the matrix. Default is “float32”.</p>
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</dd>
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</dl>
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</dd>
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<dt class="field-even">Returns<span class="colon">:</span></dt>
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<dd class="field-even"><dl class="simple">
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<dt>SubstitutionMatrix</dt><dd><p>Substitution matrix constructed from the alphabet and scores.</p>
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</dd>
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</dl>
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</dd>
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</dl>
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<p class="rubric">Examples</p>
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<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">skbio</span><span class="w"> </span><span class="kn">import</span> <span class="n">SubstitutionMatrix</span>
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<span class="gp">&gt;&gt;&gt; </span><span class="n">mat</span> <span class="o">=</span> <span class="n">SubstitutionMatrix</span><span class="o">.</span><span class="n">identity</span><span class="p">(</span><span class="s1">&#39;ACGT&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">2</span><span class="p">)</span>
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<span class="gp">&gt;&gt;&gt; </span><span class="n">mat</span><span class="o">.</span><span class="n">alphabet</span>
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<span class="go">(&#39;A&#39;, &#39;C&#39;, &#39;G&#39;, &#39;T&#39;)</span>
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<span class="gp">&gt;&gt;&gt; </span><span class="n">mat</span><span class="o">.</span><span class="n">scores</span>
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<span class="go">array([[ 1., -2., -2., -2.],</span>
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<span class="go"> [-2., 1., -2., -2.],</span>
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<span class="go"> [-2., -2., 1., -2.],</span>
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<span class="go"> [-2., -2., -2., 1.]], dtype=float32)</span>
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</pre></div>
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</div>
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</dd></dl>
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</section>
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‎docs/dev/generated/skbio.stats.composition.alr.html‎

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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.ancombc.html">skbio.stats.composition.ancombc</a></li>
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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.dirmult_ttest.html">skbio.stats.composition.dirmult_ttest</a></li>
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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.dirmult_lme.html">skbio.stats.composition.dirmult_lme</a></li>
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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.struc_zero.html">skbio.stats.composition.struc_zero</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>
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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.closure.html">skbio.stats.composition.closure</a></li>
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<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.alr_inv.html‎

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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.ancombc.html">skbio.stats.composition.ancombc</a></li>
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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.dirmult_ttest.html">skbio.stats.composition.dirmult_ttest</a></li>
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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.dirmult_lme.html">skbio.stats.composition.dirmult_lme</a></li>
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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.struc_zero.html">skbio.stats.composition.struc_zero</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>
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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.closure.html">skbio.stats.composition.closure</a></li>
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<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

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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.ancombc.html">skbio.stats.composition.ancombc</a></li>
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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.dirmult_ttest.html">skbio.stats.composition.dirmult_ttest</a></li>
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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.dirmult_lme.html">skbio.stats.composition.dirmult_lme</a></li>
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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.struc_zero.html">skbio.stats.composition.struc_zero</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>
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<li class="toctree-l2"><a class="reference internal" href="skbio.stats.composition.closure.html">skbio.stats.composition.closure</a></li>
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be significantly different. This can can be anywhere between 0 and 1
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exclusive.</p>
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</dd>
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<dt><strong>p_adjust</strong><span class="classifier">str, optional</span></dt><dd><p>Method to correct <em>p</em>-values for multiple comparisons. Options are Holm-
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Boniferroni (“holm” or “holm-bonferroni”) (default), Benjamini-
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Hochberg (“bh”, “fdr_bh” or “benjamini-hochberg”), or any method supported
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by statsmodels’ <a class="reference external" href="https://www.statsmodels.org/stable/generated/statsmodels.stats.multitest.multipletests.html#statsmodels.stats.multitest.multipletests" title="(in statsmodels 0.14.4 v0.14.4)"><code class="xref py py-func docutils literal notranslate"><span class="pre">multipletests</span></code></a> function.
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<dt><strong>p_adjust</strong><span class="classifier">str, optional</span></dt><dd><p>Method to correct <em>p</em>-values for multiple comparisons. Options are
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Holm-Boniferroni (“holm” or “holm-bonferroni”) (default), Benjamini-Hochberg
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(“bh”, “fdr_bh” or “benjamini-hochberg”), or any method supported by
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statsmodels’ <a class="reference external" href="https://www.statsmodels.org/stable/generated/statsmodels.stats.multitest.multipletests.html#statsmodels.stats.multitest.multipletests" title="(in statsmodels 0.14.4 v0.14.4)"><code class="xref py py-func docutils literal notranslate"><span class="pre">multipletests</span></code></a> function.
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Case-insensitive. If None, no correction will be performed.</p>
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<div class="versionchanged">
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<p><span class="versionmodified changed">Changed in version 0.6.0: </span>Renamed from <code class="docutils literal notranslate"><span class="pre">multiple_comparisons_correction</span></code>. The old name is kept as an alias but is deprecated.</p>

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