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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-skbio">Debian Med / python-skbio</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-skbio/commit/6885c5b39116cdcfa3433ad8e60da69a342c65b4">6885c5b3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-15T13:20:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.5.3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-skbio/commit/0962c8f33479785710a34095eb72b6cb0da7fbd7">0962c8f3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-15T13:21:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.5.3'
Update to upstream version '0.5.3'
with Debian dir 85b957ae7db66009d6c6da7eb6622963e0f4a136</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-skbio/commit/a2c9323d7136d462ca2dfa0df0dceb8ffd345c67">a2c9323d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-15T13:21:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-skbio/commit/c38b8710d6016d22c4594da2cd8489de08fbf15d">c38b8710</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-15T13:23:05Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-skbio/commit/f2418d0e0d131c4475d3f3add2f66bbe4845af84">f2418d0e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-15T13:54:34Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TODO: Needs python-hdmedians (to be packaged)
</pre>
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</ul>
<h4>28 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
</li>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
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<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
</a>
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<li class="file-stats">
<a href="#bf054b5dcafe76150d61bd77b80dd5f78820f29b">
ci/conda_requirements.txt
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<li class="file-stats">
<a href="#9fdcaf73b1f763ac7ebbb1cba65d271a7a85ef1a">
ci/pip_requirements.txt
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#4f527af5768c903b0fd5e66c83e25933c74fb224">
skbio/__init__.py
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<li class="file-stats">
<a href="#905caf0653314085d45d94634453b9fed271a8c1">
skbio/alignment/_pairwise.py
</a>
</li>
<li class="file-stats">
<a href="#c8cc8ad89bf0b0d3a634a080b2d4e0236c22c483">
skbio/diversity/_driver.py
</a>
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<li class="file-stats">
<a href="#2242175f94a5a2535849d71a0057afc39239d3b7">
skbio/diversity/_util.py
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<li class="file-stats">
<a href="#13cfb6120d51bb91f87288419de46a83fa40038d">
skbio/diversity/tests/test_util.py
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<li class="file-stats">
<a href="#eae4061f7de8aaf0ffe9fd328f82de1c62902cb1">
skbio/sequence/_grammared_sequence.py
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</li>
<li class="file-stats">
<a href="#a59a9d1ab6bbba363c9698a0f71d3020c3f04047">
skbio/stats/distance/__init__.py
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</li>
<li class="file-stats">
<a href="#6af027337d1b8e66276080d902cd559c57f4a659">
<span class="new-file">
+
skbio/stats/distance/_permdisp.py
</span>
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</li>
<li class="file-stats">
<a href="#ef4275ae7de7706dd2c3878d73aee7e936e46919">
<span class="new-file">
+
skbio/stats/distance/tests/data/moving_pictures_dm.tsv
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<li class="file-stats">
<a href="#cd334a9b00d16d3902ce297b0e3408297fa3af47">
<span class="new-file">
+
skbio/stats/distance/tests/data/moving_pictures_mf.tsv
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<li class="file-stats">
<a href="#60237a6af2901ba246b18ffc0b77db80f4610bfc">
<span class="new-file">
+
skbio/stats/distance/tests/test_permdisp.py
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</a>
</li>
<li class="file-stats">
<a href="#c6f587411e1fff773305a7254f17b301583ab8f7">
skbio/stats/ordination/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#66926f23fc6267a8a45ee0bcb544d4b6d8c78ff5">
skbio/stats/ordination/_canonical_correspondence_analysis.py
</a>
</li>
<li class="file-stats">
<a href="#c443397cd3ce71f204a6fa99ac24c98e5fcc8b14">
skbio/stats/ordination/_principal_coordinate_analysis.py
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</li>
<li class="file-stats">
<a href="#fba3bc091de94548d66122df70f408a9d18123c3">
<span class="new-file">
+
skbio/stats/ordination/tests/data/PCoA_biplot_descriptors
</span>
</a>
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<li class="file-stats">
<a href="#2752c1709b6065d169fa47e68bfd66812ca32a7b">
<span class="new-file">
+
skbio/stats/ordination/tests/data/PCoA_biplot_projected_descriptors
</span>
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<li class="file-stats">
<a href="#7605e4425f331c3f7f78961a9541055d29a4b74d">
<span class="new-file">
+
skbio/stats/ordination/tests/data/PCoA_skbio
</span>
</a>
</li>
<li class="file-stats">
<a href="#125936fde92c0e77b23cf33bdd140af1c8be8e27">
skbio/stats/ordination/tests/test_principal_coordinate_analysis.py
</a>
</li>
<li class="file-stats">
<a href="#4ed31e9f5a84645db24d6d19dc646a3259d8471f">
skbio/tree/_tree.py
</a>
</li>
<li class="file-stats">
<a href="#2fb7dcc827f95572c1c47da26ace6f71c45adcf1">
skbio/tree/tests/test_tree.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Check on http://lint.travis-ci.org/ after modifying it! Originally</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># modified from https://gist.github.com/dan-blanchard/7045057</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: teal;">sudo</span><span class="pi">:</span> <span class="no" style="color: teal;">false</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"><span class="na" style="color: teal;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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4
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="na" style="color: teal;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">c</span></span>
</pre>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="na" style="color: teal;">os</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">osx</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"><span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;"><span class="idiff left right">PYTHON_VERSION</span>=3.6 MAKE_DOC=TRUE</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;"><span class="idiff left right">PYTHON_VERSION=3.5 MAKE_DOC</span>=TRUE</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"><span class="idiff left"> </span><span class="pi"><span class="idiff">-</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">PYTHON_VERSION=3.4 USE_CYTHON=TRUE</span></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;"><span class="idiff left right">CONDA_PY</span>=3.6 MAKE_DOC=TRUE</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;"><span class="idiff left right">CONDA_PY=3.5 MAKE_DOC=TRUE USE_CYTHON</span>=TRUE</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"><span class="na" style="color: teal;">before_install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">export</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">DISPLAY=:99.0"</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">sh</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">-e</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">/etc/init.d/xvfb</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">start"</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://repo.continuum.io/miniconda/Miniconda3-3.7.3-Linux-x86_64.sh -O miniconda.sh</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">chmod +x miniconda.sh</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">./miniconda.sh -b</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH=/home/travis/miniconda3/bin:$PATH</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; fi</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh; fi</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bash miniconda.sh -b -p $HOME/miniconda</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$HOME/miniconda/bin:$PATH"</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">hash -r</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Update conda itself</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda update --yes conda</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"><span class="na" style="color: teal;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda create --yes -n env_name python=$<span class="idiff left right">PYTHON_VERSION</span></span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda create --yes -n env_name python=$<span class="idiff left right">CONDA_PY</span></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda install --yes -n env_name --file ci/conda_requirements.txt</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ ${USE_CYTHON} ]; then conda install --yes -n env_name cython; fi</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">source activate env_name</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,11 +27,14 @@ install:</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python --version</span></span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install -r ci/pip_requirements.txt</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install . --no-deps</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml"><span class="na" style="color: teal;">script</span><span class="pi">:</span></span>
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">WITH_COVERAGE=TRUE make test</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ ${MAKE_DOC} ]; then make -C doc clean html; fi</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="yaml"><span class="na" style="color: teal;">after_success</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">coveralls</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="yaml"><span class="na" style="color: teal;">notifications</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="yaml"> <span class="na" style="color: teal;">webhooks</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="yaml"> <span class="na" style="color: teal;">urls</span><span class="pi">:</span></span>
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<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># scikit-bio changelog</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 0.5.3 (2018-08-07)</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Features</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">*</span> Added <span class="sb" style="color: #d14;">`unpack`</span> and <span class="sb" style="color: #d14;">`unpack_by_func`</span> to <span class="sb" style="color: #d14;">`skbio.tree.TreeNode`</span> to unpack one or multiple internal nodes. The "unpack" operation removes an internal node and regrafts its children to its parent while retaining the overall length.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">*</span> Added <span class="sb" style="color: #d14;">`support`</span> to <span class="sb" style="color: #d14;">`skbio.tree.TreeNode`</span> to return the support value of a node.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">*</span> Added <span class="sb" style="color: #d14;">`permdisp`</span> to <span class="sb" style="color: #d14;">`skbio.stats.distance`</span> to test for the homogeniety of groups. (<span class="p">[</span><span class="nv" style="color: teal;">#1228</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/scikit-bio/issues/1228</span><span class="p">)</span>).</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p">*</span> Added <span class="sb" style="color: #d14;">`pcoa_biplot`</span> to <span class="sb" style="color: #d14;">`skbio.stats.ordination`</span> to project descriptors into a PCoA plot.</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p">*</span> Fixed pandas to 0.22.0 due to this: https://github.com/pandas-dev/pandas/issues/20527</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Backward-incompatible changes [stable]</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Backward-incompatible changes [experimental]</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Performance enhancements</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug fixes</span></span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"></span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p">*</span> Relaxing type checking in diversity calculations. (<span class="p">[</span><span class="nv" style="color: teal;">#1583</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/scikit-bio/issues/1583</span><span class="p">)</span>).</span>
</pre>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"></span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Deprecated functionality [stable]</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Deprecated functionality [experimental]</span></span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"></span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Miscellaneous</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"></span>
</pre>
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3
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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 0.5.2 (2018-04-18)</span></span>
</pre>
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4
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Features</span></span>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> :target: http://scikit-bio.org</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> :alt: scikit-bio logo</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">|Build Status| |Coverage Status| |ASV Benchmarks| |Gitter Badge| |Depsy Badge| |Anaconda <span class="idiff left right">Cloud Build| |Anaconda Cloud</span>| |License| |Downloads| |Install|</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">|Build Status| |Coverage Status| |ASV Benchmarks| |Gitter Badge| |Depsy Badge| |Anaconda <span class="idiff left right">Build Platforms| |Anaconda Build Version</span>| |License| |Downloads| |Install|</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext"> :target: https://gitter.im/biocore/scikit-bio?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext">.. |Depsy Badge| image:: http://depsy.org/api/package/pypi/scikit-bio/badge.svg</span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"> :target: http://depsy.org/package/python/scikit-bio</span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext">.. |Anaconda <span class="idiff left right">Cloud Build| image:: https://anaconda.org/conda-forge/scikit-bio/badges/build</span>.svg</span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext"> :target: https://anaconda.org/<span class="idiff left right">biocore/scikit-bio/builds</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext">.. |Anaconda <span class="idiff left right">Cloud</span>| image:: https://anaconda.org/conda-forge/scikit-bio/badges/version.svg</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">.. |Anaconda <span class="idiff left right">Build Platforms| image:: https://anaconda.org/conda-forge/scikit-bio/badges/platforms</span>.svg</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> :target: https://anaconda.org/<span class="idiff left right">conda-forge/scikit-bio</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">.. |Anaconda <span class="idiff left right">Build Version</span>| image:: https://anaconda.org/conda-forge/scikit-bio/badges/version.svg</span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="plaintext"> :target: https://anaconda.org/conda-forge/scikit-bio</span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext">.. |License| image:: https://anaconda.org/conda-forge/scikit-bio/badges/license.svg</span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext"> :target: https://anaconda.org/conda-forge/scikit-bio</span>
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<li id="bf054b5dcafe76150d61bd77b80dd5f78820f29b">
<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#bf054b5dcafe76150d61bd77b80dd5f78820f29b"><strong>ci/conda_requirements.txt</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@ pip</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">numpy<1.14.0</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">scipy</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">matplotlib</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">pandas</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">pandas<span class="idiff left right"><0.23.0</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">nose</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">pep8</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">ipython</span>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#9fdcaf73b1f763ac7ebbb1cba65d271a7a85ef1a"><strong>ci/pip_requirements.txt</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,3 +7,4 @@ Sphinx</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">sphinx-bootstrap-theme</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">numpydoc < 0.8.0</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">check-manifest</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">hdmedians</span></pre>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-skbio (0.5.3-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.2.0</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> TODO: Needs python-hdmedians (to be packaged)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 15 Aug 2018 15:21:02 +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">python-skbio (0.5.2-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +27,7 @@ Build-Depends: debhelper (>= 11~),</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> python3-sphinx,</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> python3-sphinx-bootstrap-theme,</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> libssw-dev</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.4</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.0</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-skbio</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-skbio.git</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Homepage: https://github.com/biocore/scikit-bio</span>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -120,9 +120,10 @@ setup(name='scikit-bio',</td>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># a numpy 1.14.0 conda package on `defaults` or `conda-forge`</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># channels.</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="s" style="color: #d14;">'numpy >= 1.9.2, < 1.14.0'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="s" style="color: #d14;">'pandas >= 0.19.2'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="s" style="color: #d14;">'pandas >= 0.19.2<span class="idiff left right">, < 0.23.0</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <span class="s" style="color: #d14;">'scipy >= 0.15.1'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">'nose >= 1.3.7'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="s" style="color: #d14;">'hdmedians >= 0.13'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="s" style="color: #d14;">'scikit-learn >= 0.19.1'</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">test_suite</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'nose.collector'</span><span class="p">,</span></span>
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<li id="4f527af5768c903b0fd5e66c83e25933c74fb224">
<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#4f527af5768c903b0fd5e66c83e25933c74fb224"><strong>skbio/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,7 +26,7 @@ __all__ = ['Sequence', 'DNA', 'RNA', 'Protein', 'GeneticCode',</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'TreeNode'</span><span class="p">,</span> <span class="s" style="color: #d14;">'nj'</span><span class="p">,</span> <span class="s" style="color: #d14;">'read'</span><span class="p">,</span> <span class="s" style="color: #d14;">'write'</span><span class="p">,</span> <span class="s" style="color: #d14;">'OrdinationResults'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="n" style="color: #333;">__credits__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"https://github.com/biocore/scikit-bio/graphs/contributors"</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.5.<span class="idiff left right">2</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.5.<span class="idiff left right">3</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="n" style="color: #333;">mottos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># 03/15/2014</span></span>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#905caf0653314085d45d94634453b9fed271a8c1"><strong>skbio/alignment/_pairwise.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -735,7 +735,7 @@ def local_pairwise_align_ssw(sequence1, sequence2, **kwargs):</td>
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">msa</span><span class="p">,</span> <span class="n" style="color: #333;">alignment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimal_alignment_score</span><span class="p">,</span> <span class="n" style="color: #333;">start_end</span></span>
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC738" class="line" lang="python"><span class="nd">@deprecated</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.4.0"</span><span class="p">,</span> <span class="n" style="color: #333;">until</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.5.<span class="idiff left right">3</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="python"><span class="nd">@deprecated</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.4.0"</span><span class="p">,</span> <span class="n" style="color: #333;">until</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.5.<span class="idiff left right">4</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="python"> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Will be replaced by a SubstitutionMatrix class. To track "</span></span>
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="python"> <span class="s" style="color: #d14;">"progress, see [#161]"</span></span>
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741
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="python"> <span class="s" style="color: #d14;">"(https://github.com/biocore/scikit-bio/issues/161)."</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#c8cc8ad89bf0b0d3a634a080b2d4e0236c22c483"><strong>skbio/diversity/_driver.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -182,7 +182,7 @@ def alpha_diversity(metric, counts, ids=None, validate=True, **kwargs):</td>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Series</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"><span class="nd">@deprecated</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.5.0'</span><span class="p">,</span> <span class="n" style="color: #333;">until</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.<span class="idiff left right">5.3</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"><span class="nd">@deprecated</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.5.0'</span><span class="p">,</span> <span class="n" style="color: #333;">until</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.<span class="idiff left right">6.0</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'The return type is unstable. Developer caution is '</span></span>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"> <span class="s" style="color: #d14;">'advised. The resulting DistanceMatrix object will '</span></span>
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="s" style="color: #d14;">'include zeros when distance has not been calculated, and '</span></span>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#2242175f94a5a2535849d71a0057afc39239d3b7"><strong>skbio/diversity/_util.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,10 +21,8 @@ def _validate_counts_vector(counts, suppress_cast=False):</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">asarray</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">suppress_cast</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">counts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">casting</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'safe'</span><span class="p">,</span> <span class="n" style="color: #333;">copy</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isreal</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Counts vector must contain real-valued entries."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">counts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ndim</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Only 1-D vectors are supported."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="p">(</span><span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">any</span><span class="p">():</span></span>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#13cfb6120d51bb91f87288419de46a83fa40038d"><strong>skbio/diversity/tests/test_util.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,9 +57,6 @@ class ValidationTests(TestCase):</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dtype</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_validate_counts_vector_invalid_input</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># wrong dtype</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">TypeError</span><span class="p">):</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">_validate_counts_vector</span><span class="p">([</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mf" style="color: #099;">1.2</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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63
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"></span>
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64
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># wrong number of dimensions (2-D)</span></span>
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65
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,6 +70,10 @@ class ValidationTests(TestCase):</td>
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73
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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74
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">_validate_counts_vector</span><span class="p">([</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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75
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># strings</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">_validate_counts_vector</span><span class="p">([</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'a'</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_validate_counts_matrix</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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77
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># basic valid input (n=2)</span></span>
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78
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_validate_counts_matrix</span><span class="p">([[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">],</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -101,8 +102,6 @@ class ValidationTests(TestCase):</td>
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101
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">npt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_array_equal</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mf" style="color: #099;">42.2</span><span class="p">,</span> <span class="mf" style="color: #099;">42.1</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">]))</span></span>
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102
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dtype</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>
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103
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dtype</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">TypeError</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">_validate_counts_matrix</span><span class="p">([[</span><span class="mf" style="color: #099;">0.0</span><span class="p">],</span> <span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]],</span> <span class="n" style="color: #333;">suppress_cast</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"></span>
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107
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_validate_counts_matrix_negative_counts</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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108
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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<li id="eae4061f7de8aaf0ffe9fd328f82de1c62902cb1">
<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#eae4061f7de8aaf0ffe9fd328f82de1c62902cb1"><strong>skbio/sequence/_grammared_sequence.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -281,7 +281,7 @@ class GrammaredSequence(Sequence, metaclass=GrammaredSequenceMeta):</td>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">degenerate_map</span><span class="p">)</span></span>
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"> <span class="nd">@classproperty</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"> <span class="nd">@deprecated</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.5.0'</span><span class="p">,</span> <span class="n" style="color: #333;">until</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.<span class="idiff left right">5.3</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="nd">@deprecated</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.5.0'</span><span class="p">,</span> <span class="n" style="color: #333;">until</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.<span class="idiff left right">6.0</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Renamed to definite_chars'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">nondegenerate_chars</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return non-degenerate characters.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -492,7 +492,7 @@ class GrammaredSequence(Sequence, metaclass=GrammaredSequenceMeta):</td>
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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493
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493
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">in1d</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_bytes</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_definite_char_codes</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="python"> <span class="nd">@deprecated</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.5.0'</span><span class="p">,</span> <span class="n" style="color: #333;">until</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.<span class="idiff left right">5.3</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python"> <span class="nd">@deprecated</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.5.0'</span><span class="p">,</span> <span class="n" style="color: #333;">until</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.<span class="idiff left right">6.0</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="python"> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Renamed to definites'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">nondegenerates</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="python"> <span class="s" style="color: #d14;">"""Find positions containing non-degenerate characters in the sequence.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -548,7 +548,7 @@ class GrammaredSequence(Sequence, metaclass=GrammaredSequenceMeta):</td>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># TODO: cache results</span></span>
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">definites</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">any</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="python"> <span class="nd">@deprecated</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.5.0'</span><span class="p">,</span> <span class="n" style="color: #333;">until</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.<span class="idiff left right">5.3</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python"> <span class="nd">@deprecated</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.5.0'</span><span class="p">,</span> <span class="n" style="color: #333;">until</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'0.<span class="idiff left right">6.0</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Renamed to has_definites'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">has_nondegenerates</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="python"> <span class="s" style="color: #d14;">"""Determine if sequence contains one or more non-degenerate characters</span></span>
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<li id="a59a9d1ab6bbba363c9698a0f71d3020c3f04047">
<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#a59a9d1ab6bbba363c9698a0f71d3020c3f04047"><strong>skbio/stats/distance/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -154,6 +154,7 @@ Categorical Variable Stats</td>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"><span class="s" style="color: #d14;"> anosim</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"><span class="s" style="color: #d14;"> permanova</span></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"><span class="s" style="color: #d14;"> permdisp</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"><span class="s" style="color: #d14;">Continuous Variable Stats</span></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"><span class="s" style="color: #d14;">^^^^^^^^^^^^^^^^^^^^^^^^^</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -196,9 +197,10 @@ from ._bioenv import bioenv</td>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._anosim</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">anosim</span></span>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._permanova</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">permanova</span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._mantel</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">mantel</span><span class="p">,</span> <span class="n" style="color: #333;">pwmantel</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._permdisp</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">permdisp</span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'DissimilarityMatrixError'</span><span class="p">,</span> <span class="s" style="color: #d14;">'DistanceMatrixError'</span><span class="p">,</span> <span class="s" style="color: #d14;">'MissingIDError'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="s" style="color: #d14;">'DissimilarityMatrix'</span><span class="p">,</span> <span class="s" style="color: #d14;">'DistanceMatrix'</span><span class="p">,</span> <span class="s" style="color: #d14;">'randdm'</span><span class="p">,</span> <span class="s" style="color: #d14;">'anosim'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="s" style="color: #d14;">'permanova'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bioenv'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mantel'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pwmantel'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="s" style="color: #d14;">'permanova'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bioenv'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mantel'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pwmantel'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'permdisp'</span></span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"><span class="n" style="color: #333;">test</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TestRunner</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">test</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#6af027337d1b8e66276080d902cd559c57f4a659"><strong>skbio/stats/distance/_permdisp.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Copyright (c) 2013--, scikit-bio development team.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># The full license is in the file COPYING.txt, distributed with this software.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">functools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">partial</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">scipy.stats</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">f_oneway</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">scipy.spatial.distance</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">cdist</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">hdmedians</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">hd</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._base</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">_preprocess_input</span><span class="p">,</span> <span class="n" style="color: #333;">_run_monte_carlo_stats</span><span class="p">,</span> <span class="n" style="color: #333;">_build_results</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">skbio.stats.ordination</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pcoa</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">skbio.util._decorator</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">experimental</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="nd">@experimental</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.5.2"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">permdisp</span><span class="p">(</span><span class="n" style="color: #333;">distance_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">grouping</span><span class="p">,</span> <span class="n" style="color: #333;">column</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">test</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'median'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">permutations</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">999</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test for Homogeneity of Multivariate Groups Disperisons using Marti</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="s" style="color: #d14;"> Anderson's PERMDISP2 procedure.</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;"> PERMDISP is a multivariate analogue of Levene's test for homogeneity of</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;"> multivariate variances. Distances are handled by reducing the</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;"> original distances to principal coordinates. PERMDISP calculates an</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;"> F-statistic to assess whether the dispersions between groups is significant</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;"> distance_matrix : DistanceMatrix</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;"> Distance matrix containing distances between objects (e.g., distances</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;"> between samples of microbial communities).</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;"> grouping : 1-D array_like or pandas.DataFrame</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;"> Vector indicating the assignment of objects to groups. For example,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;"> these could be strings or integers denoting which group an object</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;"> belongs to. If `grouping` is 1-D ``array_like``, it must be the same</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;"> length and in the same order as the objects in `distance_matrix`. If</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;"> `grouping` is a ``DataFrame``, the column specified by `column` will be</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="s" style="color: #d14;"> used as the grouping vector. The ``DataFrame`` must be indexed by the</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;"> IDs in `distance_matrix` (i.e., the row labels must be distance matrix</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="s" style="color: #d14;"> IDs), but the order of IDs between `distance_matrix` and the</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;"> ``DataFrame`` need not be the same. All IDs in the distance matrix must</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;"> be present in the ``DataFrame``. Extra IDs in the ``DataFrame`` are</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;"> allowed (they are ignored in the calculations).</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;"> column : str, optional</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;"> Column name to use as the grouping vector if `grouping` is a</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;"> ``DataFrame``. Must be provided if `grouping` is a ``DataFrame``.</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="s" style="color: #d14;"> Cannot be provided if `grouping` is 1-D ``array_like``.</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="s" style="color: #d14;"> test : {'centroid', 'median'}</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;"> determines whether the analysis is done using centroid or spaitial</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;"> median.</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="s" style="color: #d14;"> permutations : int, optional</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;"> Number of permutations to use when assessing statistical</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;"> significance. Must be greater than or equal to zero. If zero,</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"><span class="s" style="color: #d14;"> statistical significance calculations will be skipped and the p-value</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;"> will be ``np.nan``.</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"><span class="s" style="color: #d14;"> Returns</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"><span class="s" style="color: #d14;"> -------</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;"> pandas.Series</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"><span class="s" style="color: #d14;"> Results of the statistical test, including ``test statistic`` and</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"><span class="s" style="color: #d14;"> ``p-value``.</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"><span class="s" style="color: #d14;"> Raises</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"><span class="s" style="color: #d14;"> ------</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"><span class="s" style="color: #d14;"> TypeError</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"><span class="s" style="color: #d14;"> If, when using the spatial median test, the pcoa ordination is not of</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"><span class="s" style="color: #d14;"> type np.float32 or np.float64, the spatial median function will fail</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"><span class="s" style="color: #d14;"> and the centroid test should be used instead</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"><span class="s" style="color: #d14;"> ValueError</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"><span class="s" style="color: #d14;"> If the test is not centroid or median.</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"><span class="s" style="color: #d14;"> TypeError</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;"> If the distance matrix is not an instance of a</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"><span class="s" style="color: #d14;"> ``skbio.DistanceMatrix``.</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"><span class="s" style="color: #d14;"> ValueError</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"><span class="s" style="color: #d14;"> If there is only one group</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;"> ValueError</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"><span class="s" style="color: #d14;"> If a list and a column name are both provided</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"><span class="s" style="color: #d14;"> ValueError</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"><span class="s" style="color: #d14;"> If a list is provided for `grouping` and it's length does not match</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"><span class="s" style="color: #d14;"> the number of ids in distance_matrix</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"><span class="s" style="color: #d14;"> ValueError</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;"> If all of the values in the grouping vector are unique</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"><span class="s" style="color: #d14;"> KeyError</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;"> If there are ids in grouping that are not in distance_matrix</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;"> See Also</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"><span class="s" style="color: #d14;"> --------</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;"> permanova</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"><span class="s" style="color: #d14;"> anosim</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"><span class="s" style="color: #d14;"> Notes</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;"> -----</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"><span class="s" style="color: #d14;"> The significance of the results from this function will be the same as the</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;"> results found in vegan's betadisper, however due to floating point</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"><span class="s" style="color: #d14;"> variability the F-statistic results may vary slightly.</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;"> See [1]_ for the original method reference, as well as</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;"> ``vegan::betadisper``, available in R's vegan package [2]_.</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"><span class="s" style="color: #d14;"> References</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"><span class="s" style="color: #d14;"> .. [1] Anderson, Marti J. "Distance-Based Tests for Homogeneity of</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"><span class="s" style="color: #d14;"> Multivariate Dispersions." Biometrics 62 (2006):245-253</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"><span class="s" style="color: #d14;"> .. [2] http://cran.r-project.org/web/packages/vegan/index.html</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"><span class="s" style="color: #d14;"> Examples</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"><span class="s" style="color: #d14;"> --------</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"><span class="s" style="color: #d14;"> Load a 6x6 distance matrix and grouping vector denoting 2 groups of</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"><span class="s" style="color: #d14;"> objects:</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"><span class="s" style="color: #d14;"> >>> from skbio import DistanceMatrix</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"><span class="s" style="color: #d14;"> >>> dm = DistanceMatrix([[0, 0.5, 0.75, 1, 0.66, 0.33],</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"><span class="s" style="color: #d14;"> ... [0.5, 0, 0.25, 0.33, 0.77, 0.61],</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"><span class="s" style="color: #d14;"> ... [0.75, 0.25, 0, 0.1, 0.44, 0.55],</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"><span class="s" style="color: #d14;"> ... [1, 0.33, 0.1, 0, 0.75, 0.88],</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"><span class="s" style="color: #d14;"> ... [0.66, 0.77, 0.44, 0.75, 0, 0.77],</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"><span class="s" style="color: #d14;"> ... [0.33, 0.61, 0.55, 0.88, 0.77, 0]],</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"><span class="s" style="color: #d14;"> ... ['s1', 's2', 's3', 's4', 's5', 's6'])</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"><span class="s" style="color: #d14;"> >>> grouping = ['G1', 'G1', 'G1', 'G2', 'G2', 'G2']</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"><span class="s" style="color: #d14;"> Run PERMDISP using 99 permutations to caluculate the p-value:</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"><span class="s" style="color: #d14;"> >>> from skbio.stats.distance import permdisp</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"><span class="s" style="color: #d14;"> >>> import numpy as np</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"><span class="s" style="color: #d14;"> >>> #make output deterministic, should not be included during normal use</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"><span class="s" style="color: #d14;"> >>> np.random.seed(0)</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"><span class="s" style="color: #d14;"> >>> permdisp(dm, grouping, permutations=99)</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"><span class="s" style="color: #d14;"> method name PERMDISP</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"><span class="s" style="color: #d14;"> test statistic name F-value</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"><span class="s" style="color: #d14;"> sample size 6</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"><span class="s" style="color: #d14;"> number of groups 2</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"><span class="s" style="color: #d14;"> test statistic 1.03296</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"><span class="s" style="color: #d14;"> p-value 0.35</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"><span class="s" style="color: #d14;"> number of permutations 99</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"><span class="s" style="color: #d14;"> Name: PERMDISP results, dtype: object</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"><span class="s" style="color: #d14;"> The return value is a ``pandas.Series`` object containing the results of</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"><span class="s" style="color: #d14;"> the statistical test.</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;"> To suppress calculation of the p-value and only obtain the F statistic,</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"><span class="s" style="color: #d14;"> specify zero permutations:</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"><span class="s" style="color: #d14;"> >>> permdisp(dm, grouping, permutations=0)</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"><span class="s" style="color: #d14;"> method name PERMDISP</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"><span class="s" style="color: #d14;"> test statistic name F-value</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"><span class="s" style="color: #d14;"> sample size 6</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"><span class="s" style="color: #d14;"> number of groups 2</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"><span class="s" style="color: #d14;"> test statistic 1.03296</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"><span class="s" style="color: #d14;"> p-value NaN</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"><span class="s" style="color: #d14;"> number of permutations 0</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"><span class="s" style="color: #d14;"> Name: PERMDISP results, dtype: object</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"><span class="s" style="color: #d14;"> PERMDISP computes variances based on two types of tests, using either</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"><span class="s" style="color: #d14;"> centroids or spatial medians, also commonly referred to as a geometric</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"><span class="s" style="color: #d14;"> median. The spatial median is thought to yield a more robust test</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"><span class="s" style="color: #d14;"> statistic, and this test is used by default. Spatial medians are computed</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"><span class="s" style="color: #d14;"> using an iterative algorithm to find the optimally minimum point from all</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"><span class="s" style="color: #d14;"> other points in a group while centroids are computed using a deterministic</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"><span class="s" style="color: #d14;"> formula. As such the two different tests yeild slightly different F</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"><span class="s" style="color: #d14;"> statistics.</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"><span class="s" style="color: #d14;"> >>> np.random.seed(0)</span></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"><span class="s" style="color: #d14;"> >>> permdisp(dm, grouping, test='centroid', permutations=99)</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"><span class="s" style="color: #d14;"> method name PERMDISP</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"><span class="s" style="color: #d14;"> test statistic name F-value</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"><span class="s" style="color: #d14;"> sample size 6</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"><span class="s" style="color: #d14;"> number of groups 2</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"><span class="s" style="color: #d14;"> test statistic 3.67082</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"><span class="s" style="color: #d14;"> p-value 0.29</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"><span class="s" style="color: #d14;"> number of permutations 99</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"><span class="s" style="color: #d14;"> Name: PERMDISP results, dtype: object</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"><span class="s" style="color: #d14;"> You can also provide a ``pandas.DataFrame`` and a column denoting the</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"><span class="s" style="color: #d14;"> grouping instead of a grouping vector. The following DataFrame's</span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"><span class="s" style="color: #d14;"> Grouping column specifies the same grouping as the vector we used in the</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"><span class="s" style="color: #d14;"> previous examples.:</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"><span class="s" style="color: #d14;"> >>> import pandas as pd</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"><span class="s" style="color: #d14;"> >>> df = pd.DataFrame.from_dict(</span></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"><span class="s" style="color: #d14;"> ... {'Grouping': {'s1': 'G1', 's2': 'G1', 's3': 'G1', 's4': 'G2',</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"><span class="s" style="color: #d14;"> ... 's5': 'G2', 's6': 'G2'}})</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"><span class="s" style="color: #d14;"> >>> # make output deterministic; should not be included during normal use</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"><span class="s" style="color: #d14;"> >>> np.random.seed(0)</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"><span class="s" style="color: #d14;"> >>> permdisp(dm, df, 'Grouping', permutations=99, test='centroid')</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"><span class="s" style="color: #d14;"> method name PERMDISP</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"><span class="s" style="color: #d14;"> test statistic name F-value</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"><span class="s" style="color: #d14;"> sample size 6</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"><span class="s" style="color: #d14;"> number of groups 2</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"><span class="s" style="color: #d14;"> test statistic 3.67082</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"><span class="s" style="color: #d14;"> p-value 0.29</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"><span class="s" style="color: #d14;"> number of permutations 99</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"><span class="s" style="color: #d14;"> Name: PERMDISP results, dtype: object</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"><span class="s" style="color: #d14;"> Note that when providing a ``DataFrame``, the ordering of rows and/or</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"><span class="s" style="color: #d14;"> columns does not affect the grouping vector that is extracted. The</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"><span class="s" style="color: #d14;"> ``DataFrame`` must be indexed by the distance matrix IDs (i.e., the row</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"><span class="s" style="color: #d14;"> labels must be distance matrix IDs).</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"><span class="s" style="color: #d14;"> If IDs (rows) are present in the ``DataFrame`` but not in the distance</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"><span class="s" style="color: #d14;"> matrix, they are ignored. The previous example's ``s7`` ID illustrates this</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"><span class="s" style="color: #d14;"> behavior: note that even though the ``DataFrame`` had 7 objects, only 6</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"><span class="s" style="color: #d14;"> were used in the test (see the "Sample size" row in the results above to</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"><span class="s" style="color: #d14;"> confirm this). Thus, the ``DataFrame`` can be a superset of the distance</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"><span class="s" style="color: #d14;"> matrix IDs. Note that the reverse is not true: IDs in the distance matrix</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"><span class="s" style="color: #d14;"> *must* be present in the ``DataFrame`` or an error will be raised.</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;"> PERMDISP should be used to determine whether the dispersions between the</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"><span class="s" style="color: #d14;"> groups in your distance matrix are significantly separated.</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"><span class="s" style="color: #d14;"> A non-significant test result indicates that group dispersions are similar</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"><span class="s" style="color: #d14;"> to each other. PERMANOVA or ANOSIM should then be used in conjunction to</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"><span class="s" style="color: #d14;"> determine whether clustering within groups is significant.</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">test</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'centroid'</span><span class="p">,</span> <span class="s" style="color: #d14;">'median'</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">'Test must be centroid or median'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">ordination</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pcoa</span><span class="p">(</span><span class="n" style="color: #333;">distance_matrix</span><span class="p">)</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ordination</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">sample_size</span><span class="p">,</span> <span class="n" style="color: #333;">num_groups</span><span class="p">,</span> <span class="n" style="color: #333;">grouping</span><span class="p">,</span> <span class="n" style="color: #333;">tri_idxs</span><span class="p">,</span> <span class="n" style="color: #333;">distances</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_preprocess_input</span><span class="p">(</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">distance_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">grouping</span><span class="p">,</span> <span class="n" style="color: #333;">column</span><span class="p">)</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">test_stat_function</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">_compute_groups</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">,</span> <span class="n" style="color: #333;">test</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="n" style="color: #333;">p_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_run_monte_carlo_stats</span><span class="p">(</span><span class="n" style="color: #333;">test_stat_function</span><span class="p">,</span> <span class="n" style="color: #333;">grouping</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">permutations</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_build_results</span><span class="p">(</span><span class="s" style="color: #d14;">'PERMDISP'</span><span class="p">,</span> <span class="s" style="color: #d14;">'F-value'</span><span class="p">,</span> <span class="n" style="color: #333;">sample_size</span><span class="p">,</span> <span class="n" style="color: #333;">num_groups</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="n" style="color: #333;">p_value</span><span class="p">,</span> <span class="n" style="color: #333;">permutations</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_compute_groups</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">,</span> <span class="n" style="color: #333;">test_type</span><span class="p">,</span> <span class="n" style="color: #333;">grouping</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">samples</span><span class="p">[</span><span class="s" style="color: #d14;">'grouping'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">grouping</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">test_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'centroid'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">centroids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">'grouping'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aggregate</span><span class="p">(</span><span class="s" style="color: #d14;">'mean'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">test_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'median'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">centroids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">'grouping'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aggregate</span><span class="p">(</span><span class="n" style="color: #333;">_config_med</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="n" style="color: #333;">df</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">'grouping'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">cdist</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">[:,</span> <span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="p">[</span><span class="n" style="color: #333;">centroids</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">label</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">metric</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'euclidean'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f_oneway</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">stat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">stat</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_config_med</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"><span class="s" style="color: #d14;"> slice the vector up to the last value to exclude grouping column</span></span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"><span class="s" style="color: #d14;"> and transpose the vector to be compatible with hd.geomedian</span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">X</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">[:,</span> <span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">hd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">geomedian</span><span class="p">(</span><span class="n" style="color: #333;">X</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">T</span><span class="p">))</span></span></pre>
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<li id="ef4275ae7de7706dd2c3878d73aee7e936e46919">
<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#ef4275ae7de7706dd2c3878d73aee7e936e46919"><strong>skbio/stats/distance/tests/data/moving_pictures_dm.tsv</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"> L1S105 L1S140 L1S208 L1S257 L1S281 L1S57 L1S76 L1S8 L2S155 L2S175 L2S204 L2S222 L2S240 L2S309 L2S357 L2S382 L3S294 L3S313 L3S341 L3S360 L3S378 L4S112 L4S137 L4S63 L5S104 L5S155 L5S174 L5S203 L5S222 L5S240 L6S20 L6S68 L6S93</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">L1S105 0.0 0.5390370298457626 0.5958380256061412 0.5768343811669847 0.5923046539353664 0.44786237128294343 0.39489596582130626 0.5545584734774127 0.8628589351714164 0.8434498336351259 0.8592370856547886 0.8506877032999233 0.7889826076831608 0.8359411856255106 0.8200856211804968 0.8426252468809847 0.8588300792888636 0.7569476110839489 0.7737531468949157 0.8944159171736104 0.6033584308249973 0.8470795512030315 0.821242904747876 0.8652874911410461 0.7549182333398126 0.7223305078861331 0.7614916771466183 0.7384823167933402 0.7685949288454377 0.7217074962665071 0.7245343115615573 0.7830441925323288 0.7712136041691006</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">L1S140 0.5390370298457626 0.0 0.5799280564700269 0.5498337267462643 0.5487499420209432 0.5617578336407074 0.5274803712970444 0.5842935186320399 0.8425845430236847 0.7832827608957819 0.832335123190656 0.83707961792672 0.7311087382394217 0.7969572429804197 0.74931933992796 0.791784337383268 0.7891927506641839 0.6721331780898249 0.7493321619468443 0.8773425730913526 0.3943371737754427 0.8380071824429106 0.7797415033649835 0.8604626784828243 0.7389385379102201 0.713927118153038 0.7409814677579339 0.6893827188871452 0.739005471405395 0.7134211109446568 0.7210216228178491 0.7548606893628177 0.75650714031249</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">L1S208 0.5958380256061412 0.5799280564700269 0.0 0.3514478448812178 0.3099429863936709 0.4908395118886828 0.5060147104062029 0.5921114631534051 0.8899108348691316 0.871025922389371 0.882455510304791 0.8798738374168472 0.8153291321982421 0.8616764262370401 0.8215036618481708 0.8762874977082885 0.8826136551026731 0.8218942402038897 0.8270103157643566 0.8918833194204532 0.5595063305032598 0.8896853519676307 0.8701383470494592 0.9064920956741176 0.8245445313262268 0.7952347925702751 0.8252913142216206 0.7959214036381839 0.8153225533087411 0.7836084181624914 0.791415482862234 0.8107398191951546 0.8044123679011221</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">L1S257 0.5768343811669847 0.5498337267462643 0.3514478448812178 0.0 0.25929060246530955 0.47255177559300116 0.43222880359346527 0.5884066995223238 0.8795468292082718 0.8633179655119932 0.8688146996880899 0.8629186587174017 0.8190468684000036 0.8492352934610714 0.8120267566814204 0.8666693265827448 0.8777562843225813 0.802227485419459 0.8160964503323095 0.8817724113978568 0.5576854601824073 0.8747926182003918 0.858838497674028 0.8925129391873841 0.828703636427477 0.8010491792499632 0.8063815782189153 0.8092051698995067 0.806495056831578 0.8032210970007331 0.7958200880953574 0.8161661389998109 0.8303929119421523</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">L1S281 0.5923046539353664 0.5487499420209432 0.3099429863936709 0.25929060246530955 0.0 0.4609450181065116 0.4768241494226335 0.6336173247999576 0.8985838283907426 0.8902364311520621 0.8972881153423283 0.8878063096662511 0.842173339458122 0.8796280371215733 0.8476576569873849 0.8898292712501708 0.9039077039484619 0.8485533231569067 0.852633569868443 0.9096947429872373 0.5498250250306412 0.9022662022069642 0.8832755726058907 0.9169203743757105 0.8572110146660553 0.833803405339537 0.8394041604332061 0.8290963638641423 0.8384368165385457 0.8247152739488143 0.832089497492543 0.8365271234666928 0.8483699050146564</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">L1S57 0.44786237128294343 0.5617578336407074 0.4908395118886828 0.47255177559300116 0.4609450181065116 0.0 0.31082469034707255 0.5024096303529431 0.9113813328862811 0.9014185555334876 0.9014865706960162 0.8945638042848107 0.8714620677099987 0.8806337056845028 0.8481649374200068 0.9084204945482022 0.913489362275528 0.852617211132442 0.8535720478866394 0.9122868711391121 0.5758415360633006 0.9020100495580599 0.9027332494336695 0.9186219021297435 0.853072903040757 0.8327332298901452 0.8629325424179554 0.838123751985925 0.8659733546560768 0.8346642658091125 0.8289313199906942 0.8703637908123152 0.8629123642673379</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">L1S76 0.39489596582130626 0.5274803712970444 0.5060147104062029 0.43222880359346527 0.4768241494226335 0.31082469034707255 0.0 0.4003824579445799 0.894830907945713 0.8782305450289447 0.8768848673183877 0.8694496317335333 0.834400640278251 0.8645838229241534 0.8020621529524625 0.8821339436331491 0.8821873080715426 0.8108074314407202 0.8071422086314133 0.8931657453933083 0.5741407822604754 0.8800714967479438 0.8737823256177506 0.8981103792379882 0.8193019560519106 0.7921706586389919 0.8200532532128909 0.8020963162128805 0.8249980087726344 0.7949183972892307 0.7923436575946494 0.8310029142646927 0.8322683023877507</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">L1S8 0.5545584734774127 0.5842935186320399 0.5921114631534051 0.5884066995223238 0.6336173247999576 0.5024096303529431 0.4003824579445799 0.0 0.8984532053428095 0.8752689122693623 0.892740827989152 0.8922691853549297 0.8314474877203453 0.8600974905243383 0.8016996748131581 0.8870353495912263 0.8805255216909961 0.7980602019240324 0.829887986255906 0.8798293357284456 0.5576624158659516 0.8948846831679798 0.8816102418936791 0.9112039786090779 0.8148374423400107 0.7791385980867408 0.8123406708143702 0.8036845403456274 0.8182429195392156 0.786233773105675 0.785902469716853 0.8323093879065956 0.8268942255033314</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">L2S155 0.8628589351714164 0.8425845430236847 0.8899108348691316 0.8795468292082718 0.8985838283907426 0.9113813328862811 0.894830907945713 0.8984532053428095 0.0 0.46760603559570263 0.4249569948218847 0.43461957349574365 0.7136184283615585 0.3913207521607729 0.6347075539715223 0.7018474049205657 0.48529937944992957 0.6445967049513042 0.6384694268897185 0.4614095269789821 0.8793414820335794 0.49283220104466596 0.6490593420832039 0.47563246735903575 0.7320469060900457 0.8046481081885503 0.7992253539435805 0.7608659584888517 0.761349180972591 0.8017496796623877 0.7844856344015433 0.7648448360194874 0.7728251640763542</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">L2S175 0.8434498336351259 0.7832827608957819 0.871025922389371 0.8633179655119932 0.8902364311520621 0.9014185555334876 0.8782305450289447 0.8752689122693623 0.46760603559570263 0.0 0.4521351118370733 0.47450759266616915 0.6496968752812166 0.4163459132801876 0.5642253392315422 0.6035203651725982 0.4127343227632307 0.5009839698168453 0.5720541940600513 0.5238301647807445 0.8519601477875526 0.45057960516670714 0.6012619962408408 0.5452699437274425 0.7004211741288418 0.7254489332170817 0.7241658196524235 0.6728749977683892 0.7120770444662118 0.7067601324302817 0.7154192599371452 0.6790044090495644 0.6670904831025087</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">L2S204 0.8592370856547886 0.832335123190656 0.882455510304791 0.8688146996880899 0.8972881153423283 0.9014865706960162 0.8768848673183877 0.892740827989152 0.4249569948218847 0.4521351118370733 0.0 0.34707557932356076 0.7317461021420034 0.32542423370295653 0.5940997497062588 0.7202722055635978 0.46284470929748595 0.6399875240134363 0.5427529698531464 0.41546588368326215 0.8806954039760829 0.3819763193450203 0.6864606389600179 0.4541251117472289 0.7433650255074369 0.8140552153241122 0.8171702240197111 0.7787482342908187 0.7789238492726243 0.8145023991202386 0.797521853405542 0.7823436739920101 0.7825923091798144</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">L2S222 0.8506877032999233 0.83707961792672 0.8798738374168472 0.8629186587174017 0.8878063096662511 0.8945638042848107 0.8694496317335333 0.8922691853549297 0.43461957349574365 0.47450759266616915 0.34707557932356076 0.0 0.7373605415524003 0.38933892308526385 0.6131841736075622 0.7071347655059155 0.5297960404918108 0.6776613871707217 0.614146849517274 0.41910689292075193 0.8807526952301693 0.43694693261646017 0.6992608535946145 0.4512186030792239 0.7657709194380475 0.8264506476297601 0.8235579667989716 0.7929926795664424 0.7900065630791773 0.8272758828816869 0.8177374352486667 0.7787324503994212 0.7937870099703493</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">L2S240 0.7889826076831608 0.7311087382394217 0.8153291321982421 0.8190468684000036 0.842173339458122 0.8714620677099987 0.834400640278251 0.8314474877203453 0.7136184283615585 0.6496968752812166 0.7317461021420034 0.7373605415524003 0.0 0.7032990730427625 0.5742088858732407 0.5358811200052477 0.6113293724148627 0.5506881270264428 0.5515051266923414 0.7398454298135383 0.7579742017535656 0.7115018729258218 0.48083389190461734 0.7661067183222632 0.36560695464990867 0.4412731503394013 0.41030162605879844 0.38926922412434417 0.3758838249617733 0.43476390441875573 0.4013288162093646 0.29292532554452677 0.35832282922330977</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">L2S309 0.8359411856255106 0.7969572429804197 0.8616764262370401 0.8492352934610714 0.8796280371215733 0.8806337056845028 0.8645838229241534 0.8600974905243383 0.3913207521607729 0.4163459132801876 0.32542423370295653 0.38933892308526385 0.7032990730427625 0.0 0.5284516343093534 0.7093129471508985 0.41393505549147774 0.6241411216254367 0.5766719921218544 0.36061963338100667 0.8395112062787546 0.4200940359303599 0.6691543813483889 0.43557544512779306 0.7065436739270591 0.7784024482700062 0.7846395088210678 0.7393917740028452 0.7397915081982174 0.7798934785055419 0.7729246906860544 0.763695527435426 0.7629847033876873</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">L2S357 0.8200856211804968 0.74931933992796 0.8215036618481708 0.8120267566814204 0.8476576569873849 0.8481649374200068 0.8020621529524625 0.8016996748131581 0.6347075539715223 0.5642253392315422 0.5940997497062588 0.6131841736075622 0.5742088858732407 0.5284516343093534 0.0 0.6247944934502809 0.5283785180280727 0.44838682641972477 0.375128958725295 0.6121711834124891 0.8188660070261687 0.5950936496526126 0.542689027968325 0.6689211737896941 0.5421787179552776 0.6601284562072681 0.6793754491062178 0.5918194682678256 0.6055221091296257 0.6631138650570884 0.6559008959245738 0.6414849884779625 0.6348752854444591</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">L2S382 0.8426252468809847 0.791784337383268 0.8762874977082885 0.8666693265827448 0.8898292712501708 0.9084204945482022 0.8821339436331491 0.8870353495912263 0.7018474049205657 0.6035203651725982 0.7202722055635978 0.7071347655059155 0.5358811200052477 0.7093129471508985 0.6247944934502809 0.0 0.680488155634992 0.5879411676849041 0.6300513986721148 0.7798117418893309 0.8451713307652351 0.7053126728281367 0.29452174278276233 0.7387926847081081 0.6760422527308095 0.6989286770361658 0.6126816214335168 0.6413026519516322 0.6319640587005974 0.6916898221776602 0.6638186733377722 0.5262410574638753 0.5609030584455355</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">L3S294 0.8588300792888636 0.7891927506641839 0.8826136551026731 0.8777562843225813 0.9039077039484619 0.913489362275528 0.8821873080715426 0.8805255216909961 0.48529937944992957 0.4127343227632307 0.46284470929748595 0.5297960404918108 0.6113293724148627 0.41393505549147774 0.5283785180280727 0.680488155634992 0.0 0.5793151362285137 0.532519942057993 0.4417588676636619 0.8329083701065813 0.5166391190254049 0.6344485180123575 0.5880518426822319 0.6166977936514635 0.6976139122442497 0.6965206807593246 0.6533170380479183 0.6465722615751633 0.7007111257543401 0.697083374921763 0.7001623873009802 0.7062166839383266</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">L3S313 0.7569476110839489 0.6721331780898249 0.8218942402038897 0.802227485419459 0.8485533231569067 0.852617211132442 0.8108074314407202 0.7980602019240324 0.6445967049513042 0.5009839698168453 0.6399875240134363 0.6776613871707217 0.5506881270264428 0.6241411216254367 0.44838682641972477 0.5879411676849041 0.5793151362285137 0.0 0.45248307788083786 0.7165487737423945 0.76582414397238 0.6574105445715698 0.560831971453598 0.7171733441832148 0.5902731094836756 0.5532059333861852 0.5853434250505234 0.5025483834097694 0.561609978051379 0.5582681387584417 0.5694158492427435 0.6032070350377756 0.5911945286328084</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">L3S341 0.7737531468949157 0.7493321619468443 0.8270103157643566 0.8160964503323095 0.852633569868443 0.8535720478866394 0.8071422086314133 0.829887986255906 0.6384694268897185 0.5720541940600513 0.5427529698531464 0.614146849517274 0.5515051266923414 0.5766719921218544 0.375128958725295 0.6300513986721148 0.532519942057993 0.45248307788083786 0.0 0.6196019964860159 0.783720015310488 0.5829777947168483 0.5534737998316789 0.6520900532121093 0.5493281969319693 0.6308837007391367 0.652197593637747 0.6025364874432444 0.6084801413450426 0.6341899420458715 0.6354966927534835 0.6495259871270996 0.6352447858014029</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">L3S360 0.8944159171736104 0.8773425730913526 0.8918833194204532 0.8817724113978568 0.9096947429872373 0.9122868711391121 0.8931657453933083 0.8798293357284456 0.4614095269789821 0.5238301647807445 0.41546588368326215 0.41910689292075193 0.7398454298135383 0.36061963338100667 0.6121711834124891 0.7798117418893309 0.4417588676636619 0.7165487737423945 0.6196019964860159 0.0 0.886859306656774 0.5343546555847905 0.7414678143333879 0.5400460290177217 0.7495782488980336 0.8108767861286648 0.8149762338575348 0.7802652073770237 0.7846158292767554 0.81147352370555 0.8005244117641637 0.8006143679532055 0.8014989491687546</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">L3S378 0.6033584308249973 0.3943371737754427 0.5595063305032598 0.5576854601824073 0.5498250250306412 0.5758415360633006 0.5741407822604754 0.5576624158659516 0.8793414820335794 0.8519601477875526 0.8806954039760829 0.8807526952301693 0.7579742017535656 0.8395112062787546 0.8188660070261687 0.8451713307652351 0.8329083701065813 0.76582414397238 0.783720015310488 0.886859306656774 0.0 0.8878531310256906 0.8359164049140062 0.8993931924960518 0.7252856380797102 0.6746582064114732 0.7140756986649465 0.7000095154033142 0.7254146177064372 0.6747284675539041 0.694536665024702 0.750964397649065 0.7478762997708954</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">L4S112 0.8470795512030315 0.8380071824429106 0.8896853519676307 0.8747926182003918 0.9022662022069642 0.9020100495580599 0.8800714967479438 0.8948846831679798 0.49283220104466596 0.45057960516670714 0.3819763193450203 0.43694693261646017 0.7115018729258218 0.4200940359303599 0.5950936496526126 0.7053126728281367 0.5166391190254049 0.6574105445715698 0.5829777947168483 0.5343546555847905 0.8878531310256906 0.0 0.6481421375149321 0.3575409039402891 0.7357714051501275 0.809583225542944 0.8029186032245896 0.7654724305797693 0.7692411532770428 0.8100058186769521 0.7895581361870725 0.7651442703099545 0.7646440275794989</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">L4S137 0.821242904747876 0.7797415033649835 0.8701383470494592 0.858838497674028 0.8832755726058907 0.9027332494336695 0.8737823256177506 0.8816102418936791 0.6490593420832039 0.6012619962408408 0.6864606389600179 0.6992608535946145 0.48083389190461734 0.6691543813483889 0.542689027968325 0.29452174278276233 0.6344485180123575 0.560831971453598 0.5534737998316789 0.7414678143333879 0.8359164049140062 0.6481421375149321 0.0 0.6908078779515394 0.6039667084060777 0.680281107717286 0.5936509777076375 0.6119432909211573 0.6028821638318781 0.6703353838958876 0.6453016109359295 0.5078212308619812 0.5169165993321925</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">L4S63 0.8652874911410461 0.8604626784828243 0.9064920956741176 0.8925129391873841 0.9169203743757105 0.9186219021297435 0.8981103792379882 0.9112039786090779 0.47563246735903575 0.5452699437274425 0.4541251117472289 0.4512186030792239 0.7661067183222632 0.43557544512779306 0.6689211737896941 0.7387926847081081 0.5880518426822319 0.7171733441832148 0.6520900532121093 0.5400460290177217 0.8993931924960518 0.3575409039402891 0.6908078779515394 0.0 0.7771055341254081 0.8401318632573123 0.8278791663557197 0.8033319145222341 0.8021181534933208 0.8397629806795364 0.8174036603850671 0.8034029168891261 0.8047837943956528</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">L5S104 0.7549182333398126 0.7389385379102201 0.8245445313262268 0.828703636427477 0.8572110146660553 0.853072903040757 0.8193019560519106 0.8148374423400107 0.7320469060900457 0.7004211741288418 0.7433650255074369 0.7657709194380475 0.36560695464990867 0.7065436739270591 0.5421787179552776 0.6760422527308095 0.6166977936514635 0.5902731094836756 0.5493281969319693 0.7495782488980336 0.7252856380797102 0.7357714051501275 0.6039667084060777 0.7771055341254081 0.0 0.299746565246475 0.3717459070188454 0.30611431267503736 0.2687293485232606 0.29488133279702533 0.35282575882032935 0.4059272692757093 0.3546188970208585</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">L5S155 0.7223305078861331 0.713927118153038 0.7952347925702751 0.8010491792499632 0.833803405339537 0.8327332298901452 0.7921706586389919 0.7791385980867408 0.8046481081885503 0.7254489332170817 0.8140552153241122 0.8264506476297601 0.4412731503394013 0.7784024482700062 0.6601284562072681 0.6989286770361658 0.6976139122442497 0.5532059333861852 0.6308837007391367 0.8108767861286648 0.6746582064114732 0.809583225542944 0.680281107717286 0.8401318632573123 0.299746565246475 0.0 0.24482970831325948 0.21540954545570457 0.28453959248410193 0.08866970541518727 0.2086655812403446 0.42817224711244256 0.35580061290923976</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">L5S174 0.7614916771466183 0.7409814677579339 0.8252913142216206 0.8063815782189153 0.8394041604332061 0.8629325424179554 0.8200532532128909 0.8123406708143702 0.7992253539435805 0.7241658196524235 0.8171702240197111 0.8235579667989716 0.41030162605879844 0.7846395088210678 0.6793754491062178 0.6126816214335168 0.6965206807593246 0.5853434250505234 0.652197593637747 0.8149762338575348 0.7140756986649465 0.8029186032245896 0.5936509777076375 0.8278791663557197 0.3717459070188454 0.24482970831325948 0.0 0.2877214934590952 0.25347139824912546 0.2605730633285677 0.2559815010487754 0.27892381163313434 0.3053187587048309</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">L5S203 0.7384823167933402 0.6893827188871452 0.7959214036381839 0.8092051698995067 0.8290963638641423 0.838123751985925 0.8020963162128805 0.8036845403456274 0.7608659584888517 0.6728749977683892 0.7787482342908187 0.7929926795664424 0.38926922412434417 0.7393917740028452 0.5918194682678256 0.6413026519516322 0.6533170380479183 0.5025483834097694 0.6025364874432444 0.7802652073770237 0.7000095154033142 0.7654724305797693 0.6119432909211573 0.8033319145222341 0.30611431267503736 0.21540954545570457 0.2877214934590952 0.0 0.24311981207597314 0.2201431600708006 0.2346438472041132 0.333150002145841 0.2850632669863039</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">L5S222 0.7685949288454377 0.739005471405395 0.8153225533087411 0.806495056831578 0.8384368165385457 0.8659733546560768 0.8249980087726344 0.8182429195392156 0.761349180972591 0.7120770444662118 0.7789238492726243 0.7900065630791773 0.3758838249617733 0.7397915081982174 0.6055221091296257 0.6319640587005974 0.6465722615751633 0.561609978051379 0.6084801413450426 0.7846158292767554 0.7254146177064372 0.7692411532770428 0.6028821638318781 0.8021181534933208 0.2687293485232606 0.28453959248410193 0.25347139824912546 0.24311981207597314 0.0 0.31116489519567736 0.30117438587754664 0.29331724421227606 0.2904033216874486</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">L5S240 0.7217074962665071 0.7134211109446568 0.7836084181624914 0.8032210970007331 0.8247152739488143 0.8346642658091125 0.7949183972892307 0.786233773105675 0.8017496796623877 0.7067601324302817 0.8145023991202386 0.8272758828816869 0.43476390441875573 0.7798934785055419 0.6631138650570884 0.6916898221776602 0.7007111257543401 0.5582681387584417 0.6341899420458715 0.81147352370555 0.6747284675539041 0.8100058186769521 0.6703353838958876 0.8397629806795364 0.29488133279702533 0.08866970541518727 0.2605730633285677 0.2201431600708006 0.31116489519567736 0.0 0.21735399370958108 0.3819989872862365 0.3241682922704345</span>
</pre>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">L6S20 0.7245343115615573 0.7210216228178491 0.791415482862234 0.7958200880953574 0.832089497492543 0.8289313199906942 0.7923436575946494 0.785902469716853 0.7844856344015433 0.7154192599371452 0.797521853405542 0.8177374352486667 0.4013288162093646 0.7729246906860544 0.6559008959245738 0.6638186733377722 0.697083374921763 0.5694158492427435 0.6354966927534835 0.8005244117641637 0.694536665024702 0.7895581361870725 0.6453016109359295 0.8174036603850671 0.35282575882032935 0.2086655812403446 0.2559815010487754 0.2346438472041132 0.30117438587754664 0.21735399370958108 0.0 0.36633132081192926 0.3477206555495855</span>
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">L6S68 0.7830441925323288 0.7548606893628177 0.8107398191951546 0.8161661389998109 0.8365271234666928 0.8703637908123152 0.8310029142646927 0.8323093879065956 0.7648448360194874 0.6790044090495644 0.7823436739920101 0.7787324503994212 0.29292532554452677 0.763695527435426 0.6414849884779625 0.5262410574638753 0.7001623873009802 0.6032070350377756 0.6495259871270996 0.8006143679532055 0.750964397649065 0.7651442703099545 0.5078212308619812 0.8034029168891261 0.4059272692757093 0.42817224711244256 0.27892381163313434 0.333150002145841 0.29331724421227606 0.3819989872862365 0.36633132081192926 0.0 0.19042209104190255</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">L6S93 0.7712136041691006 0.75650714031249 0.8044123679011221 0.8303929119421523 0.8483699050146564 0.8629123642673379 0.8322683023877507 0.8268942255033314 0.7728251640763542 0.6670904831025087 0.7825923091798144 0.7937870099703493 0.35832282922330977 0.7629847033876873 0.6348752854444591 0.5609030584455355 0.7062166839383266 0.5911945286328084 0.6352447858014029 0.8014989491687546 0.7478762997708954 0.7646440275794989 0.5169165993321925 0.8047837943956528 0.3546188970208585 0.35580061290923976 0.3053187587048309 0.2850632669863039 0.2904033216874486 0.3241682922704345 0.3477206555495855 0.19042209104190255 0.0</span></pre>
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<li id="cd334a9b00d16d3902ce297b0e3408297fa3af47">
<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#cd334a9b00d16d3902ce297b0e3408297fa3af47"><strong>skbio/stats/distance/tests/data/moving_pictures_mf.tsv</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#SampleID BarcodeSequence LinkerPrimerSequence BodySite Year Month Day Subject ReportedAntibioticUsage DaysSinceExperimentStart Description</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">L1S8 AGCTGACTAGTC GTGCCAGCMGCCGCGGTAA gut 2008 10 28 subject-1 Yes 0 subject-1.gut.2008-10-28</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">L1S57 ACACACTATGGC GTGCCAGCMGCCGCGGTAA gut 2009 1 20 subject-1 No 84 subject-1.gut.2009-1-20</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">L1S76 ACTACGTGTGGT GTGCCAGCMGCCGCGGTAA gut 2009 2 17 subject-1 No 112 subject-1.gut.2009-2-17</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">L1S105 AGTGCGATGCGT GTGCCAGCMGCCGCGGTAA gut 2009 3 17 subject-1 No 140 subject-1.gut.2009-3-17</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">L2S155 ACGATGCGACCA GTGCCAGCMGCCGCGGTAA left palm 2009 1 20 subject-1 No 84 subject-1.left-palm.2009-1-20</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">L2S175 AGCTATCCACGA GTGCCAGCMGCCGCGGTAA left palm 2009 2 17 subject-1 No 112 subject-1.left-palm.2009-2-17</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">L2S204 ATGCAGCTCAGT GTGCCAGCMGCCGCGGTAA left palm 2009 3 17 subject-1 No 140 subject-1.left-palm.2009-3-17</span>
</pre>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">L2S222 CACGTGACATGT GTGCCAGCMGCCGCGGTAA left palm 2009 4 14 subject-1 No 168 subject-1.left-palm.2009-4-14</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">L3S242 ACAGTTGCGCGA GTGCCAGCMGCCGCGGTAA right palm 2008 10 28 subject-1 Yes 0 subject-1.right-palm.2008-10-28</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">L3S294 CACGACAGGCTA GTGCCAGCMGCCGCGGTAA right palm 2009 1 20 subject-1 No 84 subject-1.right-palm.2009-1-20</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">L3S313 AGTGTCACGGTG GTGCCAGCMGCCGCGGTAA right palm 2009 2 17 subject-1 No 112 subject-1.right-palm.2009-2-17</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">L3S341 CAAGTGAGAGAG GTGCCAGCMGCCGCGGTAA right palm 2009 3 17 subject-1 No 140 subject-1.right-palm.2009-3-17</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">L3S360 CATCGTATCAAC GTGCCAGCMGCCGCGGTAA right palm 2009 4 14 subject-1 No 168 subject-1.right-palm.2009-4-14</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">L5S104 CAGTGTCAGGAC GTGCCAGCMGCCGCGGTAA tongue 2008 10 28 subject-1 Yes 0 subject-1.tongue.2008-10-28</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">L5S155 ATCTTAGACTGC GTGCCAGCMGCCGCGGTAA tongue 2009 1 20 subject-1 No 84 subject-1.tongue.2009-1-20</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">L5S174 CAGACATTGCGT GTGCCAGCMGCCGCGGTAA tongue 2009 2 17 subject-1 No 112 subject-1.tongue.2009-2-17</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">L5S203 CGATGCACCAGA GTGCCAGCMGCCGCGGTAA tongue 2009 3 17 subject-1 No 140 subject-1.tongue.2009-3-17</span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">L5S222 CTAGAGACTCTT GTGCCAGCMGCCGCGGTAA tongue 2009 4 14 subject-1 No 168 subject-1.tongue.2009-4-14</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">L1S140 ATGGCAGCTCTA GTGCCAGCMGCCGCGGTAA gut 2008 10 28 subject-2 Yes 0 subject-2.gut.2008-10-28</span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">L1S208 CTGAGATACGCG GTGCCAGCMGCCGCGGTAA gut 2009 1 20 subject-2 No 84 subject-2.gut.2009-1-20</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">L1S257 CCGACTGAGATG GTGCCAGCMGCCGCGGTAA gut 2009 3 17 subject-2 No 140 subject-2.gut.2009-3-17</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">L1S281 CCTCTCGTGATC GTGCCAGCMGCCGCGGTAA gut 2009 4 14 subject-2 No 168 subject-2.gut.2009-4-14</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">L2S240 CATATCGCAGTT GTGCCAGCMGCCGCGGTAA left palm 2008 10 28 subject-2 Yes 0 subject-2.left-palm.2008-10-28</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">L2S309 CGTGCATTATCA GTGCCAGCMGCCGCGGTAA left palm 2009 1 20 subject-2 No 84 subject-2.left-palm.2009-1-20</span>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">L2S357 CTAACGCAGTCA GTGCCAGCMGCCGCGGTAA left palm 2009 3 17 subject-2 No 140 subject-2.left-palm.2009-3-17</span>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">L2S382 CTCAATGACTCA GTGCCAGCMGCCGCGGTAA left palm 2009 4 14 subject-2 No 168 subject-2.left-palm.2009-4-14</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">L3S378 ATCGATCTGTGG GTGCCAGCMGCCGCGGTAA right palm 2008 10 28 subject-2 Yes 0 subject-2.right-palm.2008-10-28</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">L4S63 CTCGTGGAGTAG GTGCCAGCMGCCGCGGTAA right palm 2009 1 20 subject-2 No 84 subject-2.right-palm.2009-1-20</span>
</pre>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">L4S112 GCGTTACACACA GTGCCAGCMGCCGCGGTAA right palm 2009 3 17 subject-2 No 140 subject-2.right-palm.2009-3-17</span>
</pre>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">L4S137 GAACTGTATCTC GTGCCAGCMGCCGCGGTAA right palm 2009 4 14 subject-2 No 168 subject-2.right-palm.2009-4-14</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">L5S240 CTGGACTCATAG GTGCCAGCMGCCGCGGTAA tongue 2008 10 28 subject-2 Yes 0 subject-2.tongue.2008-10-28</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">L6S20 GAGGCTCATCAT GTGCCAGCMGCCGCGGTAA tongue 2009 1 20 subject-2 No 84 subject-2.tongue.2009-1-20</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">L6S68 GATACGTCCTGA GTGCCAGCMGCCGCGGTAA tongue 2009 3 17 subject-2 No 140 subject-2.tongue.2009-3-17</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">L6S93 GATTAGCACTCT GTGCCAGCMGCCGCGGTAA tongue 2009 4 14 subject-2 No 168 subject-2.tongue.2009-4-14</span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#60237a6af2901ba246b18ffc0b77db80f4610bfc"><strong>skbio/stats/distance/tests/test_permdisp.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Copyright (c) 2013--, scikit-bio development team.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># The full license is in the file COPYING.txt, distributed with this software.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">functools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">partial</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span><span class="p">,</span> <span class="n" style="color: #333;">main</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy.testing</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">npt</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pandas.util.testing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">assert_series_equal</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">scipy.stats</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">f_oneway</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">hdmedians</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">hd</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">skbio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">DistanceMatrix</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">skbio.stats.ordination</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pcoa</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">skbio.stats.distance</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">permdisp</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">skbio.stats.distance._permdisp</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_compute_groups</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">skbio.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_data_path</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">testPERMDISP</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test with 2 groups of equal size</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># when assigned different labels, results should be the same</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">grouping_eq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bar'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bar'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bar'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">grouping_eq_relab</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'pyt'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pyt'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pyt'</span><span class="p">,</span> <span class="s" style="color: #d14;">'hon'</span><span class="p">,</span> <span class="s" style="color: #d14;">'hon'</span><span class="p">,</span> <span class="s" style="color: #d14;">'hon'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exp_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'method name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'test statistic name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample size'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">'number of groups'</span><span class="p">,</span> <span class="s" style="color: #d14;">'test statistic'</span><span class="p">,</span> <span class="s" style="color: #d14;">'p-value'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">'number of permutations'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test with 3 groups of different sizes</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># when assigned different labels results should be the same</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">grouping_uneq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bar'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bar'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bar'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">'qw'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qw'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qw'</span><span class="p">,</span> <span class="s" style="color: #d14;">'qw'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">grouping_uneq_relab</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">23</span><span class="p">,</span> <span class="mi" style="color: #099;">23</span><span class="p">,</span> <span class="mi" style="color: #099;">23</span><span class="p">,</span> <span class="mi" style="color: #099;">23</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">grouping_un_mixed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'a'</span><span class="p">,</span> <span class="s" style="color: #d14;">'a'</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="s" style="color: #d14;">'b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">eq_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'s1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'s2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'s3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'s4'</span><span class="p">,</span> <span class="s" style="color: #d14;">'s5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'s6'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">uneq_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'s1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'s2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'s3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'s4'</span><span class="p">,</span> <span class="s" style="color: #d14;">'s5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'s6'</span><span class="p">,</span> <span class="s" style="color: #d14;">'s7'</span><span class="p">,</span> <span class="s" style="color: #d14;">'s8'</span><span class="p">,</span> <span class="s" style="color: #d14;">'s9'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># matrix for equal grouping</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">eq_mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DistanceMatrix</span><span class="p">([[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]],</span> <span class="n" style="color: #333;">eq_ids</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># matrix for unequal grouping</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uneq_mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DistanceMatrix</span><span class="p">([[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]],</span> <span class="n" style="color: #333;">uneq_ids</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># null matrix for equal grouping</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">null_mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DistanceMatrix</span><span class="p">([[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]],</span> <span class="n" style="color: #333;">eq_ids</span><span class="p">)</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">unif_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'PC.354'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PC.355'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PC.356'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PC.481'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PC.593'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PC.607'</span><span class="p">,</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="s" style="color: #d14;">'PC.634'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PC.635'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PC.636'</span><span class="p">]</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unifrac_dm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DistanceMatrix</span><span class="p">(</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="p">[[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">0.595483768391</span><span class="p">,</span> <span class="mf" style="color: #099;">0.618074717633</span><span class="p">,</span> <span class="mf" style="color: #099;">0.582763100909</span><span class="p">,</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="mf" style="color: #099;">0.566949022108</span><span class="p">,</span> <span class="mf" style="color: #099;">0.714717232268</span><span class="p">,</span> <span class="mf" style="color: #099;">0.772001731764</span><span class="p">,</span> <span class="mf" style="color: #099;">0.690237118413</span><span class="p">,</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="mf" style="color: #099;">0.740681707488</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.595483768391</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">0.581427669668</span><span class="p">,</span> <span class="mf" style="color: #099;">0.613726772383</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="mf" style="color: #099;">0.65945132763</span><span class="p">,</span> <span class="mf" style="color: #099;">0.745176523638</span><span class="p">,</span> <span class="mf" style="color: #099;">0.733836123821</span><span class="p">,</span> <span class="mf" style="color: #099;">0.720305073505</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="mf" style="color: #099;">0.680785600439</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.618074717633</span><span class="p">,</span> <span class="mf" style="color: #099;">0.581427669668</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">0.672149021573</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="mf" style="color: #099;">0.699416863323</span><span class="p">,</span> <span class="mf" style="color: #099;">0.71405573754</span><span class="p">,</span> <span class="mf" style="color: #099;">0.759178215168</span><span class="p">,</span> <span class="mf" style="color: #099;">0.689701276341</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="mf" style="color: #099;">0.725100672826</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.582763100909</span><span class="p">,</span> <span class="mf" style="color: #099;">0.613726772383</span><span class="p">,</span> <span class="mf" style="color: #099;">0.672149021573</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="mf" style="color: #099;">0.64756120797</span><span class="p">,</span> <span class="mf" style="color: #099;">0.666018240373</span><span class="p">,</span> <span class="mf" style="color: #099;">0.66532968784</span><span class="p">,</span> <span class="mf" style="color: #099;">0.650464714994</span><span class="p">,</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="mf" style="color: #099;">0.632524644216</span><span class="p">],</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.566949022108</span><span class="p">,</span> <span class="mf" style="color: #099;">0.65945132763</span><span class="p">,</span> <span class="mf" style="color: #099;">0.699416863323</span><span class="p">,</span> <span class="mf" style="color: #099;">0.64756120797</span><span class="p">,</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">0.703720200713</span><span class="p">,</span> <span class="mf" style="color: #099;">0.748240937349</span><span class="p">,</span> <span class="mf" style="color: #099;">0.73416971958</span><span class="p">,</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="mf" style="color: #099;">0.727154987937</span><span class="p">],</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.714717232268</span><span class="p">,</span> <span class="mf" style="color: #099;">0.745176523638</span><span class="p">,</span> <span class="mf" style="color: #099;">0.71405573754</span><span class="p">,</span> <span class="mf" style="color: #099;">0.666018240373</span><span class="p">,</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="mf" style="color: #099;">0.703720200713</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">0.707316869557</span><span class="p">,</span> <span class="mf" style="color: #099;">0.636288883818</span><span class="p">,</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="mf" style="color: #099;">0.699880573956</span><span class="p">],</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.772001731764</span><span class="p">,</span> <span class="mf" style="color: #099;">0.733836123821</span><span class="p">,</span> <span class="mf" style="color: #099;">0.759178215168</span><span class="p">,</span> <span class="mf" style="color: #099;">0.66532968784</span><span class="p">,</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="mf" style="color: #099;">0.748240937349</span><span class="p">,</span> <span class="mf" style="color: #099;">0.707316869557</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">0.565875193399</span><span class="p">,</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="mf" style="color: #099;">0.560605525642</span><span class="p">],</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.690237118413</span><span class="p">,</span> <span class="mf" style="color: #099;">0.720305073505</span><span class="p">,</span> <span class="mf" style="color: #099;">0.689701276341</span><span class="p">,</span> <span class="mf" style="color: #099;">0.650464714994</span><span class="p">,</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="mf" style="color: #099;">0.73416971958</span><span class="p">,</span> <span class="mf" style="color: #099;">0.636288883818</span><span class="p">,</span> <span class="mf" style="color: #099;">0.565875193399</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="mf" style="color: #099;">0.575788039321</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.740681707488</span><span class="p">,</span> <span class="mf" style="color: #099;">0.680785600439</span><span class="p">,</span> <span class="mf" style="color: #099;">0.725100672826</span><span class="p">,</span> <span class="mf" style="color: #099;">0.632524644216</span><span class="p">,</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="mf" style="color: #099;">0.727154987937</span><span class="p">,</span> <span class="mf" style="color: #099;">0.699880573956</span><span class="p">,</span> <span class="mf" style="color: #099;">0.560605525642</span><span class="p">,</span> <span class="mf" style="color: #099;">0.575788039321</span><span class="p">,</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="mf" style="color: #099;">0.0</span><span class="p">]],</span> <span class="n" style="color: #333;">unif_ids</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unif_grouping</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'Control'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Control'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Control'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Control'</span><span class="p">,</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="s" style="color: #d14;">'Control'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Fast'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Fast'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Fast'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Fast'</span><span class="p">]</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_series_equal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">assert_series_equal</span><span class="p">,</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">check_index_type</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">check_series_type</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_centroids_eq_groups</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="mf" style="color: #099;">1.2886811963240687</span><span class="p">,</span> <span class="mf" style="color: #099;">1.890538910062923</span><span class="p">,</span> <span class="mf" style="color: #099;">1.490527658097728</span><span class="p">],</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">2.17349240061718</span><span class="p">,</span> <span class="mf" style="color: #099;">2.3192679626679946</span><span class="p">,</span> <span class="mf" style="color: #099;">2.028338553903792</span><span class="p">]]</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">exp_stat</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f_oneway</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">dm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pcoa</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">eq_mat</span><span class="p">)</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">dm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dm</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_compute_groups</span><span class="p">(</span><span class="n" style="color: #333;">dm</span><span class="p">,</span> <span class="s" style="color: #d14;">'centroid'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">grouping_eq</span><span class="p">)</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp_stat</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">obs_relab</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_compute_groups</span><span class="p">(</span><span class="n" style="color: #333;">dm</span><span class="p">,</span> <span class="s" style="color: #d14;">'centroid'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">grouping_eq_relab</span><span class="p">)</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs_relab</span><span class="p">,</span> <span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_centroids_uneq_groups</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"><span class="s" style="color: #d14;"> the expected result here was calculated by hand</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="mf" style="color: #099;">2.5847022428144935</span><span class="p">,</span> <span class="mf" style="color: #099;">2.285624595858895</span><span class="p">,</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="mf" style="color: #099;">1.7022431146340287</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">1.724817266046108</span><span class="p">,</span> <span class="mf" style="color: #099;">1.724817266046108</span><span class="p">],</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">2.4333280644972795</span><span class="p">,</span> <span class="mf" style="color: #099;">2.389000390879655</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="mf" style="color: #099;">2.8547180589306036</span><span class="p">,</span> <span class="mf" style="color: #099;">3.218568759338847</span><span class="p">]]</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">exp_stat</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f_oneway</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">dm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pcoa</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uneq_mat</span><span class="p">)</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">dm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dm</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_compute_groups</span><span class="p">(</span><span class="n" style="color: #333;">dm</span><span class="p">,</span> <span class="s" style="color: #d14;">'centroid'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">grouping_uneq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp_stat</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">obs_relab</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_compute_groups</span><span class="p">(</span><span class="n" style="color: #333;">dm</span><span class="p">,</span> <span class="s" style="color: #d14;">'centroid'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">grouping_uneq_relab</span><span class="p">)</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">obs_relab</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_centroids_mixedgroups</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="mf" style="color: #099;">2.5847022428144935</span><span class="p">,</span> <span class="mf" style="color: #099;">2.285624595858895</span><span class="p">,</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="mf" style="color: #099;">1.7022431146340287</span><span class="p">],</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">1.724817266046108</span><span class="p">,</span> <span class="mf" style="color: #099;">1.724817266046108</span><span class="p">],</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">2.4333280644972795</span><span class="p">,</span> <span class="mf" style="color: #099;">2.389000390879655</span><span class="p">,</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="mf" style="color: #099;">2.8547180589306036</span><span class="p">,</span> <span class="mf" style="color: #099;">3.218568759338847</span><span class="p">]]</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">dm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pcoa</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uneq_mat</span><span class="p">)</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">dm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dm</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">exp_stat</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f_oneway</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">obs_mixed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_compute_groups</span><span class="p">(</span><span class="n" style="color: #333;">dm</span><span class="p">,</span> <span class="s" style="color: #d14;">'centroid'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">grouping_un_mixed</span><span class="p">)</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">exp_stat</span><span class="p">,</span> <span class="n" style="color: #333;">obs_mixed</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_centroids_null</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">dm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pcoa</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">null_mat</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">dm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dm</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">obs_null</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_compute_groups</span><span class="p">(</span><span class="n" style="color: #333;">dm</span><span class="p">,</span> <span class="s" style="color: #d14;">'centroid'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">grouping_eq</span><span class="p">)</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">obs_null</span><span class="p">)</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_centroid_normal</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Series</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exp_index</span><span class="p">,</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'PERMDISP'</span><span class="p">,</span> <span class="s" style="color: #d14;">'F-value'</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mf" style="color: #099;">0.244501519876</span><span class="p">,</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="mf" style="color: #099;">0.63</span><span class="p">,</span> <span class="mi" style="color: #099;">99</span><span class="p">],</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'PERMDISP results'</span><span class="p">)</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">grouping</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'Control'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Control'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Control'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Control'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Control'</span><span class="p">,</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="s" style="color: #d14;">'Fast'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Fast'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Fast'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Fast'</span><span class="p">]</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">random</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seed</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">permdisp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unifrac_dm</span><span class="p">,</span> <span class="n" style="color: #333;">grouping</span><span class="p">,</span> <span class="n" style="color: #333;">test</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'centroid'</span><span class="p">,</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">permutations</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">99</span><span class="p">)</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_series_equal</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_median_normal</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Series</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exp_index</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'PERMDISP'</span><span class="p">,</span> <span class="s" style="color: #d14;">'F-value'</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mf" style="color: #099;">0.139475441876</span><span class="p">,</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="mf" style="color: #099;">0.61</span><span class="p">,</span> <span class="mi" style="color: #099;">99</span><span class="p">],</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'PERMDISP results'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">random</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seed</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">permdisp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unifrac_dm</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unif_grouping</span><span class="p">,</span> <span class="n" style="color: #333;">test</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'median'</span><span class="p">,</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">permutations</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">99</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_series_equal</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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195
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_not_distance_matrix</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">dm</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">grouping</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'Control'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Control'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Control'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Control'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Control'</span><span class="p">,</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="s" style="color: #d14;">'Fast'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Fast'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Fast'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Fast'</span><span class="p">]</span></span>
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200
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">npt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">TypeError</span><span class="p">,</span> <span class="n" style="color: #333;">permdisp</span><span class="p">,</span> <span class="n" style="color: #333;">dm</span><span class="p">,</span> <span class="n" style="color: #333;">grouping</span><span class="p">,</span> <span class="n" style="color: #333;">permutations</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mismatched_group</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">gr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bar'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">npt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="n" style="color: #333;">permdisp</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unifrac_dm</span><span class="p">,</span> <span class="n" style="color: #333;">gr</span><span class="p">)</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_group</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">gr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'f'</span><span class="p">,</span> <span class="s" style="color: #d14;">'f'</span><span class="p">,</span> <span class="s" style="color: #d14;">'f'</span><span class="p">,</span> <span class="s" style="color: #d14;">'f'</span><span class="p">,</span> <span class="s" style="color: #d14;">'f'</span><span class="p">,</span> <span class="s" style="color: #d14;">'f'</span><span class="p">,</span> <span class="s" style="color: #d14;">'f'</span><span class="p">,</span> <span class="s" style="color: #d14;">'f'</span><span class="p">,</span> <span class="s" style="color: #d14;">'f'</span><span class="p">]</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">npt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="n" style="color: #333;">permdisp</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unifrac_dm</span><span class="p">,</span> <span class="n" style="color: #333;">gr</span><span class="p">)</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_no_permuations</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">permdisp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">eq_mat</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">grouping_eq</span><span class="p">,</span> <span class="n" style="color: #333;">permutations</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">pval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">obs</span><span class="p">[</span><span class="s" style="color: #d14;">'p-value'</span><span class="p">]</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">pval</span><span class="p">)</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_hdmedians</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mf" style="color: #099;">2.01956244</span><span class="p">,</span> <span class="mf" style="color: #099;">1.53164546</span><span class="p">,</span> <span class="mf" style="color: #099;">2.60571752</span><span class="p">,</span> <span class="mf" style="color: #099;">0.91424179</span><span class="p">,</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="mf" style="color: #099;">1.76214416</span><span class="p">,</span> <span class="mf" style="color: #099;">1.69943057</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">hd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">geomedian</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">eq_mat</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">data</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">npt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_almost_equal</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">,</span> <span class="n" style="color: #333;">decimal</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_confirm_betadispr_results</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">mp_dm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DistanceMatrix</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'moving_pictures_dm.tsv'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">mp_mf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'moving_pictures_mf.tsv'</span><span class="p">),</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">mp_mf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_index</span><span class="p">(</span><span class="s" style="color: #d14;">'#SampleID'</span><span class="p">,</span> <span class="n" style="color: #333;">inplace</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">obs_med_mp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">permdisp</span><span class="p">(</span><span class="n" style="color: #333;">mp_dm</span><span class="p">,</span> <span class="n" style="color: #333;">mp_mf</span><span class="p">,</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">column</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'BodySite'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">obs_cen_mp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">permdisp</span><span class="p">(</span><span class="n" style="color: #333;">mp_dm</span><span class="p">,</span> <span class="n" style="color: #333;">mp_mf</span><span class="p">,</span> <span class="n" style="color: #333;">column</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'BodySite'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">test</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'centroid'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">exp_data_m</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'PERMDISP'</span><span class="p">,</span> <span class="s" style="color: #d14;">'F-value'</span><span class="p">,</span> <span class="mi" style="color: #099;">33</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mf" style="color: #099;">10.1956</span><span class="p">,</span> <span class="mf" style="color: #099;">0.001</span><span class="p">,</span> <span class="mi" style="color: #099;">999</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">exp_data_c</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'PERMDISP'</span><span class="p">,</span> <span class="s" style="color: #d14;">'F-value'</span><span class="p">,</span> <span class="mi" style="color: #099;">33</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mf" style="color: #099;">17.4242</span><span class="p">,</span> <span class="mf" style="color: #099;">0.001</span><span class="p">,</span> <span class="mi" style="color: #099;">999</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">exp_ind</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'method name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'test statistic name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample size'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="s" style="color: #d14;">'number of groups'</span><span class="p">,</span> <span class="s" style="color: #d14;">'test statistic'</span><span class="p">,</span> <span class="s" style="color: #d14;">'p-value'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="s" style="color: #d14;">'number of permutations'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">exp_med_mp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Series</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">exp_data_m</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">exp_ind</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'object'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'PERMDISP results'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">exp_cen_mp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Series</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">exp_data_c</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">exp_ind</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'object'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'PERMDISP results'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_series_equal</span><span class="p">(</span><span class="n" style="color: #333;">exp_med_mp</span><span class="p">,</span> <span class="n" style="color: #333;">obs_med_mp</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_series_equal</span><span class="p">(</span><span class="n" style="color: #333;">exp_cen_mp</span><span class="p">,</span> <span class="n" style="color: #333;">obs_cen_mp</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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<li id="c6f587411e1fff773305a7254f17b301583ab8f7">
<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#c6f587411e1fff773305a7254f17b301583ab8f7"><strong>skbio/stats/ordination/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,6 +17,7 @@ Functions</td>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;"> ca</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;"> pcoa</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> pcoa_biplot</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> cca</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> rda</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;"> mean_and_std</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -126,11 +127,11 @@ from skbio.util import TestRunner</td>
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126
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._redundancy_analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">rda</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._correspondence_analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ca</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._canonical_correspondence_analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">cca</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._principal_coordinate_analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pcoa</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._principal_coordinate_analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pcoa</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pcoa_biplot</span></span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._ordination_results</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">OrdinationResults</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">mean_and_std</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">svd_rank</span><span class="p">,</span> <span class="n" style="color: #333;">corr</span><span class="p">,</span> <span class="n" style="color: #333;">e_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">f_matrix</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'ca'</span><span class="p">,</span> <span class="s" style="color: #d14;">'rda'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cca'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pcoa'</span><span class="p">,</span> <span class="s" style="color: #d14;">'OrdinationResults'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'ca'</span><span class="p">,</span> <span class="s" style="color: #d14;">'rda'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cca'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pcoa'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left">pcoa_biplot'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'</span>OrdinationResults'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="s" style="color: #d14;">'mean_and_std'</span><span class="p">,</span> <span class="s" style="color: #d14;">'scale'</span><span class="p">,</span> <span class="s" style="color: #d14;">'svd_rank'</span><span class="p">,</span> <span class="s" style="color: #d14;">'corr'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="s" style="color: #d14;">'e_matrix'</span><span class="p">,</span> <span class="s" style="color: #d14;">'f_matrix'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#66926f23fc6267a8a45ee0bcb544d4b6d8c78ff5"><strong>skbio/stats/ordination/_canonical_correspondence_analysis.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,7 +44,7 @@ def cca(y, x, scaling=1):</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;"> Samples by constraints table (n, q)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;"> scaling : int, {1, 2}, optional</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"><span class="s" style="color: #d14;"> Scaling type 1 maintains :math:`\chi^2` distances between rows.</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;"> Scaling type 2 preserve<span class="idiff left right">r</span> :math:`\chi^2` distances between columns.</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;"> Scaling type 2 preserve<span class="idiff left right">s</span> :math:`\chi^2` distances between columns.</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"><span class="s" style="color: #d14;"> For a more detailed explanation of the interpretation, check Legendre &</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;"> Legendre 1998, section 9.4.3.</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#c443397cd3ce71f204a6fa99ac24c98e5fcc8b14"><strong>skbio/stats/ordination/_principal_coordinate_analysis.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,7 @@ from scipy.linalg import eigh</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">skbio.stats.distance</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">DistanceMatrix</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">skbio.util._decorator</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">experimental</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._ordination_results</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">OrdinationResults</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">e_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">f_matrix</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">e_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">f_matrix</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">scale</span></span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># - In cogent, after computing eigenvalues/vectors, the imaginary part</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># is dropped, if any. We know for a fact that the eigenvalues are</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -142,3 +142,64 @@ def pcoa(distance_matrix):</td>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">axis_labels</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">proportion_explained</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Series</span><span class="p">(</span><span class="n" style="color: #333;">proportion_explained</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">axis_labels</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"><span class="nd">@experimental</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.5.3"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pcoa_biplot</span><span class="p">(</span><span class="n" style="color: #333;">ordination</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="s" style="color: #d14;">"""Compute the projection of descriptors into a PCoA matrix</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"><span class="s" style="color: #d14;"> This implementation is as described in Chapter 9 of Legendre & Legendre,</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"><span class="s" style="color: #d14;"> Numerical Ecology 3rd edition.</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"><span class="s" style="color: #d14;"> ordination: OrdinationResults</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"><span class="s" style="color: #d14;"> The computed principal coordinates analysis of dimensions (n, c) where</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"><span class="s" style="color: #d14;"> the matrix ``y`` will be projected onto.</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"><span class="s" style="color: #d14;"> y: DataFrame</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"><span class="s" style="color: #d14;"> Samples by features table of dimensions (n, m). These can be</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"><span class="s" style="color: #d14;"> environmental features or abundance counts. This table should be</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"><span class="s" style="color: #d14;"> normalized in cases of dimensionally heterogenous physical variables.</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"><span class="s" style="color: #d14;"> Returns</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"><span class="s" style="color: #d14;"> -------</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"><span class="s" style="color: #d14;"> OrdinationResults</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"><span class="s" style="color: #d14;"> The modified input object that includes projected features onto the</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"><span class="s" style="color: #d14;"> ordination space in the ``features`` attribute.</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># acknowledge that most saved ordinations lack a name, however if they have</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># a name, it should be PCoA</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ordination</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">short_method_name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">''</span> <span class="ow" style="font-weight: 600;">and</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">ordination</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">short_method_name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'PCoA'</span><span class="p">):</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">'This biplot computation can only be performed in a '</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="s" style="color: #d14;">'PCoA matrix.'</span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">ordination</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">):</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">'The eigenvectors and the descriptors must describe '</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="s" style="color: #d14;">'the same samples.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">eigvals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ordination</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">eigvals</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">coordinates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ordination</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coordinates</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># align the descriptors and eigenvectors in a sample-wise fashion</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reindex</span><span class="p">(</span><span class="n" style="color: #333;">coordinates</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">)</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># S_pc from equation 9.44</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Represents the covariance matrix between the features matrix and the</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># column-centered eigenvectors of the pcoa.</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">spc</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dot</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">(</span><span class="n" style="color: #333;">coordinates</span><span class="p">,</span> <span class="n" style="color: #333;">ddof</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># U_proj from equation 9.55, is the matrix of descriptors to be projected.</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Only get the power of non-zero values, otherwise this will raise a</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># divide by zero warning. There shouldn't be negative eigenvalues(?)</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">Uproj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">spc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dot</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">power</span><span class="p">(</span><span class="n" style="color: #333;">eigvals</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">0.5</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">eigvals</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)))</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">ordination</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">features</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Uproj</span><span class="p">,</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">(),</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">coordinates</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">())</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ordination</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#fba3bc091de94548d66122df70f408a9d18123c3"><strong>skbio/stats/ordination/tests/data/PCoA_biplot_descriptors</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Taxon PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Root;k__Bacteria;Other 0.0202702702703 0.0469798657718 0.0266666666667 0.027397260274 0.0134228187919 0.0134228187919 0.0136054421769 0.0469798657718 0.02</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Root;k__Bacteria;p__Actinobacteria 0.00675675675676 0.00671140939597 0.0 0.00684931506849 0.0 0.0 0.0 0.0201342281879 0.02</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Root;k__Bacteria;p__Bacteroidetes 0.695945945946 0.523489932886 0.193333333333 0.143835616438 0.0738255033557 0.389261744966 0.285714285714 0.275167785235 0.653333333333</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Root;k__Bacteria;p__Deferribacteres 0.0472972972973 0.0134228187919 0.0 0.0 0.0 0.0 0.0 0.0201342281879 0.0333333333333</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Root;k__Bacteria;p__Firmicutes 0.209459459459 0.395973154362 0.773333333333 0.787671232877 0.89932885906 0.41610738255 0.700680272109 0.456375838926 0.22</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Root;k__Bacteria;p__Proteobacteria 0.00675675675676 0.00671140939597 0.0 0.0 0.0 0.0335570469799 0.0 0.0201342281879 0.0133333333333</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Root;k__Bacteria;p__TM7 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0133333333333</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Root;k__Bacteria;p__ 0.0135135135135 0.00671140939597 0.00666666666667 0.0342465753425 0.0134228187919 0.147651006711 0.0 0.161073825503 0.0266666666667</span></pre>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#2752c1709b6065d169fa47e68bfd66812ca32a7b"><strong>skbio/stats/ordination/tests/data/PCoA_biplot_projected_descriptors</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">"","Axis.1","Axis.2","Axis.3","Axis.4","Axis.5","Axis.6","Axis.7","Axis.8"</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">"Root;k__Bacteria;Other",-0.0251703458354009,-0.0387419997798285,0.0370307944752097,-0.0182485866183309,-0.00129741030252842,0.000814106793625313,-0.0173701207829898,0.0361211055519348</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">"Root;k__Bacteria;p__Actinobacteria",-0.0243896442435075,-0.0173750855733946,0.00412122918478027,-0.00122921164491863,-0.0133154056835269,-0.0154481346200809,0.0110025326657988,-0.0193889181281414</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">"Root;k__Bacteria;p__Bacteroidetes",-0.715120229604841,0.317840715450945,-0.183247320427738,0.616597812375811,0.261720590975174,-0.0233954969961052,0.0235684811385711,0.108576064612194</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">"Root;k__Bacteria;p__Deferribacteres",-0.0581057801759818,0.0109676872979955,0.000973434160884227,0.0403394413149601,-0.0126657203131676,0.0312522995897358,0.00445295277091873,-0.0391828157435708</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">"Root;k__Bacteria;p__Firmicutes",0.826514889978526,0.0338669291769973,0.258683679610306,-0.820041925817023,-0.236331008329088,0.0820371240664409,-0.146993916645359,-0.114613637622136</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">"Root;k__Bacteria;p__Proteobacteria",-0.00665357958782869,-0.0351957821869525,-0.0269691957766513,0.0384070851104123,0.019915981256556,-0.0152225877254676,0.019285238587548,0.0101464789573946</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">"Root;k__Bacteria;p__TM7",-0.00936607225354557,0.00504668520861811,-0.00329562583232389,-0.00189853964818609,0.00398022745872819,-0.0160400884328152,0.0128760393792986,-0.0162949930598132</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">"Root;k__Bacteria;p__",0.0122907617222583,-0.276409149593715,-0.0872969953941216,0.146073924926225,-0.022007255063595,-0.0439972226754927,0.0931787928855206,0.0346367154320729</span></pre>
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<li id="7605e4425f331c3f7f78961a9541055d29a4b74d">
<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#7605e4425f331c3f7f78961a9541055d29a4b74d"><strong>skbio/stats/ordination/tests/data/PCoA_skbio</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Eigvals 9</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">0.5123672604605048 0.30071909442702155 0.2679120660041405 0.20898868107836532 0.19169895326008157 0.16054234528018121 0.1501769571197782 0.12245774816668883 0.0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Proportion explained 9</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">0.2675738327765797 0.1570446960499008 0.1399118637740237 0.109140272453788 0.10011104850250738 0.08384011619116792 0.07842699390110737 0.06395117635092507 0.0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Species 0 0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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8
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Site 9 9</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">PC.636 -0.25846546118284214 0.17399954688273864 -0.03828757925519388 0.1944775056196811 -0.08311760208440848 0.2624303332005185 -0.023163639223487725 0.018479403958060633 -0.0</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">PC.635 -0.27100113539100923 -0.01859513190633933 0.08648419263485602 -0.11806424531525102 0.19880835843691802 -0.021172359953453967 -0.19102402756537798 -0.1556465923768283 -0.0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">PC.356 0.2350778981747308 0.0962519254488697 0.3457927267138699 0.003208625776186833 0.09637776755188007 0.04570253869527276 0.1854728132858981 -0.04040939717932225 -0.0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">PC.481 0.026140766432533637 -0.011145967653319279 -0.14766060301460832 -0.29087660852960373 -0.20394547280060757 0.06197123847575147 0.10164132870879576 -0.1056909987185146 -0.0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">PC.354 0.2850075522831214 -0.019254988848331458 -0.062326337538532166 -0.13812679985198154 0.10479860242276298 0.09517207306283292 -0.12963609754202599 0.22068717037162142 -0.0</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">PC.593 0.20463632624145503 -0.13936115093164061 -0.2915138196228669 0.18156678682059035 0.1595801327151684 -0.024641213016179383 0.08662524044412884 -0.09962214768709698 -0.0</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">PC.355 0.23348240321199026 0.22525797406849948 0.018862309626814986 0.10772998183109622 -0.1771089995718839 -0.19290583515124646 -0.14981947140833857 -0.03835490374645002 -0.0</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">PC.607 -0.09496319113225948 -0.42097480249530345 0.1548694548694144 0.08984275092805967 -0.15261819448811528 -0.0334232691500879 -0.02512247773026579 0.05089885364091516 -0.0</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">PC.634 -0.35991515863772167 0.11382259543482588 -0.06622034441375366 -0.029757997278778266 0.05722540781828547 -0.1931335061634077 0.14502633103067314 0.14965861173761527 -0.0</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Biplot 0 0</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Site constraints 0 0</span></pre>
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<li id="125936fde92c0e77b23cf33bdd140af1c8be8e27">
<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#125936fde92c0e77b23cf33bdd140af1c8be8e27"><strong>skbio/stats/ordination/tests/test_principal_coordinate_analysis.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,11 +9,12 @@</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy.testing</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">npt</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">copy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">deepcopy</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span><span class="p">,</span> <span class="n" style="color: #333;">main</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">skbio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">DistanceMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">OrdinationResults</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">skbio.stats.distance</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">DissimilarityMatrixError</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">skbio.stats.ordination</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pcoa</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">skbio.stats.ordination</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pcoa</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pcoa_biplot</span></span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">skbio.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_data_path</span><span class="p">,</span> <span class="n" style="color: #333;">assert_ordination_results_equal</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -126,5 +127,106 @@ class TestPCoA(TestCase):</td>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">pcoa</span><span class="p">([[</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">]])</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestPCoABiplot</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Crawford dataset for unweighted UniFrac</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'PCoA_sample_data_3'</span><span class="p">)</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ordination</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pcoa</span><span class="p">(</span><span class="n" style="color: #333;">DistanceMatrix</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">))</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'PCoA_biplot_descriptors'</span><span class="p">)</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">descriptors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_table</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">index_col</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Taxon'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">T</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pcoa_biplot_from_ape</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test against a reference implementation from R's ape package</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"><span class="s" style="color: #d14;"> The test data was generated with the R script below and using a</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"><span class="s" style="color: #d14;"> modified version of pcoa.biplot that returns the U matrix.</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"><span class="s" style="color: #d14;"> library(ape)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"><span class="s" style="color: #d14;"> # files can be found in the test data folder of the ordination module</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"><span class="s" style="color: #d14;"> y = t(read.table('PCoA_biplot_descriptors', row.names = 1, header = 1))</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"><span class="s" style="color: #d14;"> dm = read.table('PCoA_sample_data_3', row.names = 1, header = 1)</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"><span class="s" style="color: #d14;"> h = pcoa(dm)</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"><span class="s" style="color: #d14;"> # biplot.pcoa will only calculate the biplot for two axes at a time</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"><span class="s" style="color: #d14;"> acc = NULL</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"><span class="s" style="color: #d14;"> for (axes in c(1, 3, 5, 7)) {</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"><span class="s" style="color: #d14;"> new = biplot.pcoa(h, y, plot.axes=c(axes, axes+1),</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"><span class="s" style="color: #d14;"> rn = rep('.', length(colnames(dm))) )</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"><span class="s" style="color: #d14;"> if(is.null(acc)) {</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"><span class="s" style="color: #d14;"> acc = new</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"><span class="s" style="color: #d14;"> else {</span></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"><span class="s" style="color: #d14;"> b = acc</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"><span class="s" style="color: #d14;"> acc <- cbind(acc, new)</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"><span class="s" style="color: #d14;"> write.csv(acc, file='PCoA_biplot_projected_descriptors')</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pcoa_biplot</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ordination</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">descriptors</span><span class="p">)</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># we'll build a dummy ordination results object based on the expected</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># the main thing we'll compare and modify is the features dataframe</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">deepcopy</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">)</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'PCoA_biplot_projected_descriptors'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># R won't calculate the last dimension, so pad with zeros to make the</span></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># arrays comparable</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">exp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">features</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_table</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">','</span><span class="p">,</span> <span class="n" style="color: #333;">index_col</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">exp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="s" style="color: #d14;">'Axis.9'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">zeros_like</span><span class="p">(</span><span class="n" style="color: #333;">exp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="s" style="color: #d14;">'Axis.8'</span><span class="p">])</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># make the order comparable</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">exp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">features</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">features</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reindex</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">features</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">)</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">assert_ordination_results_equal</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">,</span> <span class="n" style="color: #333;">ignore_directionality</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">ignore_axis_labels</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pcoa_biplot_subset_input</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># create a 2D copy of the full ordination</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">two_dims</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">deepcopy</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ordination</span><span class="p">)</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">two_dims</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">eigvals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">two_dims</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">eigvals</span><span class="p">[:</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">two_dims</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">two_dims</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iloc</span><span class="p">[:,</span> <span class="p">:</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">two_dims</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">proportion_explained</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">two_dims</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">proportion_explained</span><span class="p">[:</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># only look at the features</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">subset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pcoa_biplot</span><span class="p">(</span><span class="n" style="color: #333;">two_dims</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">descriptors</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">features</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">full</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pcoa_biplot</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ordination</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">descriptors</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">features</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># the biplot should be identical regardless of the number of axes used</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">testing</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_almost_equal</span><span class="p">(</span><span class="n" style="color: #333;">subset</span><span class="p">,</span> <span class="n" style="color: #333;">full</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iloc</span><span class="p">[:,</span> <span class="p">:</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mismatching_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">new_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">descriptors</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">new_index</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Not.an.id'</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">descriptors</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Index</span><span class="p">(</span><span class="n" style="color: #333;">new_index</span><span class="p">)</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'The eigenvectors and the '</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="s" style="color: #d14;">'descriptors must describe the same '</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="s" style="color: #d14;">'samples.'</span><span class="p">):</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">pcoa_biplot</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ordination</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">descriptors</span><span class="p">)</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_not_a_pcoa</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ordination</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">short_method_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'RDA'</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ordination</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">long_method_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Redundancy Analysis'</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'This biplot computation can'</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="s" style="color: #d14;">' only be performed in a PCoA matrix.'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">pcoa_biplot</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ordination</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">descriptors</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_from_seralized_results</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># the current implementation of ordination results loses some</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># information, test that pcoa_biplot works fine regardless</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrdinationResults</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'PCoA_skbio'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">serialized</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pcoa_biplot</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">descriptors</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">in_memory</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pcoa_biplot</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ordination</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">descriptors</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">assert_ordination_results_equal</span><span class="p">(</span><span class="n" style="color: #333;">serialized</span><span class="p">,</span> <span class="n" style="color: #333;">in_memory</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">ignore_directionality</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">ignore_axis_labels</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">ignore_method_names</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#4ed31e9f5a84645db24d6d19dc646a3259d8471f"><strong>skbio/tree/_tree.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3098,3 +3098,118 @@ class TreeNode(SkbioObject):</td>
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3098
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<pre style="margin: 0;"> <span id="LC3098" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3099" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span></span>
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<pre style="margin: 0;"> <span id="LC3100" class="line" lang="python"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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3101
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<pre style="margin: 0;">+<span id="LC3101" class="line" lang="python"></span>
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3102
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<pre style="margin: 0;">+<span id="LC3102" class="line" lang="python"> <span class="nd">@experimental</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.5.3"</span><span class="p">)</span></span>
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3103
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<pre style="margin: 0;">+<span id="LC3103" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">support</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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3104
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<pre style="margin: 0;">+<span id="LC3104" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return support value of a node if available.</span></span>
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3105
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<pre style="margin: 0;">+<span id="LC3105" class="line" lang="python"></span>
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3106
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<pre style="margin: 0;">+<span id="LC3106" class="line" lang="python"><span class="s" style="color: #d14;"> Returns</span></span>
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3107
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<pre style="margin: 0;">+<span id="LC3107" class="line" lang="python"><span class="s" style="color: #d14;"> -------</span></span>
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3108
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<pre style="margin: 0;">+<span id="LC3108" class="line" lang="python"><span class="s" style="color: #d14;"> float or None</span></span>
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3109
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<pre style="margin: 0;">+<span id="LC3109" class="line" lang="python"><span class="s" style="color: #d14;"> support value of the node, or None if not available</span></span>
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3110
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<pre style="margin: 0;">+<span id="LC3110" class="line" lang="python"></span>
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3111
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<pre style="margin: 0;">+<span id="LC3111" class="line" lang="python"><span class="s" style="color: #d14;"> Notes</span></span>
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3112
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<pre style="margin: 0;">+<span id="LC3112" class="line" lang="python"><span class="s" style="color: #d14;"> -----</span></span>
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3113
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<pre style="margin: 0;">+<span id="LC3113" class="line" lang="python"><span class="s" style="color: #d14;"> A "support value" is defined as the numeric form of a whole node label</span></span>
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3114
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<pre style="margin: 0;">+<span id="LC3114" class="line" lang="python"><span class="s" style="color: #d14;"> without ":", or the part preceding the first ":" in the node label.</span></span>
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3115
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<pre style="margin: 0;">+<span id="LC3115" class="line" lang="python"></span>
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3116
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<pre style="margin: 0;">+<span id="LC3116" class="line" lang="python"><span class="s" style="color: #d14;"> For examples: "(a,b)1.0", "(a,b)1.0:2.5", and "(a,b)'1.0:species_A'".</span></span>
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3117
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<pre style="margin: 0;">+<span id="LC3117" class="line" lang="python"><span class="s" style="color: #d14;"> In these cases the support values are all 1.0.</span></span>
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3118
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<pre style="margin: 0;">+<span id="LC3118" class="line" lang="python"></span>
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3119
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<pre style="margin: 0;">+<span id="LC3119" class="line" lang="python"><span class="s" style="color: #d14;"> For examples: "(a,b):1.0" and "(a,b)species_A". In these cases there</span></span>
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3120
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<pre style="margin: 0;">+<span id="LC3120" class="line" lang="python"><span class="s" style="color: #d14;"> are no support values.</span></span>
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3121
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<pre style="margin: 0;">+<span id="LC3121" class="line" lang="python"></span>
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3122
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<pre style="margin: 0;">+<span id="LC3122" class="line" lang="python"><span class="s" style="color: #d14;"> Examples</span></span>
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3123
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<pre style="margin: 0;">+<span id="LC3123" class="line" lang="python"><span class="s" style="color: #d14;"> --------</span></span>
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3124
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<pre style="margin: 0;">+<span id="LC3124" class="line" lang="python"><span class="s" style="color: #d14;"> >>> from skbio import TreeNode</span></span>
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3125
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<pre style="margin: 0;">+<span id="LC3125" class="line" lang="python"><span class="s" style="color: #d14;"> >>> tree = TreeNode.read(['((a,b)99,(c,d):1.0);'])</span></span>
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3126
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<pre style="margin: 0;">+<span id="LC3126" class="line" lang="python"><span class="s" style="color: #d14;"> >>> tree.lca(['a', 'b']).support()</span></span>
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3127
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<pre style="margin: 0;">+<span id="LC3127" class="line" lang="python"><span class="s" style="color: #d14;"> 99.0</span></span>
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3128
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<pre style="margin: 0;">+<span id="LC3128" class="line" lang="python"><span class="s" style="color: #d14;"> >>> tree.lca(['c', 'd']).support() is None</span></span>
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3129
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<pre style="margin: 0;">+<span id="LC3129" class="line" lang="python"><span class="s" style="color: #d14;"> True</span></span>
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3130
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<pre style="margin: 0;">+<span id="LC3130" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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3131
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<pre style="margin: 0;">+<span id="LC3131" class="line" lang="python"> <span class="n" style="color: #333;">support</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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3132
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<pre style="margin: 0;">+<span id="LC3132" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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3133
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<pre style="margin: 0;">+<span id="LC3133" class="line" lang="python"> <span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">partition</span><span class="p">(</span><span class="s" style="color: #d14;">':'</span><span class="p">)</span></span>
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3134
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<pre style="margin: 0;">+<span id="LC3134" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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3135
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<pre style="margin: 0;">+<span id="LC3135" class="line" lang="python"> <span class="n" style="color: #333;">support</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">left</span><span class="p">)</span></span>
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3136
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<pre style="margin: 0;">+<span id="LC3136" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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3137
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<pre style="margin: 0;">+<span id="LC3137" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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3138
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<pre style="margin: 0;">+<span id="LC3138" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">support</span></span>
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3139
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<pre style="margin: 0;">+<span id="LC3139" class="line" lang="python"></span>
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3140
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<pre style="margin: 0;">+<span id="LC3140" class="line" lang="python"> <span class="nd">@experimental</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.5.3"</span><span class="p">)</span></span>
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3141
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<pre style="margin: 0;">+<span id="LC3141" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">unpack</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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3142
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<pre style="margin: 0;">+<span id="LC3142" class="line" lang="python"> <span class="s" style="color: #d14;">"""Unpack an internal node in place.</span></span>
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3143
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<pre style="margin: 0;">+<span id="LC3143" class="line" lang="python"></span>
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3144
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<pre style="margin: 0;">+<span id="LC3144" class="line" lang="python"><span class="s" style="color: #d14;"> Notes</span></span>
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3145
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<pre style="margin: 0;">+<span id="LC3145" class="line" lang="python"><span class="s" style="color: #d14;"> -----</span></span>
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<pre style="margin: 0;">+<span id="LC3146" class="line" lang="python"><span class="s" style="color: #d14;"> This function sequentially: 1) elongates child nodes by branch length</span></span>
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<pre style="margin: 0;">+<span id="LC3147" class="line" lang="python"><span class="s" style="color: #d14;"> of self (omit if there is no branch length), 2) removes self from</span></span>
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<pre style="margin: 0;">+<span id="LC3148" class="line" lang="python"><span class="s" style="color: #d14;"> parent node, and 3) grafts child nodes to parent node.</span></span>
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3149
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<pre style="margin: 0;">+<span id="LC3149" class="line" lang="python"></span>
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3150
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<pre style="margin: 0;">+<span id="LC3150" class="line" lang="python"><span class="s" style="color: #d14;"> Raises</span></span>
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3151
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<pre style="margin: 0;">+<span id="LC3151" class="line" lang="python"><span class="s" style="color: #d14;"> ------</span></span>
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3152
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<pre style="margin: 0;">+<span id="LC3152" class="line" lang="python"><span class="s" style="color: #d14;"> ValueError</span></span>
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3153
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<pre style="margin: 0;">+<span id="LC3153" class="line" lang="python"><span class="s" style="color: #d14;"> if input node is root or tip</span></span>
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3154
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<pre style="margin: 0;">+<span id="LC3154" class="line" lang="python"></span>
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3155
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<pre style="margin: 0;">+<span id="LC3155" class="line" lang="python"><span class="s" style="color: #d14;"> See also</span></span>
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3156
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<pre style="margin: 0;">+<span id="LC3156" class="line" lang="python"><span class="s" style="color: #d14;"> --------</span></span>
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3157
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<pre style="margin: 0;">+<span id="LC3157" class="line" lang="python"><span class="s" style="color: #d14;"> unpack_by_func</span></span>
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3158
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<pre style="margin: 0;">+<span id="LC3158" class="line" lang="python"><span class="s" style="color: #d14;"> prune</span></span>
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3159
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<pre style="margin: 0;">+<span id="LC3159" class="line" lang="python"></span>
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3160
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<pre style="margin: 0;">+<span id="LC3160" class="line" lang="python"><span class="s" style="color: #d14;"> Examples</span></span>
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3161
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<pre style="margin: 0;">+<span id="LC3161" class="line" lang="python"><span class="s" style="color: #d14;"> --------</span></span>
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3162
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<pre style="margin: 0;">+<span id="LC3162" class="line" lang="python"><span class="s" style="color: #d14;"> >>> from skbio import TreeNode</span></span>
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3163
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<pre style="margin: 0;">+<span id="LC3163" class="line" lang="python"><span class="s" style="color: #d14;"> >>> tree = TreeNode.read(['((c:2.0,d:3.0)a:1.0,(e:2.0,f:1.0)b:2.0);'])</span></span>
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3164
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<pre style="margin: 0;">+<span id="LC3164" class="line" lang="python"><span class="s" style="color: #d14;"> >>> tree.find('b').unpack()</span></span>
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3165
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<pre style="margin: 0;">+<span id="LC3165" class="line" lang="python"><span class="s" style="color: #d14;"> >>> print(tree)</span></span>
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3166
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<pre style="margin: 0;">+<span id="LC3166" class="line" lang="python"><span class="s" style="color: #d14;"> ((c:2.0,d:3.0)a:1.0,e:4.0,f:3.0);</span></span>
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3167
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<pre style="margin: 0;">+<span id="LC3167" class="line" lang="python"><span class="s" style="color: #d14;"> <BLANKLINE></span></span>
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3168
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<pre style="margin: 0;">+<span id="LC3168" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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3169
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<pre style="margin: 0;">+<span id="LC3169" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_root</span><span class="p">():</span></span>
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3170
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<pre style="margin: 0;">+<span id="LC3170" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">TreeError</span><span class="p">(</span><span class="s" style="color: #d14;">'Cannot unpack root.'</span><span class="p">)</span></span>
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3171
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<pre style="margin: 0;">+<span id="LC3171" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_tip</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC3172" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">TreeError</span><span class="p">(</span><span class="s" style="color: #d14;">'Cannot unpack tip.'</span><span class="p">)</span></span>
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3173
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<pre style="margin: 0;">+<span id="LC3173" class="line" lang="python"> <span class="n" style="color: #333;">parent</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parent</span></span>
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3174
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<pre style="margin: 0;">+<span id="LC3174" class="line" lang="python"> <span class="n" style="color: #333;">blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="ow" style="font-weight: 600;">or</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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3175
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<pre style="margin: 0;">+<span id="LC3175" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">child</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">:</span></span>
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3176
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<pre style="margin: 0;">+<span id="LC3176" class="line" lang="python"> <span class="n" style="color: #333;">clen</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">child</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="ow" style="font-weight: 600;">or</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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3177
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<pre style="margin: 0;">+<span id="LC3177" class="line" lang="python"> <span class="n" style="color: #333;">child</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">clen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">blen</span> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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3178
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<pre style="margin: 0;">+<span id="LC3178" class="line" lang="python"> <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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3179
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<pre style="margin: 0;">+<span id="LC3179" class="line" lang="python"> <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">)</span></span>
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3180
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<pre style="margin: 0;">+<span id="LC3180" class="line" lang="python"></span>
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3181
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<pre style="margin: 0;">+<span id="LC3181" class="line" lang="python"> <span class="nd">@experimental</span><span class="p">(</span><span class="n" style="color: #333;">as_of</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.5.3"</span><span class="p">)</span></span>
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3182
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<pre style="margin: 0;">+<span id="LC3182" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">unpack_by_func</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">func</span><span class="p">):</span></span>
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3183
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<pre style="margin: 0;">+<span id="LC3183" class="line" lang="python"> <span class="s" style="color: #d14;">"""Unpack internal nodes of a tree that meet certain criteria.</span></span>
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3184
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<pre style="margin: 0;">+<span id="LC3184" class="line" lang="python"></span>
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3185
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<pre style="margin: 0;">+<span id="LC3185" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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3186
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<pre style="margin: 0;">+<span id="LC3186" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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3187
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<pre style="margin: 0;">+<span id="LC3187" class="line" lang="python"><span class="s" style="color: #d14;"> func : function</span></span>
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3188
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<pre style="margin: 0;">+<span id="LC3188" class="line" lang="python"><span class="s" style="color: #d14;"> a function that accepts a TreeNode and returns `True` or `False`,</span></span>
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3189
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<pre style="margin: 0;">+<span id="LC3189" class="line" lang="python"><span class="s" style="color: #d14;"> where `True` indicates the node is to be unpacked</span></span>
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3190
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<pre style="margin: 0;">+<span id="LC3190" class="line" lang="python"></span>
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3191
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<pre style="margin: 0;">+<span id="LC3191" class="line" lang="python"><span class="s" style="color: #d14;"> See also</span></span>
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3192
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<pre style="margin: 0;">+<span id="LC3192" class="line" lang="python"><span class="s" style="color: #d14;"> --------</span></span>
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3193
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<pre style="margin: 0;">+<span id="LC3193" class="line" lang="python"><span class="s" style="color: #d14;"> unpack</span></span>
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3194
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<pre style="margin: 0;">+<span id="LC3194" class="line" lang="python"><span class="s" style="color: #d14;"> prune</span></span>
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3195
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<pre style="margin: 0;">+<span id="LC3195" class="line" lang="python"></span>
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3196
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<pre style="margin: 0;">+<span id="LC3196" class="line" lang="python"><span class="s" style="color: #d14;"> Examples</span></span>
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3197
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<pre style="margin: 0;">+<span id="LC3197" class="line" lang="python"><span class="s" style="color: #d14;"> --------</span></span>
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3198
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<pre style="margin: 0;">+<span id="LC3198" class="line" lang="python"><span class="s" style="color: #d14;"> >>> from skbio import TreeNode</span></span>
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3199
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<pre style="margin: 0;">+<span id="LC3199" class="line" lang="python"><span class="s" style="color: #d14;"> >>> tree = TreeNode.read(['((c:2,d:3)a:1,(e:1,f:2)b:2);'])</span></span>
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3200
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<pre style="margin: 0;">+<span id="LC3200" class="line" lang="python"><span class="s" style="color: #d14;"> >>> tree.unpack_by_func(lambda x: x.length <= 1)</span></span>
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3201
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<pre style="margin: 0;">+<span id="LC3201" class="line" lang="python"><span class="s" style="color: #d14;"> >>> print(tree)</span></span>
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3202
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<pre style="margin: 0;">+<span id="LC3202" class="line" lang="python"><span class="s" style="color: #d14;"> ((e:1.0,f:2.0)b:2.0,c:3.0,d:4.0);</span></span>
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3203
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<pre style="margin: 0;">+<span id="LC3203" class="line" lang="python"><span class="s" style="color: #d14;"> <BLANKLINE></span></span>
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3204
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<pre style="margin: 0;">+<span id="LC3204" class="line" lang="python"><span class="s" style="color: #d14;"> >>> tree = TreeNode.read(['(((a,b)85,(c,d)78)75,(e,(f,g)64)80);'])</span></span>
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3205
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<pre style="margin: 0;">+<span id="LC3205" class="line" lang="python"><span class="s" style="color: #d14;"> >>> tree.unpack_by_func(lambda x: x.support() < 75)</span></span>
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3206
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<pre style="margin: 0;">+<span id="LC3206" class="line" lang="python"><span class="s" style="color: #d14;"> >>> print(tree)</span></span>
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3207
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<pre style="margin: 0;">+<span id="LC3207" class="line" lang="python"><span class="s" style="color: #d14;"> (((a,b)85,(c,d)78)75,(e,f,g)80);</span></span>
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3208
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<pre style="margin: 0;">+<span id="LC3208" class="line" lang="python"><span class="s" style="color: #d14;"> <BLANKLINE></span></span>
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3209
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<pre style="margin: 0;">+<span id="LC3209" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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3210
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<pre style="margin: 0;">+<span id="LC3210" class="line" lang="python"> <span class="n" style="color: #333;">nodes_to_unpack</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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3211
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<pre style="margin: 0;">+<span id="LC3211" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">non_tips</span><span class="p">(</span><span class="n" style="color: #333;">include_self</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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3212
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<pre style="margin: 0;">+<span id="LC3212" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">func</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">):</span></span>
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3213
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<pre style="margin: 0;">+<span id="LC3213" class="line" lang="python"> <span class="n" style="color: #333;">nodes_to_unpack</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">)</span></span>
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3214
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<pre style="margin: 0;">+<span id="LC3214" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">nodes_to_unpack</span><span class="p">:</span></span>
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3215
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<pre style="margin: 0;">+<span id="LC3215" class="line" lang="python"> <span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unpack</span><span class="p">()</span></span></pre>
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<li id="2fb7dcc827f95572c1c47da26ace6f71c45adcf1">
<a href="https://salsa.debian.org/med-team/python-skbio/compare/ba9bddb165769afd7052c5cbe2737a0fa6a0ab3a...f2418d0e0d131c4475d3f3add2f66bbe4845af84#2fb7dcc827f95572c1c47da26ace6f71c45adcf1"><strong>skbio/tree/tests/test_tree.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1303,6 +1303,135 @@ class TreeTests(TestCase):</td>
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1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="n" style="color: #333;">MissingNodeError</span><span class="p">):</span></span>
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1304
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1304
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<pre style="margin: 0;"> <span id="LC1304" class="line" lang="python"> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">simple_t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shuffle</span><span class="p">(</span><span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'y'</span><span class="p">]))</span></span>
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1305
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1305
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<pre style="margin: 0;"> <span id="LC1305" class="line" lang="python"></span>
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1306
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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_support</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1307
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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="python"> <span class="s" style="color: #d14;">"""Get support value of a node."""</span></span>
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1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test nodes with support alone as label</span></span>
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1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'((a,b)75,(c,d)90);'</span><span class="p">])</span></span>
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1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="python"> <span class="n" style="color: #333;">node1</span><span class="p">,</span> <span class="n" style="color: #333;">node2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span></span>
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1311
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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">node1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">support</span><span class="p">(),</span> <span class="mf" style="color: #099;">75.0</span><span class="p">)</span></span>
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1312
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<pre style="margin: 0;">+<span id="LC1312" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">node2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">support</span><span class="p">(),</span> <span class="mf" style="color: #099;">90.0</span><span class="p">)</span></span>
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1313
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<pre style="margin: 0;">+<span id="LC1313" class="line" lang="python"></span>
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1314
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<pre style="margin: 0;">+<span id="LC1314" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test nodes with support and branch length</span></span>
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1315
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<pre style="margin: 0;">+<span id="LC1315" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'((a,b)0.85:1.23,(c,d)0.95:4.56);'</span><span class="p">])</span></span>
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1316
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<pre style="margin: 0;">+<span id="LC1316" class="line" lang="python"> <span class="n" style="color: #333;">node1</span><span class="p">,</span> <span class="n" style="color: #333;">node2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span></span>
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1317
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<pre style="margin: 0;">+<span id="LC1317" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">node1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">support</span><span class="p">(),</span> <span class="mf" style="color: #099;">0.85</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1318
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">node2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">support</span><span class="p">(),</span> <span class="mf" style="color: #099;">0.95</span><span class="p">)</span></span>
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1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="python"></span>
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1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test support values that are negative or scientific notation (not a</span></span>
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1321
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># common scenario but can happen)</span></span>
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1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'((a,b)-1.23,(c,d)1.23e-4);'</span><span class="p">])</span></span>
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1323
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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="python"> <span class="n" style="color: #333;">node1</span><span class="p">,</span> <span class="n" style="color: #333;">node2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1324
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<pre style="margin: 0;">+<span id="LC1324" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">node1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">support</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.23</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1325
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<pre style="margin: 0;">+<span id="LC1325" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">node2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">support</span><span class="p">(),</span> <span class="mf" style="color: #099;">0.000123</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1326
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<pre style="margin: 0;">+<span id="LC1326" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1327
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<pre style="margin: 0;">+<span id="LC1327" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test nodes with support and extra label (not a common scenario but</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1328
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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># can happen)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1329
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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'((a,b)</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">80:X</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">,(c,d)</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">60:Y</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">);'</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1330
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="python"> <span class="n" style="color: #333;">node1</span><span class="p">,</span> <span class="n" style="color: #333;">node2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">node1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">support</span><span class="p">(),</span> <span class="mf" style="color: #099;">80.0</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">node2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">support</span><span class="p">(),</span> <span class="mf" style="color: #099;">60.0</span><span class="p">)</span></span>
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1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test nodes without label, with non-numeric label, and with branch</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># length only</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'((a,b),(c,d)x,(e,f):1.0);'</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">children</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1338
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIsNone</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">support</span><span class="p">())</span></span>
</pre>
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1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="python"></span>
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1340
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_unpack</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="python"> <span class="s" style="color: #d14;">"""Unpack an internal node."""</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1342
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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test unpacking a node without branch length</span></span>
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1343
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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'((c,d)a,(e,f)b);'</span><span class="p">])</span></span>
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1344
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<pre style="margin: 0;">+<span id="LC1344" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">'b'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unpack</span><span class="p">()</span></span>
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1345
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'((c,d)a,e,f);</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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1346
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">),</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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1347
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<pre style="margin: 0;">+<span id="LC1347" class="line" lang="python"></span>
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1348
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<pre style="margin: 0;">+<span id="LC1348" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test unpacking a node with branch length</span></span>
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1349
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'((c:2.0,d:3.0)a:1.0,(e:2.0,f:1.0)b:2.0);'</span><span class="p">])</span></span>
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1350
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<pre style="margin: 0;">+<span id="LC1350" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">'b'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unpack</span><span class="p">()</span></span>
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1351
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<pre style="margin: 0;">+<span id="LC1351" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'((c:2.0,d:3.0)a:1.0,e:4.0,f:3.0);'</span></span>
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1352
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<pre style="margin: 0;">+<span id="LC1352" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(),</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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1353
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<pre style="margin: 0;">+<span id="LC1353" class="line" lang="python"></span>
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1354
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<pre style="margin: 0;">+<span id="LC1354" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test attempting to unpack root</span></span>
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1355
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<pre style="margin: 0;">+<span id="LC1355" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'((d,e)b,(f,g)c)a;'</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1356
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<pre style="margin: 0;">+<span id="LC1356" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Cannot unpack root.'</span></span>
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1357
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<pre style="margin: 0;">+<span id="LC1357" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="n" style="color: #333;">TreeError</span><span class="p">,</span> <span class="n" style="color: #333;">msg</span><span class="p">):</span></span>
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1358
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<pre style="margin: 0;">+<span id="LC1358" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">'a'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unpack</span><span class="p">()</span></span>
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1359
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<pre style="margin: 0;">+<span id="LC1359" class="line" lang="python"></span>
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1360
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<pre style="margin: 0;">+<span id="LC1360" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test attempting to unpack tip</span></span>
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1361
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<pre style="margin: 0;">+<span id="LC1361" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Cannot unpack tip.'</span></span>
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1362
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<pre style="margin: 0;">+<span id="LC1362" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="n" style="color: #333;">TreeError</span><span class="p">,</span> <span class="n" style="color: #333;">msg</span><span class="p">):</span></span>
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1363
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<pre style="margin: 0;">+<span id="LC1363" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">'d'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unpack</span><span class="p">()</span></span>
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1364
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<pre style="margin: 0;">+<span id="LC1364" class="line" lang="python"></span>
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1365
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<pre style="margin: 0;">+<span id="LC1365" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_unpack_by_func</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1366
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<pre style="margin: 0;">+<span id="LC1366" class="line" lang="python"> <span class="s" style="color: #d14;">"""Unpack internal nodes of a tree by a function."""</span></span>
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1367
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<pre style="margin: 0;">+<span id="LC1367" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># unpack internal nodes with branch length <= 1.0</span></span>
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1368
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<pre style="margin: 0;">+<span id="LC1368" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">func</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">):</span></span>
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1369
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<pre style="margin: 0;">+<span id="LC1369" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">1.0</span></span>
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1370
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<pre style="margin: 0;">+<span id="LC1370" class="line" lang="python"></span>
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1371
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<pre style="margin: 0;">+<span id="LC1371" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># will unpack node 'a', but not tip 'e'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1372
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<pre style="margin: 0;">+<span id="LC1372" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># will add the branch length of 'a' to its child nodes 'c' and 'd'</span></span>
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1373
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<pre style="margin: 0;">+<span id="LC1373" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'((c:2,d:3)a:1,(e:1,f:2)b:2);'</span><span class="p">])</span></span>
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1374
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unpack_by_func</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="p">)</span></span>
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1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'((e:1.0,f:2.0)b:2.0,c:3.0,d:4.0);'</span></span>
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1376
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(),</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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1377
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<pre style="margin: 0;">+<span id="LC1377" class="line" lang="python"></span>
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1378
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<pre style="margin: 0;">+<span id="LC1378" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># unpack internal nodes with branch length < 2.01</span></span>
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1379
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<pre style="margin: 0;">+<span id="LC1379" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># will unpack both 'a' and 'b'</span></span>
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1380
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<pre style="margin: 0;">+<span id="LC1380" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'((c:2,d:3)a:1,(e:1,f:2)b:2);'</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1381
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<pre style="margin: 0;">+<span id="LC1381" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unpack_by_func</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">2.0</span><span class="p">)</span></span>
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1382
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<pre style="margin: 0;">+<span id="LC1382" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'(c:3.0,d:4.0,e:3.0,f:4.0);'</span></span>
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1383
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<pre style="margin: 0;">+<span id="LC1383" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(),</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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1384
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<pre style="margin: 0;">+<span id="LC1384" class="line" lang="python"></span>
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1385
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<pre style="margin: 0;">+<span id="LC1385" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># unpack two nested nodes 'a' and 'c' simultaneously</span></span>
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1386
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<pre style="margin: 0;">+<span id="LC1386" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'(((e:3,f:2)c:1,d:3)a:1,b:4);'</span><span class="p">])</span></span>
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1387
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<pre style="margin: 0;">+<span id="LC1387" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unpack_by_func</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">2.0</span><span class="p">)</span></span>
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1388
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<pre style="margin: 0;">+<span id="LC1388" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'(b:4.0,d:4.0,e:5.0,f:4.0);'</span></span>
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1389
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<pre style="margin: 0;">+<span id="LC1389" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(),</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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1390
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<pre style="margin: 0;">+<span id="LC1390" class="line" lang="python"></span>
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1391
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<pre style="margin: 0;">+<span id="LC1391" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test a complicated scenario (unpacking nodes 'g', 'h' and 'm')</span></span>
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1392
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<pre style="margin: 0;">+<span id="LC1392" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">func</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">):</span></span>
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1393
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<pre style="margin: 0;">+<span id="LC1393" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">2.0</span></span>
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1394
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<pre style="margin: 0;">+<span id="LC1394" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'(((a:1.04,b:2.32,c:1.44)d:3.20,'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1395
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<pre style="margin: 0;">+<span id="LC1395" class="line" lang="python"> <span class="s" style="color: #d14;">'(e:3.91,f:2.47)g:1.21)h:1.75,'</span></span>
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1396
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<pre style="margin: 0;">+<span id="LC1396" class="line" lang="python"> <span class="s" style="color: #d14;">'(i:4.14,(j:2.06,k:1.58)l:3.32)m:0.77);'</span><span class="p">])</span></span>
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1397
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<pre style="margin: 0;">+<span id="LC1397" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unpack_by_func</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="p">)</span></span>
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1398
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<pre style="margin: 0;">+<span id="LC1398" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'((a:1.04,b:2.32,c:1.44)d:4.95,e:6.87,f:5.43,i:4.91,'</span></span>
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1399
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<pre style="margin: 0;">+<span id="LC1399" class="line" lang="python"> <span class="s" style="color: #d14;">'(j:2.06,k:1.58)l:4.09);'</span><span class="p">)</span></span>
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1400
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<pre style="margin: 0;">+<span id="LC1400" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(),</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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1401
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<pre style="margin: 0;">+<span id="LC1401" class="line" lang="python"></span>
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1402
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<pre style="margin: 0;">+<span id="LC1402" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># unpack nodes with support < 75</span></span>
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1403
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<pre style="margin: 0;">+<span id="LC1403" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">func</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">):</span></span>
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1404
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<pre style="margin: 0;">+<span id="LC1404" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">support</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">75</span></span>
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1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'(((a,b)85,(c,d)78)75,(e,(f,g)64)80);'</span><span class="p">])</span></span>
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1406
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<pre style="margin: 0;">+<span id="LC1406" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unpack_by_func</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="p">)</span></span>
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1407
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<pre style="margin: 0;">+<span id="LC1407" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'(((a,b)85,(c,d)78)75,(e,f,g)80);'</span></span>
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1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(),</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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1409
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="python"></span>
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1410
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># unpack nodes with support < 85</span></span>
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1411
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'(((a,b)85,(c,d)78)75,(e,(f,g)64)80);'</span><span class="p">])</span></span>
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1412
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<pre style="margin: 0;">+<span id="LC1412" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unpack_by_func</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">support</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">85</span><span class="p">)</span></span>
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1413
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'((a,b)85,c,d,e,f,g);'</span></span>
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1414
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<pre style="margin: 0;">+<span id="LC1414" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(),</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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1415
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<pre style="margin: 0;">+<span id="LC1415" class="line" lang="python"></span>
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1416
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<pre style="margin: 0;">+<span id="LC1416" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># unpack nodes with support < 0.95</span></span>
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1417
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'(((a,b)0.97,(c,d)0.98)1.0,(e,(f,g)0.88)0.96);'</span><span class="p">])</span></span>
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1418
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<pre style="margin: 0;">+<span id="LC1418" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unpack_by_func</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">support</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.95</span><span class="p">)</span></span>
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1419
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<pre style="margin: 0;">+<span id="LC1419" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'(((a,b)0.97,(c,d)0.98)1.0,(e,f,g)0.96);'</span></span>
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1420
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<pre style="margin: 0;">+<span id="LC1420" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(),</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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1421
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<pre style="margin: 0;">+<span id="LC1421" class="line" lang="python"></span>
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1422
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<pre style="margin: 0;">+<span id="LC1422" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test a case where there are branch lengths, none support values and</span></span>
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1423
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<pre style="margin: 0;">+<span id="LC1423" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># node labels</span></span>
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1424
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<pre style="margin: 0;">+<span id="LC1424" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">func</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1425
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<pre style="margin: 0;">+<span id="LC1425" class="line" lang="python"> <span class="n" style="color: #333;">sup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">support</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1426
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<pre style="margin: 0;">+<span id="LC1426" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sup</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sup</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">75</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1427
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<pre style="margin: 0;">+<span id="LC1427" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TreeNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">([</span><span class="s" style="color: #d14;">'(((a:1.02,b:0.33)85:0.12,(c:0.86,d:2.23)'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1428
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<pre style="margin: 0;">+<span id="LC1428" class="line" lang="python"> <span class="s" style="color: #d14;">'70:3.02)75:0.95,(e:1.43,(f:1.69,g:1.92)64:0.20)'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1429
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<pre style="margin: 0;">+<span id="LC1429" class="line" lang="python"> <span class="s" style="color: #d14;">'node:0.35)root;'</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1430
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<pre style="margin: 0;">+<span id="LC1430" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unpack_by_func</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1431
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<pre style="margin: 0;">+<span id="LC1431" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'(((a:1.02,b:0.33)85:0.12,c:3.88,d:5.25)75:0.95,'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1432
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<pre style="margin: 0;">+<span id="LC1432" class="line" lang="python"> <span class="s" style="color: #d14;">'(e:1.43,f:1.89,g:2.12)node:0.35)root;'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1433
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<pre style="margin: 0;">+<span id="LC1433" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(),</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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1434
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<pre style="margin: 0;">+<span id="LC1434" class="line" lang="python"></span>
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1306
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1435
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<pre style="margin: 0;"> <span id="LC1435" class="line" lang="python"></span>
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1307
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1436
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<pre style="margin: 0;"> <span id="LC1436" class="line" lang="python"><span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""</span></span>
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1308
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1437
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<pre style="margin: 0;"> <span id="LC1437" class="line" lang="python"><span class="s" style="color: #d14;">(</span></span>
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