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<h3>
Andrius Merkys pushed to branch master
at <a href="https://salsa.debian.org/med-team/beast-mcmc">Debian Med / beast-mcmc</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/beast-mcmc/commit/0f836acd455bbfdebd1bbac4550c9913d553fcc7">0f836acd</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2019-05-21T08:30:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Preparing to use newer version of libejml-java. Performing the source transition using convert_to_ejml31.py script from libejml-java.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beast-mcmc/commit/6d7d364263c8bcf0b412e034008bbc92681b44eb">6d7d3642</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2019-05-21T08:41:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Migrating non-automigrated org.ejml.alg.dense.misc.UnrolledInverseFromMinor.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beast-mcmc/commit/d65b3ffc5b9f27d3f03bf5292f796c26cc515caf">d65b3ffc</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2019-05-21T09:03:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Migrating non-automigrated org.ejml.alg.dense.decomposition.lu.LUDecompositionAlt_D64.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beast-mcmc/commit/26c4975815e4b06d0a8e2ba3f66674d12a186d83">26c49758</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2019-05-21T09:18:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Finishing migration.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beast-mcmc/commit/a15aca9e2917d681657e95f72ad5a979a9bd35ef">a15aca9e</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2019-05-21T09:25:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding versioned b-dep on libejml-java.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beast-mcmc/commit/8b6ddc1a4c86353dd71310d418ffb0ba2a3b06af">8b6ddc1a</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2019-05-21T09:27:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding patch description for update-ejml.patch.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beast-mcmc/commit/d5cab6e953b9b255fc9b227c1a34b0a1f026f1f4">d5cab6e9</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2019-05-21T09:28:52Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Preparing for the next upload.
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#60bc9af5ec216f8a84f4c14ada50ecf18d619e42">
debian/patches/fix_classpath_in_build_xml.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#da07bcb0f06a82597c6bdf5125f96c597b960ea1">
<span class="new-file">
+
debian/patches/update-ejml.patch
</span>
</a>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/beast-mcmc/compare/0e8c48145b38c678c18a9d1cbd04eb7aa70df039...d5cab6e953b9b255fc9b227c1a34b0a1f026f1f4#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">beast-mcmc (1.10.4+dfsg-2) UNRELEASED; urgency=medium</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">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Migrating to libejml-java 0.38.</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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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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">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andrius Merkys <merkys@debian.org> Tue, 21 May 2019 05:27:43 -0400</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">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext">beast-mcmc (1.10.4+dfsg-1) unstable; urgency=medium</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="LC10" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/beast-mcmc/compare/0e8c48145b38c678c18a9d1cbd04eb7aa70df039...d5cab6e953b9b255fc9b227c1a34b0a1f026f1f4#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" 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="22" 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">@@ -22,7 +22,7 @@ Build-Depends: debhelper (>= 11~),</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> junit4,</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> libmtj-java,</span>
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<td class="diff-line-num old_line" data-linenumber="24" 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="LC24" class="line" lang="plaintext"> libitext1-java,</span>
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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> libejml-java,</span>
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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">
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> libejml-java<span class="idiff left right"> (>= 0.38)</span>,</span>
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<td class="diff-line-num old_line" data-linenumber="26" 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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<td class="diff-line-num new_line" data-linenumber="26" 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="LC26" class="line" lang="plaintext"> libjlapack-java</span>
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<td class="diff-line-num old_line" data-linenumber="27" 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="LC27" class="line" lang="plaintext">Standards-Version: 4.2.1</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/beast-mcmc</span>
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<a href="https://salsa.debian.org/med-team/beast-mcmc/compare/0e8c48145b38c678c18a9d1cbd04eb7aa70df039...d5cab6e953b9b255fc9b227c1a34b0a1f026f1f4#60bc9af5ec216f8a84f4c14ada50ecf18d619e42"><strong>debian/patches/fix_classpath_in_build_xml.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" 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">@@ -13,7 +13,7 @@ Forwarded: no</td>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> <property name="dist" location="${build}/dist"/></span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> </span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> <property name="main_class_BEAST" value="dr.app.beast.BeastMain"/></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -48,6 +49,<span class="idiff left right">2</span>1 @@</span></span>
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<td class="diff-line-num new old_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">
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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="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -48,6 +49,<span class="idiff left right">3</span>1 @@</span></span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> </span>
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18
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> <path id="classpath"></span>
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<td class="diff-line-num old_line" data-linenumber="19" 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">
19
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<td class="diff-line-num new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> <fileset dir="${lib}" includes="**/*.jar"/></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" 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="31" 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">@@ -31,11 +31,21 @@ Forwarded: no</td>
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<td class="diff-line-num old_line" data-linenumber="31" 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">
31
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="${deblib}" includes="mtj.jar"/></span></span>
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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
32
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="${deblib}" includes="options.jar"/></span></span>
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<td class="diff-line-num old_line" data-linenumber="33" 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">
33
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="${deblib}" includes="EJML.jar"/></span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="${deblib}" includes="ejml-all.jar"/></span></span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="35" 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">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="${deblib}" includes="ejml-all.jar"/></span></span>
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<td class="diff-line-num new old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="${deblib}" includes="ejml-cdense.jar"/></span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="37" 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">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="${deblib}" includes="ejml-core.jar"/></span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="${deblib}" includes="ejml-ddense.jar"/></span></span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="39" 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">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="${deblib}" includes="ejml-dsparse.jar"/></span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="${deblib}" includes="ejml-experimental.jar"/></span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="41" 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">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="${deblib}" includes="ejml-fdense.jar"/></span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="${deblib}" includes="ejml-simple.jar"/></span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="${deblib}" includes="ejml-zdense.jar"/></span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
34
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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="${deblib}" includes="jlapack-lapack.jar"/></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> </path></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> <!-- start --></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">59,17 +175</span>,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">61,17 +187</span>,6 @@</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> <include name="org/virion/jam/**/*.png"/></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> <include name="dr/**/*.properties"/></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> </fileset></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">@@ -53,7 +63,7 @@ Forwarded: no</td>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> </jar></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"> <!-- Put everything in ${build} into the beauti.jar file --></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -22<span class="idiff left right">6,11 +231</span>,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -22<span class="idiff left right">8,11 +243</span>,6 @@</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> <fileset dir="${src}"></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"> <include name="dr/**/*.png"/></span>
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59
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"> </fileset></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">@@ -67,7 +77,7 @@ Forwarded: no</td>
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67
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"> <!-- Put everything in ${build} into the trace.jar file --></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/.classpath</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/.classpath</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,20 +1,<span class="idiff left right">18</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,20 +1,<span class="idiff left right">27</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"> <?xml version="1.0" encoding="UTF-8"?></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"> <classpath></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"> <classpathentry kind="src" path="src"/></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">@@ -98,6 +108,15 @@ Forwarded: no</td>
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98
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/mtj.jar"/></span></span>
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99
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/commons-math.jar"/></span></span>
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100
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/EJML.jar"/></span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/ejml-all.jar"/></span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/ejml-cdense.jar"/></span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/ejml-core.jar"/></span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/ejml-ddense.jar"/></span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/ejml-dsparse.jar"/></span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/ejml-experimental.jar"/></span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/ejml-fdense.jar"/></span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/ejml-simple.jar"/></span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/ejml-zdense.jar"/></span></span>
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101
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/jlapack-lapack.jar"/></span></span>
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102
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="diff"> <classpathentry kind="output" path="bin"/></span>
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103
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="diff"> </classpath></span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/beast-mcmc/compare/0e8c48145b38c678c18a9d1cbd04eb7aa70df039...d5cab6e953b9b255fc9b227c1a34b0a1f026f1f4#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -3,3 +3,4 @@ fix_classpath_in_build_xml.patch</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">create_soname.patch</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">fix_encoding.patch</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">ignore_mac_install.patch</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">update-ejml.patch</span></pre>
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<li id="da07bcb0f06a82597c6bdf5125f96c597b960ea1">
<a href="https://salsa.debian.org/med-team/beast-mcmc/compare/0e8c48145b38c678c18a9d1cbd04eb7aa70df039...d5cab6e953b9b255fc9b227c1a34b0a1f026f1f4#da07bcb0f06a82597c6bdf5125f96c597b960ea1"><strong>debian/patches/update-ejml.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andrius Merkys <merkys@debian.org></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Description: Migrating to libejml-java v0.38.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/dr/evomodel/treedatalikelihood/continuous/cdi/ContinuousDiffusionIntegrator.java</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/dr/evomodel/treedatalikelihood/continuous/cdi/ContinuousDiffusionIntegrator.java</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -413,7 +413,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> final double vi = branchLengths[imo];</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> final double vj = branchLengths[jmo];</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> if (DEBUG) {</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> System.err.println("updatePreOrderPartial for node " + iBuffer);</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -427,33 +427,33 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> final double pk = prePartials[kbo + dimTrait];</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> final double pj = partials[jbo + dimTrait];</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pk = wrap(prePartials, kbo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// // final DenseMatrix64F Pj = wrap(partials, jbo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pk = wrap(prePartials, kbo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// // final DMatrixRMaj Pj = wrap(partials, jbo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// // final DenseMatrix64F Vk = wrap(prePartials, kbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vj = wrap(partials, jbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// // final DMatrixRMaj Vk = wrap(prePartials, kbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vj = wrap(partials, jbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> // B. Inflate variance along sibling branch using matrix inversion</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> final double pjp = Double.isInfinite(pj) ?</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> 1.0 / vj : pj / (1.0 + pj * vj);</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// // final DenseMatrix64F Vjp = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vjp = matrix0;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Vj, vj, Vd, Vjp);</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// // final DMatrixRMaj Vjp = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vjp = matrix0;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Vj, vj, Vd, Vjp);</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// // final DenseMatrix64F Pjp = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pjp = matrix1;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// // final DMatrixRMaj Pjp = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pjp = matrix1;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> // InversionResult cj = safeInvert(Vjp, Pjp, false);</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> //</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// // final DenseMatrix64F Pip = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pip = matrix2;</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Pk, Pjp, Pip);</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// // final DMatrixRMaj Pip = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pip = matrix2;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Pk, Pjp, Pip);</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> final double pip = pjp + pk;</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// // final DenseMatrix64F Vip = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vip = matrix3;</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// // final DMatrixRMaj Vip = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vip = matrix3;</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> // InversionResult cip = safeInvert(Pip, Vip, false);</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> // // C. Compute prePartial mean</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -484,11 +484,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> final double pi = Double.isInfinite(pip) ?</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> 1.0 / vi : pip / (1.0 + pip * vi);</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vi = Vip;</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(vi, Vd, Vip, Vi);</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vi = Vip;</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(vi, Vd, Vip, Vi);</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// // final DenseMatrix64F Pi = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pi = matrix4;</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// // final DMatrixRMaj Pi = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pi = matrix4;</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> // InversionResult ci = safeInvert(Vi, Pi, false);</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> // // X. Store precision results for node</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/dr/evomodel/treedatalikelihood/continuous/cdi/MultivariateIntegrator.java</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/dr/evomodel/treedatalikelihood/continuous/cdi/MultivariateIntegrator.java</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2,8 +2,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> import dr.math.matrixAlgebra.WrappedVector;</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> import dr.math.matrixAlgebra.missingData.InversionResult;</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.data.DenseMatrix64F;</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.ops.CommonOps;</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.data.DMatrixRMaj;</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.dense.row.CommonOps_DDRM;</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> import java.util.HashMap;</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> import java.util.Map;</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -56,13 +56,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> private final Map<String, Long> times;</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F matrix0;</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F matrix1;</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F matrix2;</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F matrix3;</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F matrix4;</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F matrix5;</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F matrix6;</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj matrix0;</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj matrix1;</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj matrix2;</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj matrix3;</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj matrix4;</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj matrix5;</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj matrix6;</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> </span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> double[] vector0;</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -70,13 +70,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> inverseDiffusions = new double[dimTrait * dimTrait * diffusionCount];</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> vector0 = new double[dimTrait];</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- matrix0 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- matrix1 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- matrix2 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- matrix3 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- matrix4 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- matrix5 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- matrix6 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ matrix0 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ matrix1 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ matrix2 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ matrix3 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ matrix4 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ matrix5 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ matrix6 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> }</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> </span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> @Override</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -86,9 +86,9 @@</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> assert (inverseDiffusions != null);</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> </span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> final int offset = dimTrait * dimTrait * precisionIndex;</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F precision = wrap(diffusions, offset, dimTrait, dimTrait);</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F variance = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.invert(precision, variance);</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj precision = wrap(diffusions, offset, dimTrait, dimTrait);</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj variance = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.invert(precision, variance);</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> unwrap(variance, inverseDiffusions, offset);</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> </span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> if (DEBUG) {</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -124,7 +124,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> final double vi = branchLengths[imo];</span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> final double vj = branchLengths[jmo];</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> </span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> if (DEBUG) {</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> System.err.println("updatePreOrderPartial for node " + iBuffer);</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -137,27 +137,27 @@</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> for (int trait = 0; trait < numTraits; ++trait) {</span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> // A. Get current precision of k and j</span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pk = wrap(prePartials, kbo + dimTrait, dimTrait, dimTrait);</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pj = wrap(partials, jbo + dimTrait, dimTrait, dimTrait);</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pk = wrap(prePartials, kbo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pj = wrap(partials, jbo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vk = wrap(prePartials, kbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vj = wrap(partials, jbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vk = wrap(prePartials, kbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vj = wrap(partials, jbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> </span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> // B. Inflate variance along sibling branch using matrix inversion</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vjp = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vjp = matrix0;</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Vj, vj, Vd, Vjp);</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vjp = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vjp = matrix0;</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Vj, vj, Vd, Vjp);</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> </span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pjp = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pjp = matrix1;</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pjp = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pjp = matrix1;</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> InversionResult cj = safeInvert(Vjp, Pjp, false);</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> </span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pip = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pip = matrix2;</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Pk, Pjp, Pip);</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pip = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pip = matrix2;</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Pk, Pjp, Pip);</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> </span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vip = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vip = matrix3;</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vip = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vip = matrix3;</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> InversionResult cip = safeInvert(Pip, Vip, false);</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> </span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> // C. Compute prePartial mean</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -180,11 +180,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> // C. Inflate variance along node branch</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vi = Vip;</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(vi, Vd, Vip, Vi);</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vi = Vip;</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(vi, Vd, Vip, Vi);</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pi = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pi = matrix4;</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pi = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pi = matrix4;</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> InversionResult ci = safeInvert(Vi, Pi, false);</span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> // X. Store precision results for node</span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -242,7 +242,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> final double vi = branchLengths[imo];</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> final double vj = branchLengths[jmo];</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> if (DEBUG) {</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> System.err.println("variance diffusion: " + Vd);</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -269,11 +269,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> final double lpi = partials[ibo + dimTrait + 2 * dimTrait * dimTrait];</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> final double lpj = partials[jbo + dimTrait + 2 * dimTrait * dimTrait];</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pi = wrap(partials, ibo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pj = wrap(partials, jbo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pi = wrap(partials, ibo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pj = wrap(partials, jbo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vi = wrap(partials, ibo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vj = wrap(partials, jbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vi = wrap(partials, ibo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vj = wrap(partials, jbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> if (TIMING) {</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> endTime("peel1");</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -286,23 +286,23 @@</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> final double lpjp = Double.isInfinite(lpj) ?</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> 1.0 / vj : lpj / (1.0 + lpj * vj);</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vip = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vjp = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vip = matrix0;</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vjp = matrix1;</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vip = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vjp = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vip = matrix0;</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vjp = matrix1;</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> </span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Vi, vi, Vd, Vip);</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Vj, vj, Vd, Vjp);</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Vi, vi, Vd, Vip);</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Vj, vj, Vd, Vjp);</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> </span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> if (TIMING) {</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> endTime("peel2");</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> startTime("peel2a");</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"> }</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> </span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pip = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pjp = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pip = matrix2;</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pjp = matrix3;</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pip = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pjp = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pip = matrix2;</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pjp = matrix3;</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> </span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> InversionResult ci = safeInvert(Vip, Pip, true);</span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> InversionResult cj = safeInvert(Vjp, Pjp, true);</span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -317,13 +317,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> // A. Partial precision and variance (for later use) using one matrix inversion</span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> final double lpk = lpip + lpjp;</span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pk = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pk = matrix4;</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pk = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pk = matrix4;</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Pip, Pjp, Pk);</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Pip, Pjp, Pk);</span></span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vk = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vk = matrix5;</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vk = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vk = matrix5;</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> InversionResult ck = safeInvert(Pk, Vk, true);</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> // B. Partial mean</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -433,9 +433,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vt = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vt = matrix6;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="297" 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">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Vip, Vjp, Vt);</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vt = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vt = matrix6;</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Vip, Vjp, Vt);</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> </span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> if (DEBUG) {</span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> System.err.println("Vt: " + Vt);</span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -445,7 +445,7 @@</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> - ck.getEffectiveDimension();</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> </span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> remainder += -dimensionChange * LOG_SQRT_2_PI - 0.5 *</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// (Math.log(CommonOps.det(Vip)) + Math.log(CommonOps.det(Vjp)) - Math.log(CommonOps.det(Vk)))</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// (Math.log(CommonOps_DDRM.det(Vip)) + Math.log(CommonOps_DDRM.det(Vjp)) - Math.log(CommonOps_DDRM.det(Vk)))</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> (Math.log(ci.getDeterminant()) + Math.log(cj.getDeterminant()) + Math.log(ck.getDeterminant()))</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"> - 0.5 * (SSi + SSj - SSk);</span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -469,7 +469,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> assert (false);</span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pt = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pt = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> InversionResult ct = safeInvert(Vt, Pt, false);</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> int opo = dimTrait * dimTrait * trait;</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -551,29 +551,29 @@</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> int rootOffset = dimPartial * rootBufferIndex;</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> int priorOffset = dimPartial * priorBufferIndex;</span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> // TODO For each trait in parallel</span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> for (int trait = 0; trait < numTraits; ++trait) {</span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Proot = wrap(partials, rootOffset + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pprior = wrap(partials, priorOffset + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Proot = wrap(partials, rootOffset + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pprior = wrap(partials, priorOffset + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vroot = wrap(partials, rootOffset + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vprior = wrap(partials, priorOffset + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vroot = wrap(partials, rootOffset + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vprior = wrap(partials, priorOffset + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> // TODO Block below is for the conjugate prior ONLY</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vtmp = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.mult(Vd, Vprior, Vtmp);</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vtmp = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.mult(Vd, Vprior, Vtmp);</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> Vprior.set(Vtmp);</span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vtotal = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Vroot, Vprior, Vtotal);</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vtotal = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Vroot, Vprior, Vtotal);</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Ptotal = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.invert(Vtotal, Ptotal); // TODO Can return determinant at same time to avoid extra QR decomp</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Ptotal = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.invert(Vtotal, Ptotal); // TODO Can return determinant at same time to avoid extra QR decomp</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> double SS = 0;</span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"> for (int g = 0; g < dimTrait; ++g) {</span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -586,7 +586,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final double logLike = -dimTrait * LOG_SQRT_2_PI - 0.5 * Math.log(CommonOps.det(Vtotal)) - 0.5 * SS;</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final double logLike = -dimTrait * LOG_SQRT_2_PI - 0.5 * Math.log(CommonOps_DDRM.det(Vtotal)) - 0.5 * SS;</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"> final double remainder = remainders[rootBufferIndex * numTraits + trait];</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> logLikelihoods[trait] = logLike + remainder;</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/dr/evomodel/treedatalikelihood/continuous/cdi/SafeMultivariateIntegrator.java</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/dr/evomodel/treedatalikelihood/continuous/cdi/SafeMultivariateIntegrator.java</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2,8 +2,8 @@</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> </span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> import dr.math.matrixAlgebra.WrappedVector;</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> import dr.math.matrixAlgebra.missingData.InversionResult;</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.data.DenseMatrix64F;</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.ops.CommonOps;</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.data.DMatrixRMaj;</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.dense.row.CommonOps_DDRM;</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> </span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"> import static dr.math.matrixAlgebra.missingData.InversionResult.Code.NOT_OBSERVED;</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"> import static dr.math.matrixAlgebra.missingData.MissingOps.*;</span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -53,13 +53,13 @@</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> </span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> // private final Map<String, Long> times;</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> //</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// private DenseMatrix64F matrix0;</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// private DenseMatrix64F matrix1;</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// private DenseMatrix64F matrix2;</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// private DenseMatrix64F matrix3;</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// private DenseMatrix64F matrix4;</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// private DenseMatrix64F matrix5;</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// private DenseMatrix64F matrix6;</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// private DMatrixRMaj matrix0;</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// private DMatrixRMaj matrix1;</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// private DMatrixRMaj matrix2;</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// private DMatrixRMaj matrix3;</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// private DMatrixRMaj matrix4;</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// private DMatrixRMaj matrix5;</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// private DMatrixRMaj matrix6;</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"> //</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> // private double[] vector0;</span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> </span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -67,13 +67,13 @@</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"> // inverseDiffusions = new double[dimTrait * dimTrait * diffusionCount];</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> //</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> // vector0 = new double[dimTrait];</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// matrix0 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// matrix1 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// matrix2 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// matrix3 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// matrix4 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// matrix5 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// matrix6 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// matrix0 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// matrix1 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// matrix2 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// matrix3 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// matrix4 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// matrix5 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// matrix6 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"> // }</span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"> // @Override</span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -83,9 +83,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"> // assert (inverseDiffusions != null);</span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> // final int offset = dimTrait * dimTrait * precisionIndex;</span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// DenseMatrix64F precision = wrap(diffusions, offset, dimTrait, dimTrait);</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// DenseMatrix64F variance = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.invert(precision, variance);</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// DMatrixRMaj precision = wrap(diffusions, offset, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// DMatrixRMaj variance = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.invert(precision, variance);</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"> // unwrap(variance, inverseDiffusions, offset);</span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"> // if (DEBUG) {</span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -121,7 +121,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> // final double vi = branchLengths[imo];</span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"> // final double vj = branchLengths[jmo];</span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"> // if (DEBUG) {</span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> // System.err.println("updatePreOrderPartial for node " + iBuffer);</span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -134,27 +134,27 @@</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"> // for (int trait = 0; trait < numTraits; ++trait) {</span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"> // // A. Get current precision of k and j</span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pk = wrap(prePartials, kbo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-//// final DenseMatrix64F Pj = wrap(partials, jbo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pk = wrap(prePartials, kbo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+//// final DMatrixRMaj Pj = wrap(partials, jbo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-//// final DenseMatrix64F Vk = wrap(prePartials, kbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vj = wrap(partials, jbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+//// final DMatrixRMaj Vk = wrap(prePartials, kbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vj = wrap(partials, jbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"> // // B. Inflate variance along sibling branch using matrix inversion</span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-//// final DenseMatrix64F Vjp = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vjp = matrix0;</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Vj, vj, Vd, Vjp);</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+//// final DMatrixRMaj Vjp = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vjp = matrix0;</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Vj, vj, Vd, Vjp);</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-//// final DenseMatrix64F Pjp = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pjp = matrix1;</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+//// final DMatrixRMaj Pjp = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pjp = matrix1;</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"> // InversionResult cj = safeInvert(Vjp, Pjp, false);</span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-//// final DenseMatrix64F Pip = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pip = matrix2;</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Pk, Pjp, Pip);</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+//// final DMatrixRMaj Pip = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pip = matrix2;</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Pk, Pjp, Pip);</span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-//// final DenseMatrix64F Vip = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vip = matrix3;</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+//// final DMatrixRMaj Vip = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vip = matrix3;</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"> // InversionResult cip = safeInvert(Pip, Vip, false);</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"> // // C. Compute prePartial mean</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -177,11 +177,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"> // }</span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"> // // C. Inflate variance along node branch</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vi = Vip;</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(vi, Vd, Vip, Vi);</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vi = Vip;</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(vi, Vd, Vip, Vi);</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"> //</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-//// final DenseMatrix64F Pi = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pi = matrix4;</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+//// final DMatrixRMaj Pi = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pi = matrix4;</span></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> // InversionResult ci = safeInvert(Vi, Pi, false);</span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"> //</span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"> // // X. Store precision results for node</span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -239,8 +239,8 @@</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"> final double vi = branchLengths[imo];</span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"> final double vj = branchLengths[jmo];</span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"> </span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pd = wrap(diffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pd = wrap(diffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"> </span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"> if (DEBUG) {</span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"> System.err.println("variance diffusion: " + Vd);</span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -267,8 +267,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"> final double lpi = partials[ibo + dimTrait + 2 * dimTrait * dimTrait];</span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"> final double lpj = partials[jbo + dimTrait + 2 * dimTrait * dimTrait];</span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pi = wrap(partials, ibo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pj = wrap(partials, jbo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pi = wrap(partials, ibo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pj = wrap(partials, jbo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"> if (TIMING) {</span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"> endTime("peel1");</span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -284,8 +284,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"> InversionResult ci;</span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"> InversionResult cj;</span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pip = matrix2;</span></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pjp = matrix3;</span></span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pip = matrix2;</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pjp = matrix3;</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> // boolean useVariance = anyDiagonalInfinities(Pi) || anyDiagonalInfinities(Pj);</span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"> final boolean useVariancei = anyDiagonalInfinities(Pi);</span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -293,77 +293,77 @@</span></span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> if (useVariancei) {</span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"> </span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vip = matrix0;</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vi = wrap(partials, ibo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Vi, vi, Vd, Vip);</span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vip = matrix0;</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vi = wrap(partials, ibo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Vi, vi, Vd, Vip);</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"> ci = safeInvert(Vip, Pip, true);</span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"> } else {</span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F PiPlusPd = matrix0;</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Pi, 1.0 / vi, Pd, PiPlusPd);</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F PiPlusPdInv = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj PiPlusPd = matrix0;</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Pi, 1.0 / vi, Pd, PiPlusPd);</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj PiPlusPdInv = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"> safeInvert(PiPlusPd, PiPlusPdInv, false);</span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.mult(PiPlusPdInv, Pi, Pip);</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.mult(Pi, Pip, PiPlusPdInv);</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Pi, -1, PiPlusPdInv, Pip);</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.mult(PiPlusPdInv, Pi, Pip);</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.mult(Pi, Pip, PiPlusPdInv);</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Pi, -1, PiPlusPdInv, Pip);</span></span>
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"> ci = safeDeterminant(Pip, false);</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"> }</span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"> </span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"> if (useVariancej) {</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"> </span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vjp = matrix1;</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vj = wrap(partials, jbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Vj, vj, Vd, Vjp);</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vjp = matrix1;</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vj = wrap(partials, jbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Vj, vj, Vd, Vjp);</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"> cj = safeInvert(Vjp, Pjp, true);</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"> </span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"> } else {</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"> </span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F PjPlusPd = matrix1;</span></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Pj, 1.0 / vj, Pd, PjPlusPd);</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F PjPlusPdInv = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj PjPlusPd = matrix1;</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Pj, 1.0 / vj, Pd, PjPlusPd);</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj PjPlusPdInv = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"> safeInvert(PjPlusPd, PjPlusPdInv, false);</span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.mult(PjPlusPdInv, Pj, Pjp);</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.mult(Pj, Pjp, PjPlusPdInv);</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Pj, -1, PjPlusPdInv, Pjp);</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.mult(PjPlusPdInv, Pj, Pjp);</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.mult(Pj, Pjp, PjPlusPdInv);</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Pj, -1, PjPlusPdInv, Pjp);</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"> cj = safeDeterminant(Pjp, false);</span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"> }</span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"> </span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"> // if (useVariance) {</span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"> //</span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vip = matrix0;</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vjp = matrix1;</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vip = matrix0;</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vjp = matrix1;</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"> //</span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vi = wrap(partials, ibo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vj = wrap(partials, jbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vi = wrap(partials, ibo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vj = wrap(partials, jbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"> //</span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Vi, vi, Vd, Vip);</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Vj, vj, Vd, Vjp);</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Vi, vi, Vd, Vip);</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Vj, vj, Vd, Vjp);</span></span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"> // ci = safeInvert(Vip, Pip, true);</span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"> // cj = safeInvert(Vjp, Pjp, true);</span>
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"> // } else {</span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F PiPlusPd = matrix0;</span></span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F PjPlusPd = matrix1;</span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj PiPlusPd = matrix0;</span></span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj PjPlusPd = matrix1;</span></span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Pi, 1.0 / vi, Pd, PiPlusPd);</span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Pj, 1.0 / vj, Pd, PjPlusPd);</span></span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Pi, 1.0 / vi, Pd, PiPlusPd);</span></span>
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Pj, 1.0 / vj, Pd, PjPlusPd);</span></span>
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F PiPlusPdInv = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F PjPlusPdInv = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj PiPlusPdInv = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj PjPlusPdInv = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"> // safeInvert(PiPlusPd, PiPlusPdInv, false);</span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"> // safeInvert(PjPlusPd, PjPlusPdInv, false);</span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.mult(PiPlusPdInv, Pi, Pip);</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.mult(PjPlusPdInv, Pj, Pjp);</span></span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.mult(PiPlusPdInv, Pi, Pip);</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.mult(PjPlusPdInv, Pj, Pjp);</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.mult(Pi, Pip, PiPlusPdInv);</span></span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.mult(Pj, Pjp, PjPlusPdInv);</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.mult(Pi, Pip, PiPlusPdInv);</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.mult(Pj, Pjp, PjPlusPdInv);</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Pi, -1, PiPlusPdInv, Pip);</span></span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Pj, -1, PjPlusPdInv, Pjp);</span></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Pi, -1, PiPlusPdInv, Pip);</span></span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Pj, -1, PjPlusPdInv, Pjp);</span></span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"> // ci = safeDeterminant(Pip, false);</span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"> // cj = safeDeterminant(Pjp, false);</span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -385,12 +385,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"> // A. Partial precision and variance (for later use) using one matrix inversion</span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"> final double lpk = lpip + lpjp;</span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pk = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pk = matrix4;</span></span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Pip, Pjp, Pk);</span></span>
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pk = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pk = matrix4;</span></span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Pip, Pjp, Pk);</span></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vk = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vk = matrix5;</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vk = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vk = matrix5;</span></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff"> // if (useVariance) {</span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"> //// InversionResult ck =</span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -524,9 +524,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vt = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vt = matrix6;</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Vip, Vjp, Vt);</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vt = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vt = matrix6;</span></span>
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Vip, Vjp, Vt);</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"> // if (DEBUG) {</span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"> // System.err.println("Vt: " + Vt);</span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -536,16 +536,16 @@</span></span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff"> - ck.getEffectiveDimension();</span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"> </span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"> // System.err.println(ci.getDeterminant());</span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// System.err.println(CommonOps.det(Vip));</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// System.err.println(CommonOps_DDRM.det(Vip));</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"> //</span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff"> // System.err.println(cj.getDeterminant());</span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// System.err.println(CommonOps.det(Vjp));</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// System.err.println(CommonOps_DDRM.det(Vjp));</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"> //</span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"> // System.err.println(1.0 / ck.getDeterminant());</span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// System.err.println(CommonOps.det(Vk));</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// System.err.println(CommonOps_DDRM.det(Vk));</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"> </span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff"> remainder += -dimensionChange * LOG_SQRT_2_PI - 0.5 *</span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// (Math.log(CommonOps.det(Vip)) + Math.log(CommonOps.det(Vjp)) - Math.log(CommonOps.det(Vk)))</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// (Math.log(CommonOps_DDRM.det(Vip)) + Math.log(CommonOps_DDRM.det(Vjp)) - Math.log(CommonOps_DDRM.det(Vk)))</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"> (Math.log(ci.getDeterminant()) + Math.log(cj.getDeterminant()) + Math.log(ck.getDeterminant()))</span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"> - 0.5 * (SSi + SSj - SSk);</span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"> </span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -632,42 +632,42 @@</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"> int rootOffset = dimPartial * rootBufferIndex;</span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"> int priorOffset = dimPartial * priorBufferIndex;</span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"> </span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pd = wrap(diffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pd = wrap(diffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"> // TODO For each trait in parallel</span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"> for (int trait = 0; trait < numTraits; ++trait) {</span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"> </span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Proot = wrap(partials, rootOffset + dimTrait, dimTrait, dimTrait);</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pprior = wrap(partials, priorOffset + dimTrait, dimTrait, dimTrait);</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Proot = wrap(partials, rootOffset + dimTrait, dimTrait, dimTrait);</span></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pprior = wrap(partials, priorOffset + dimTrait, dimTrait, dimTrait);</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"> </span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vroot = wrap(partials, rootOffset + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vprior = wrap(partials, priorOffset + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vroot = wrap(partials, rootOffset + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vprior = wrap(partials, priorOffset + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"> // TODO Block below is for the conjugate prior ONLY</span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"> {</span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vtmp = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.mult(Vd, Vprior, Vtmp);</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vtmp = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.mult(Vd, Vprior, Vtmp);</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="diff"> // Vprior.set(Vtmp);</span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Ptmp = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.mult(Pd, Pprior, Ptmp);</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Ptmp = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.mult(Pd, Pprior, Ptmp);</span></span>
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="diff"> Pprior.set(Ptmp); // TODO What does this do?</span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="diff"> }</span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="diff"> </span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vtotal = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Vroot, Vprior, Vtotal);</span></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vtotal = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Vroot, Vprior, Vtotal);</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="diff"> </span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Ptotal = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.invert(Vtotal, Ptotal); // TODO Can return determinant at same time to avoid extra QR decomp</span></span>
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Ptotal = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.invert(Vtotal, Ptotal); // TODO Can return determinant at same time to avoid extra QR decomp</span></span>
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F tmp1 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F tmp2 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Proot, Pprior, Ptotal);</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.invert(Ptotal, Vtotal);</span></span>
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.mult(Vtotal, Proot, tmp1);</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.mult(Proot, tmp1, tmp2);</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Proot, -1.0, tmp2, Ptotal);</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj tmp1 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj tmp2 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Proot, Pprior, Ptotal);</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.invert(Ptotal, Vtotal);</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.mult(Vtotal, Proot, tmp1);</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.mult(Proot, tmp1, tmp2);</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Proot, -1.0, tmp2, Ptotal);</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"> </span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="diff"> double SS = 0;</span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="diff"> for (int g = 0; g < dimTrait; ++g) {</span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -681,8 +681,8 @@</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="diff"> }</span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"> </span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"> final double logLike = -dimTrait * LOG_SQRT_2_PI</span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// - 0.5 * Math.log(CommonOps.det(Vtotal))</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- + 0.5 * Math.log(CommonOps.det(Ptotal))</span></span>
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// - 0.5 * Math.log(CommonOps_DDRM.det(Vtotal))</span></span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ + 0.5 * Math.log(CommonOps_DDRM.det(Ptotal))</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="diff"> - 0.5 * SS;</span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="diff"> final double remainder = remainders[rootBufferIndex * numTraits + trait];</span>
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/dr/evomodel/treedatalikelihood/continuous/cdi/SafeMultivariateWithDriftIntegrator.java</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/dr/evomodel/treedatalikelihood/continuous/cdi/SafeMultivariateWithDriftIntegrator.java</span></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2,8 +2,8 @@</span></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="diff"> </span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="diff"> import dr.math.matrixAlgebra.WrappedVector;</span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="diff"> import dr.math.matrixAlgebra.missingData.InversionResult;</span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.data.DenseMatrix64F;</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.ops.CommonOps;</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.data.DMatrixRMaj;</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.dense.row.CommonOps_DDRM;</span></span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="diff"> </span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="diff"> import static dr.math.matrixAlgebra.missingData.InversionResult.Code.NOT_OBSERVED;</span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="diff"> import static dr.math.matrixAlgebra.missingData.MissingOps.*;</span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -65,9 +65,9 @@</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"> assert (inverseDiffusions != null);</span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="diff"> </span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="diff"> final int offset = dimTrait * dimTrait * precisionIndex;</span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F precision = wrap(diffusions, offset, dimTrait, dimTrait);</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F variance = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.invert(precision, variance);</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj precision = wrap(diffusions, offset, dimTrait, dimTrait);</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj variance = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.invert(precision, variance);</span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="diff"> unwrap(variance, inverseDiffusions, offset);</span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="diff"> </span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="diff"> if (DEBUG) {</span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -199,14 +199,14 @@</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="diff"> // final double vi = variances[imo];</span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="diff"> // final double vj = variances[jmo];</span>
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pd = wrap(diffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vd = wrap(inverseDiffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pd = wrap(diffusions, precisionOffset, dimTrait, dimTrait);</span></span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vdi = wrap(variances, imo, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vdj = wrap(variances, jmo, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vdi = wrap(variances, imo, dimTrait, dimTrait);</span></span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vdj = wrap(variances, jmo, dimTrait, dimTrait);</span></span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pdi = wrap(precisions, imo, dimTrait, dimTrait); // TODO Only if needed</span></span>
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pdj = wrap(precisions, jmo, dimTrait, dimTrait); // TODO Only if needed</span></span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pdi = wrap(precisions, imo, dimTrait, dimTrait); // TODO Only if needed</span></span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pdj = wrap(precisions, jmo, dimTrait, dimTrait); // TODO Only if needed</span></span>
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="diff"> </span>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="diff"> // TODO End fix</span>
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -237,8 +237,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="diff"> // final double lpi = partials[ibo + dimTrait + 2 * dimTrait * dimTrait];</span>
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="diff"> // final double lpj = partials[jbo + dimTrait + 2 * dimTrait * dimTrait];</span>
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pi = wrap(partials, ibo + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pj = wrap(partials, jbo + dimTrait, dimTrait, dimTrait);</span></span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pi = wrap(partials, ibo + dimTrait, dimTrait, dimTrait);</span></span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pj = wrap(partials, jbo + dimTrait, dimTrait, dimTrait);</span></span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="diff"> </span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="diff"> if (TIMING) {</span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="diff"> endTime("peel1");</span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -254,8 +254,8 @@</span></span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="diff"> InversionResult ci;</span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="diff"> InversionResult cj;</span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="diff"> </span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pip = matrix2;</span></span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pjp = matrix3;</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pip = matrix2;</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pjp = matrix3;</span></span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="diff"> </span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="diff"> // boolean useVariance = anyDiagonalInfinities(Pi) || anyDiagonalInfinities(Pj);</span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="diff"> final boolean useVariancei = anyDiagonalInfinities(Pi);</span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -263,43 +263,43 @@</span></span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="diff"> </span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="diff"> if (useVariancei) {</span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="diff"> </span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vip = matrix0;</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vi = wrap(partials, ibo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Vi, vi, Vd, Vip); // TODO Fix</span></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Vi, Vdi, Vip);</span></span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vip = matrix0;</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vi = wrap(partials, ibo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Vi, vi, Vd, Vip); // TODO Fix</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Vi, Vdi, Vip);</span></span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="diff"> ci = safeInvert(Vip, Pip, true);</span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="diff"> </span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="diff"> } else {</span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="diff"> </span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F PiPlusPd = matrix0;</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Pi, 1.0 / vi, Pd, PiPlusPd); // TODO Fix</span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Pi, Pdi, PiPlusPd);</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F PiPlusPdInv = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj PiPlusPd = matrix0;</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Pi, 1.0 / vi, Pd, PiPlusPd); // TODO Fix</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Pi, Pdi, PiPlusPd);</span></span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj PiPlusPdInv = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="diff"> safeInvert(PiPlusPd, PiPlusPdInv, false);</span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.mult(PiPlusPdInv, Pi, Pip);</span></span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.mult(Pi, Pip, PiPlusPdInv);</span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Pi, -1, PiPlusPdInv, Pip);</span></span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.mult(PiPlusPdInv, Pi, Pip);</span></span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.mult(Pi, Pip, PiPlusPdInv);</span></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Pi, -1, PiPlusPdInv, Pip);</span></span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="diff"> ci = safeDeterminant(Pip, false);</span>
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="diff"> if (useVariancej) {</span>
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vjp = matrix1;</span></span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vj = wrap(partials, jbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Vj, vj, Vd, Vjp); // TODO Fix</span></span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Vj, Vdj, Vjp);</span></span>
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vjp = matrix1;</span></span>
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vj = wrap(partials, jbo + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Vj, vj, Vd, Vjp); // TODO Fix</span></span>
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Vj, Vdj, Vjp);</span></span>
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="diff"> cj = safeInvert(Vjp, Pjp, true);</span>
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="diff"> } else {</span>
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F PjPlusPd = matrix1;</span></span>
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Pj, 1.0 / vj, Pd, PjPlusPd); // TODO Fix</span></span>
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Pj, Pdj, PjPlusPd);</span></span>
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F PjPlusPdInv = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj PjPlusPd = matrix1;</span></span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Pj, 1.0 / vj, Pd, PjPlusPd); // TODO Fix</span></span>
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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Pj, Pdj, PjPlusPd);</span></span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj PjPlusPdInv = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="diff"> safeInvert(PjPlusPd, PjPlusPdInv, false);</span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.mult(PjPlusPdInv, Pj, Pjp);</span></span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.mult(Pj, Pjp, PjPlusPdInv);</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Pj, -1, PjPlusPdInv, Pjp);</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.mult(PjPlusPdInv, Pj, Pjp);</span></span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.mult(Pj, Pjp, PjPlusPdInv);</span></span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Pj, -1, PjPlusPdInv, Pjp);</span></span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="diff"> cj = safeDeterminant(Pjp, false);</span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="diff"> }</span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -313,12 +313,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="diff"> // A. Partial precision and variance (for later use) using one matrix inversion</span>
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918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="diff"> // final double lpk = lpip + lpjp;</span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="diff"> </span>
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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Pk = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pk = matrix4;</span></span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(Pip, Pjp, Pk);</span></span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Pk = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pk = matrix4;</span></span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(Pip, Pjp, Pk);</span></span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="diff"> </span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vk = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vk = matrix5;</span></span>
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929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vk = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="930" 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">
930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vk = matrix5;</span></span>
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931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="diff"> </span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="diff"> // if (useVariance) {</span>
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933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="diff"> //// InversionResult ck =</span>
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<td class="diff-line-num new new_line" data-linenumber="934" 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">
934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -475,9 +475,9 @@</span></span>
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935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="936" 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">
936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="diff"> }</span>
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937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="938" 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">
938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vt = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="939" 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">
939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F Vt = matrix6;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="940" 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">
940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.add(Vip, Vjp, Vt);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="941" 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">
941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vt = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="942" 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">
942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj Vt = matrix6;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="943" 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">
943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.add(Vip, Vjp, Vt);</span></span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="diff"> </span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="diff"> // if (DEBUG) {</span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="diff"> // System.err.println("Vt: " + Vt);</span>
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<td class="diff-line-num new new_line" data-linenumber="947" 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">
947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -487,16 +487,16 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="948" 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">
948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="diff"> - ck.getEffectiveDimension();</span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="diff"> </span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="diff"> // System.err.println(ci.getDeterminant());</span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// System.err.println(CommonOps.det(Vip));</span></span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// System.err.println(CommonOps_DDRM.det(Vip));</span></span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="diff"> //</span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="diff"> // System.err.println(cj.getDeterminant());</span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// System.err.println(CommonOps.det(Vjp));</span></span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// System.err.println(CommonOps_DDRM.det(Vjp));</span></span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="diff"> //</span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="diff"> // System.err.println(1.0 / ck.getDeterminant());</span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// System.err.println(CommonOps.det(Vk));</span></span>
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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// System.err.println(CommonOps_DDRM.det(Vk));</span></span>
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961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="diff"> </span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="diff"> remainder += -dimensionChange * LOG_SQRT_2_PI - 0.5 *</span>
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// (Math.log(CommonOps.det(Vip)) + Math.log(CommonOps.det(Vjp)) - Math.log(CommonOps.det(Vk)))</span></span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// (Math.log(CommonOps_DDRM.det(Vip)) + Math.log(CommonOps_DDRM.det(Vjp)) - Math.log(CommonOps_DDRM.det(Vk)))</span></span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="diff"> (Math.log(ci.getDeterminant()) + Math.log(cj.getDeterminant()) + Math.log(ck.getDeterminant()))</span>
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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="diff"> - 0.5 * (SSi + SSj - SSk);</span>
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967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="diff"> </span>
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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/dr/evomodel/treedatalikelihood/continuous/IntegratedFactorAnalysisLikelihood.java</span></span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/dr/evomodel/treedatalikelihood/continuous/IntegratedFactorAnalysisLikelihood.java</span></span>
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970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -38,7 +38,7 @@</span></span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="diff"> import dr.math.matrixAlgebra.WrappedVector;</span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="diff"> import dr.math.matrixAlgebra.missingData.InversionResult;</span>
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973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="diff"> import dr.xml.*;</span>
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974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.data.DenseMatrix64F;</span></span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.data.DMatrixRMaj;</span></span>
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976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="diff"> </span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="diff"> import java.util.ArrayList;</span>
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978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="diff"> import java.util.Arrays;</span>
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -229,7 +229,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="diff"> private final double nuggetPrecision;</span>
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- private void computePrecisionForTaxon(final DenseMatrix64F precision, final int taxon,</span></span>
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ private void computePrecisionForTaxon(final DMatrixRMaj precision, final int taxon,</span></span>
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="diff"> final int numFactors) {</span>
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="diff"> final double[] observed = observedIndicators[taxon];</span>
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -249,7 +249,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- private InversionResult fillInMeanForTaxon(final WrappedVector output, final DenseMatrix64F precision, final int taxon) {</span></span>
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ private InversionResult fillInMeanForTaxon(final WrappedVector output, final DMatrixRMaj precision, final int taxon) {</span></span>
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="diff"> final double[] observed = observedIndicators[taxon];</span>
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="diff"> final Parameter Y = traitParameter.getParameter(taxon);</span>
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -269,8 +269,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="diff"> tmp[row] = sum;</span>
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F B = DenseMatrix64F.wrap(numFactors, 1, tmp);</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F X = DenseMatrix64F.wrap(numFactors, 1, tmp2);</span></span>
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj B = DMatrixRMaj.wrap(numFactors, 1, tmp);</span></span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj X = DMatrixRMaj.wrap(numFactors, 1, tmp2);</span></span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="diff"> </span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="diff"> InversionResult ci = safeSolve(precision, B, X, true);</span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="diff"> </span>
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1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -294,7 +294,7 @@</span></span>
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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="diff"> return sum;</span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="diff"> }</span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="diff"> </span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- private double computeFactorInnerProduct(final WrappedVector mean, final DenseMatrix64F precision) {</span></span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ private double computeFactorInnerProduct(final WrappedVector mean, final DMatrixRMaj precision) {</span></span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="diff"> // Compute \mu_i^t P_i \mu^t</span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="diff"> double sum = 0;</span>
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1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="diff"> for (int row = 0; row < numFactors; ++row) {</span>
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1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -334,7 +334,7 @@</span></span>
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1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="diff"> return logDet;</span>
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1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="diff"> }</span>
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1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="diff"> </span>
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1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- private void makeCompletedUnobserved(final DenseMatrix64F matrix, double diagonal) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1022" 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">
1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ private void makeCompletedUnobserved(final DMatrixRMaj matrix, double diagonal) {</span></span>
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1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="diff"> for (int row = 0; row < numFactors; ++row) {</span>
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1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="diff"> for (int col = 0; col < numFactors; ++col) {</span>
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1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="diff"> double x = (row == col) ? diagonal : 0.0;</span>
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<td class="diff-line-num new new_line" data-linenumber="1026" 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">
1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -345,8 +345,8 @@</span></span>
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1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="diff"> </span>
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1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="diff"> private void computePartialsAndRemainders() {</span>
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1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="diff"> </span>
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1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F precision = new DenseMatrix64F(numFactors, numFactors);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1031" 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">
1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F variance = new DenseMatrix64F(numFactors, numFactors);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1032" 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">
1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj precision = new DMatrixRMaj(numFactors, numFactors);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1033" 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">
1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj variance = new DMatrixRMaj(numFactors, numFactors);</span></span>
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1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1035" 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">
1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="diff"> int partialsOffset = 0;</span>
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<td class="diff-line-num new new_line" data-linenumber="1036" 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">
1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="diff"> for (int taxon = 0; taxon < numTaxa; ++taxon) {</span>
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<td class="diff-line-num new new_line" data-linenumber="1037" 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">
1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/dr/evomodel/treedatalikelihood/continuous/RepeatedMeasuresTraitLikelihood.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1038" 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">
1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/dr/evomodel/treedatalikelihood/continuous/RepeatedMeasuresTraitLikelihood.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1039" 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">
1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -39,7 +39,7 @@</span></span>
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1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="diff"> import dr.math.matrixAlgebra.WrappedVector;</span>
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1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="diff"> import dr.math.matrixAlgebra.missingData.InversionResult;</span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="diff"> import dr.xml.*;</span>
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<td class="diff-line-num new new_line" data-linenumber="1043" 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">
1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.data.DenseMatrix64F;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1044" 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">
1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.data.DMatrixRMaj;</span></span>
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1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="diff"> </span>
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1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="diff"> import java.util.ArrayList;</span>
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1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="diff"> import java.util.Arrays;</span>
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1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -230,7 +230,7 @@</span></span>
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1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="diff"> </span>
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1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="diff"> private final double nuggetPrecision;</span>
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1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="diff"> </span>
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1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// private void computePrecisionForTaxon(final DenseMatrix64F precision, final int taxon,</span></span>
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1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// private void computePrecisionForTaxon(final DMatrixRMaj precision, final int taxon,</span></span>
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1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="diff"> // final int numFactors) {</span>
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<td class="diff-line-num new new_line" data-linenumber="1055" 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">
1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="diff"> //</span>
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1056
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<pre style="margin: 0;">+<span id="LC1056" class="line" lang="diff"> // final double[] observed = observedIndicators[taxon];</span>
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<td class="diff-line-num new new_line" data-linenumber="1057" 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">
1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -250,7 +250,7 @@</span></span>
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1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="diff"> // }</span>
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<td class="diff-line-num new new_line" data-linenumber="1059" 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">
1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="diff"> // }</span>
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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="diff"> </span>
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1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// private InversionResult fillInMeanForTaxon(final WrappedVector output, final DenseMatrix64F precision, final int taxon) {</span></span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// private InversionResult fillInMeanForTaxon(final WrappedVector output, final DMatrixRMaj precision, final int taxon) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1063" 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">
1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="diff"> //</span>
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1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="diff"> // final double[] observed = observedIndicators[taxon];</span>
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1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="diff"> // final Parameter Y = traitParameter.getParameter(taxon);</span>
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1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -270,8 +270,8 @@</span></span>
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1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="diff"> // tmp[row] = sum;</span>
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<td class="diff-line-num new new_line" data-linenumber="1068" 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">
1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="diff"> // }</span>
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1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="diff"> //</span>
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1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// DenseMatrix64F B = DenseMatrix64F.wrap(numFactors, 1, tmp);</span></span>
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1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// DenseMatrix64F X = DenseMatrix64F.wrap(numFactors, 1, tmp2);</span></span>
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1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// DMatrixRMaj B = DMatrixRMaj.wrap(numFactors, 1, tmp);</span></span>
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1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// DMatrixRMaj X = DMatrixRMaj.wrap(numFactors, 1, tmp2);</span></span>
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1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="diff"> //</span>
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1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="diff"> // InversionResult ci = safeSolve(precision, B, X, true);</span>
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1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="diff"> //</span>
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1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -295,7 +295,7 @@</span></span>
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1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="diff"> // return sum;</span>
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1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="diff"> // }</span>
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1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1081" 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">
1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// private double computeFactorInnerProduct(final WrappedVector mean, final DenseMatrix64F precision) {</span></span>
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1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// private double computeFactorInnerProduct(final WrappedVector mean, final DMatrixRMaj precision) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1083" 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">
1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="diff"> // // Compute \mu_i^t P_i \mu^t</span>
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<td class="diff-line-num new new_line" data-linenumber="1084" 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">
1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="diff"> // double sum = 0;</span>
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<td class="diff-line-num new new_line" data-linenumber="1085" 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">
1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="diff"> // for (int row = 0; row < numFactors; ++row) {</span>
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<td class="diff-line-num new new_line" data-linenumber="1086" 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">
1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -320,7 +320,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1087" 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">
1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="diff"> // return det;</span>
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<td class="diff-line-num new new_line" data-linenumber="1088" 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">
1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="diff"> // }</span>
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1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="diff"> </span>
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1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// private void makeCompletedUnobserved(final DenseMatrix64F matrix, double diagonal) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1091" 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">
1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// private void makeCompletedUnobserved(final DMatrixRMaj matrix, double diagonal) {</span></span>
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1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="diff"> // for (int row = 0; row < numFactors; ++row) {</span>
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1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="diff"> // for (int col = 0; col < numFactors; ++col) {</span>
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<td class="diff-line-num new new_line" data-linenumber="1094" 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">
1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="diff"> // double x = (row == col) ? diagonal : 0.0;</span>
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<td class="diff-line-num new new_line" data-linenumber="1095" 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">
1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -331,8 +331,8 @@</span></span>
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1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="diff"> </span>
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1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="diff"> private void computePartialsAndRemainders() {</span>
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1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="diff"> </span>
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1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F precision = new DenseMatrix64F(numFactors, numFactors);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1100" 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">
1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// final DenseMatrix64F variance = new DenseMatrix64F(numFactors, numFactors);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1101" 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">
1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj precision = new DMatrixRMaj(numFactors, numFactors);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1102" 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">
1102
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// final DMatrixRMaj variance = new DMatrixRMaj(numFactors, numFactors);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1103" 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">
1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="diff"> //</span>
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1104
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="diff"> // int partialsOffset = 0;</span>
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="diff"> // for (int taxon = 0; taxon < numTaxa; ++taxon) {</span>
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1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/dr/evomodel/treedatalikelihood/preorder/AbstractValuesViaFullConditionalDelegate.java</span></span>
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1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/dr/evomodel/treedatalikelihood/preorder/AbstractValuesViaFullConditionalDelegate.java</span></span>
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1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -5,7 +5,7 @@</span></span>
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1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="diff"> import dr.evomodel.continuous.MultivariateDiffusionModel;</span>
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1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="diff"> import dr.evomodel.treedatalikelihood.continuous.*;</span>
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1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="diff"> import dr.math.matrixAlgebra.WrappedVector;</span>
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1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.data.DenseMatrix64F;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1113" 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">
1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.data.DMatrixRMaj;</span></span>
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1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="diff"> </span>
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1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="diff"> import static dr.math.matrixAlgebra.missingData.MissingOps.wrap;</span>
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1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="diff"> </span>
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1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -63,7 +63,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="diff"> System.err.println("Missing tip = " + node.getNumber() + " (" + nodeBuffer + "), trait = " + trait);</span>
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1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="diff"> </span>
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1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="diff"> final WrappedVector preMean = new WrappedVector.Raw(conditionalNodeBuffer, partialOffset, dimTrait);</span>
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1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F preVar = wrap(conditionalNodeBuffer, partialOffset + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj preVar = wrap(conditionalNodeBuffer, partialOffset + dimTrait + dimTrait * dimTrait, dimTrait, dimTrait);</span></span>
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1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="diff"> final WrappedVector postObs = new WrappedVector.Raw(partialNodeBuffer, partialOffset, dimTrait);</span>
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1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="diff"> </span>
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1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/dr/evomodel/treedatalikelihood/preorder/ConditionalVarianceAndTransform2.java</span></span>
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<pre style="margin: 0;">+<span id="LC1127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/dr/evomodel/treedatalikelihood/preorder/ConditionalVarianceAndTransform2.java</span></span>
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1128
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,8 +1,8 @@</span></span>
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1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="diff"> package dr.evomodel.treedatalikelihood.preorder;</span>
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1130
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1131" 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">
1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="diff"> import dr.math.matrixAlgebra.WrappedVector;</span>
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<td class="diff-line-num new new_line" data-linenumber="1132" 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">
1132
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<pre style="margin: 0;">+<span id="LC1132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.data.DenseMatrix64F;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1133" 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">
1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.ops.CommonOps;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1134" 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">
1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.data.DMatrixRMaj;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1135" 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">
1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.dense.row.CommonOps_DDRM;</span></span>
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1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="diff"> </span>
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1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="diff"> import static dr.math.matrixAlgebra.missingData.MissingOps.gatherRowsAndColumns;</span>
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1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1139" 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">
1139
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -23,8 +23,8 @@</span></span>
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1140
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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="diff"> * \bar{\Sigma} = \Sigma_{11} - \Sigma_{12}\Sigma_{22}^1\Sigma{21}</span>
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1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="diff"> */</span>
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1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1143" 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">
1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final private DenseMatrix64F sBar;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1144" 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">
1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final private DenseMatrix64F affineTransform;</span></span>
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1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final private DMatrixRMaj sBar;</span></span>
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1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final private DMatrixRMaj affineTransform;</span></span>
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1147
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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="diff"> </span>
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1148
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<pre style="margin: 0;">+<span id="LC1148" class="line" lang="diff"> private final int[] missingIndices;</span>
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1149
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<pre style="margin: 0;">+<span id="LC1149" class="line" lang="diff"> private final int[] notMissingIndices;</span>
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1150
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -36,9 +36,9 @@</span></span>
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1151
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<pre style="margin: 0;">+<span id="LC1151" class="line" lang="diff"> private static final boolean DEBUG = false;</span>
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1152
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<pre style="margin: 0;">+<span id="LC1152" class="line" lang="diff"> </span>
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1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="diff"> private double[][] cholesky = null;</span>
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1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- private DenseMatrix64F sBarInv = null;</span></span>
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1155
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<pre style="margin: 0;">+<span id="LC1155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ private DMatrixRMaj sBarInv = null;</span></span>
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1156
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<pre style="margin: 0;">+<span id="LC1156" class="line" lang="diff"> </span>
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1157
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ConditionalVarianceAndTransform2(final DenseMatrix64F variance,</span></span>
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1158
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<pre style="margin: 0;">+<span id="LC1158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ConditionalVarianceAndTransform2(final DMatrixRMaj variance,</span></span>
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1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="diff"> final int[] missingIndices, final int[] notMissingIndices) {</span>
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1160
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="diff"> </span>
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1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="diff"> assert (missingIndices.length + notMissingIndices.length == variance.getNumRows());</span>
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1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -51,44 +51,44 @@</span></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="diff"> System.err.println("variance:\n" + variance);</span>
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1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="diff"> }</span>
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1165
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<pre style="margin: 0;">+<span id="LC1165" class="line" lang="diff"> </span>
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1166
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<pre style="margin: 0;">+<span id="LC1166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F S22 = new DenseMatrix64F(notMissingIndices.length, notMissingIndices.length);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1167" 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">
1167
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj S22 = new DMatrixRMaj(notMissingIndices.length, notMissingIndices.length);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1168" 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">
1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="diff"> gatherRowsAndColumns(variance, S22, notMissingIndices, notMissingIndices);</span>
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1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="diff"> </span>
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1170
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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="diff"> if (DEBUG) {</span>
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1171
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<pre style="margin: 0;">+<span id="LC1171" class="line" lang="diff"> System.err.println("S22:\n" + S22);</span>
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1172
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<pre style="margin: 0;">+<span id="LC1172" class="line" lang="diff"> }</span>
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1173
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<pre style="margin: 0;">+<span id="LC1173" class="line" lang="diff"> </span>
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1174
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<pre style="margin: 0;">+<span id="LC1174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F S22Inv = new DenseMatrix64F(notMissingIndices.length, notMissingIndices.length);</span></span>
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1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.invert(S22, S22Inv);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1176" 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">
1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj S22Inv = new DMatrixRMaj(notMissingIndices.length, notMissingIndices.length);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1177" 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">
1177
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<pre style="margin: 0;">+<span id="LC1177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.invert(S22, S22Inv);</span></span>
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1178
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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1179" 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">
1179
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<pre style="margin: 0;">+<span id="LC1179" class="line" lang="diff"> if (DEBUG) {</span>
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<td class="diff-line-num new new_line" data-linenumber="1180" 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">
1180
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<pre style="margin: 0;">+<span id="LC1180" class="line" lang="diff"> System.err.println("S22Inv:\n" + S22Inv);</span>
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<td class="diff-line-num new new_line" data-linenumber="1181" 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">
1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="1182" 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">
1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1183" 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">
1183
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<pre style="margin: 0;">+<span id="LC1183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F S12 = new DenseMatrix64F(missingIndices.length, notMissingIndices.length);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1184" 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">
1184
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<pre style="margin: 0;">+<span id="LC1184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj S12 = new DMatrixRMaj(missingIndices.length, notMissingIndices.length);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1185" 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">
1185
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<pre style="margin: 0;">+<span id="LC1185" class="line" lang="diff"> gatherRowsAndColumns(variance, S12, missingIndices, notMissingIndices);</span>
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<td class="diff-line-num new new_line" data-linenumber="1186" 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">
1186
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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1187" 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">
1187
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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="diff"> if (DEBUG) {</span>
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<td class="diff-line-num new new_line" data-linenumber="1188" 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">
1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="diff"> System.err.println("S12:\n" + S12);</span>
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<td class="diff-line-num new new_line" data-linenumber="1189" 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">
1189
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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="diff"> }</span>
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1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1191" 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">
1191
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<pre style="margin: 0;">+<span id="LC1191" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F S12S22Inv = new DenseMatrix64F(missingIndices.length, notMissingIndices.length);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1192" 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">
1192
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<pre style="margin: 0;">+<span id="LC1192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.mult(S12, S22Inv, S12S22Inv);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1193" 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">
1193
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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj S12S22Inv = new DMatrixRMaj(missingIndices.length, notMissingIndices.length);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1194" 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">
1194
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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.mult(S12, S22Inv, S12S22Inv);</span></span>
</pre>
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1195
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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="diff"> </span>
</pre>
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1196
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<pre style="margin: 0;">+<span id="LC1196" class="line" lang="diff"> if (DEBUG) {</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1197" 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">
1197
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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="diff"> System.err.println("S12S22Inv:\n" + S12S22Inv);</span>
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1198
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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="diff"> }</span>
</pre>
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1199
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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="diff"> </span>
</pre>
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1200
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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F S12S22InvS21 = new DenseMatrix64F(missingIndices.length, missingIndices.length);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1201" 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">
1201
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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.multTransB(S12S22Inv, S12, S12S22InvS21);</span></span>
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<pre style="margin: 0;">+<span id="LC1202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj S12S22InvS21 = new DMatrixRMaj(missingIndices.length, missingIndices.length);</span></span>
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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.multTransB(S12S22Inv, S12, S12S22InvS21);</span></span>
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1204
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<pre style="margin: 0;">+<span id="LC1204" class="line" lang="diff"> </span>
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1205
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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="diff"> if (DEBUG) {</span>
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<pre style="margin: 0;">+<span id="LC1206" class="line" lang="diff"> System.err.println("S12S22InvS21:\n" + S12S22InvS21);</span>
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1207
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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="diff"> }</span>
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1208
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<pre style="margin: 0;">+<span id="LC1208" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sBar = new DenseMatrix64F(missingIndices.length, missingIndices.length);</span></span>
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1210
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sBar = new DMatrixRMaj(missingIndices.length, missingIndices.length);</span></span>
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1211
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<pre style="margin: 0;">+<span id="LC1211" class="line" lang="diff"> gatherRowsAndColumns(variance, sBar, missingIndices, missingIndices);</span>
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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.subtract(sBar, S12S22InvS21, sBar);</span></span>
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1213
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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.subtract(sBar, S12S22InvS21, sBar);</span></span>
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<pre style="margin: 0;">+<span id="LC1214" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="diff"> if (DEBUG) {</span>
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<pre style="margin: 0;">+<span id="LC1217" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -141,18 +141,18 @@</span></span>
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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="diff"> return cholesky;</span>
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC1220" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// public final DenseMatrix64F getAffineTransform() {</span></span>
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<pre style="margin: 0;">+<span id="LC1222" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// public final DMatrixRMaj getAffineTransform() {</span></span>
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<pre style="margin: 0;">+<span id="LC1223" class="line" lang="diff"> // return affineTransform;</span>
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<pre style="margin: 0;">+<span id="LC1224" class="line" lang="diff"> // }</span>
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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1226" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F getConditionalVariance() {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1227" 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">
1227
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<pre style="margin: 0;">+<span id="LC1227" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj getConditionalVariance() {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1228" 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">
1228
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<pre style="margin: 0;">+<span id="LC1228" class="line" lang="diff"> return sBar;</span>
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<td class="diff-line-num new new_line" data-linenumber="1229" 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">
1229
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<pre style="margin: 0;">+<span id="LC1229" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="1230" 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">
1230
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<pre style="margin: 0;">+<span id="LC1230" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1231" 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">
1231
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<pre style="margin: 0;">+<span id="LC1231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F getConditionalPrecision() {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1232" 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">
1232
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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj getConditionalPrecision() {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1233" 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">
1233
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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="diff"> if (sBarInv == null) {</span>
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<td class="diff-line-num new new_line" data-linenumber="1234" 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">
1234
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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sBarInv = new DenseMatrix64F(numMissing, numMissing);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1235" 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">
1235
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<pre style="margin: 0;">+<span id="LC1235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.invert(sBar, sBarInv);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1236" 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">
1236
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<pre style="margin: 0;">+<span id="LC1236" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sBarInv = new DMatrixRMaj(numMissing, numMissing);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1237" 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">
1237
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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.invert(sBar, sBarInv);</span></span>
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1238
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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="diff"> }</span>
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1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="diff"> return sBarInv;</span>
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1240
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<pre style="margin: 0;">+<span id="LC1240" class="line" lang="diff"> }</span>
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1241
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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/dr/evomodel/treedatalikelihood/preorder/MultivariateConditionalOnTipsRealizedDelegate.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1242" 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">
1242
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<pre style="margin: 0;">+<span id="LC1242" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/dr/evomodel/treedatalikelihood/preorder/MultivariateConditionalOnTipsRealizedDelegate.java</span></span>
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1243
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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -6,8 +6,8 @@</span></span>
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1244
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<pre style="margin: 0;">+<span id="LC1244" class="line" lang="diff"> import dr.math.distributions.MultivariateNormalDistribution;</span>
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1245
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<pre style="margin: 0;">+<span id="LC1245" class="line" lang="diff"> import dr.math.matrixAlgebra.Matrix;</span>
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<td class="diff-line-num new new_line" data-linenumber="1246" 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">
1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="diff"> import dr.math.matrixAlgebra.WrappedVector;</span>
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<td class="diff-line-num new new_line" data-linenumber="1247" 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">
1247
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.data.DenseMatrix64F;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1248" 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">
1248
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<pre style="margin: 0;">+<span id="LC1248" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.ops.CommonOps;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1249" 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">
1249
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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.data.DMatrixRMaj;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1250" 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">
1250
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<pre style="margin: 0;">+<span id="LC1250" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.dense.row.CommonOps_DDRM;</span></span>
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1251
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<pre style="margin: 0;">+<span id="LC1251" class="line" lang="diff"> </span>
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1252
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<pre style="margin: 0;">+<span id="LC1252" class="line" lang="diff"> import static dr.math.matrixAlgebra.missingData.MissingOps.*;</span>
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1253
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<pre style="margin: 0;">+<span id="LC1253" class="line" lang="diff"> </span>
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1254
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<pre style="margin: 0;">+<span id="LC1254" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -41,14 +41,14 @@</span></span>
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1255
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<pre style="margin: 0;">+<span id="LC1255" class="line" lang="diff"> // scalar, dT + 2 * dT * dT, 1</span>
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1256
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<pre style="margin: 0;">+<span id="LC1256" class="line" lang="diff"> </span>
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1257
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<pre style="margin: 0;">+<span id="LC1257" class="line" lang="diff"> // Integrate out against prior</span>
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1258
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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F rootPrec = wrap(partialNodeBuffer, offsetPartial + dimTrait, dimTrait, dimTrait);</span></span>
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1259
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<pre style="margin: 0;">+<span id="LC1259" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F priorPrec = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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1260
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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.mult(Pd, wrap(partialPriorBuffer, offsetPartial + dimTrait, dimTrait, dimTrait), priorPrec);</span></span>
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1261
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj rootPrec = wrap(partialNodeBuffer, offsetPartial + dimTrait, dimTrait, dimTrait);</span></span>
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1262
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<pre style="margin: 0;">+<span id="LC1262" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj priorPrec = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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1263
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.mult(Pd, wrap(partialPriorBuffer, offsetPartial + dimTrait, dimTrait, dimTrait), priorPrec);</span></span>
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1264
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<pre style="margin: 0;">+<span id="LC1264" class="line" lang="diff"> </span>
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1265
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<pre style="margin: 0;">+<span id="LC1265" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F totalPrec = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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1266
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<pre style="margin: 0;">+<span id="LC1266" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(rootPrec, priorPrec, totalPrec);</span></span>
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1267
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<pre style="margin: 0;">+<span id="LC1267" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj totalPrec = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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1268
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<pre style="margin: 0;">+<span id="LC1268" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(rootPrec, priorPrec, totalPrec);</span></span>
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1269
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<pre style="margin: 0;">+<span id="LC1269" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F totalVar = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj totalVar = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="diff"> safeInvert(totalPrec, totalVar, false);</span>
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1273
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="diff"> final double[] tmp = new double[dimTrait];</span>
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1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -93,7 +93,7 @@</span></span>
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1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="diff"> }</span>
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1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="diff"> }</span>
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1278
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="diff"> </span>
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1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// boolean extremeValue(final DenseMatrix64F x) {</span></span>
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1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// boolean extremeValue(final DMatrixRMaj x) {</span></span>
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1281
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="diff"> // return extremeValue(new WrappedVector.Raw(x.getData(), 0, x.getNumElements()));</span>
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1282
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="diff"> // }</span>
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1283
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="diff"> //</span>
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1284
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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -130,7 +130,7 @@</span></span>
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1285
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="diff"> final int offsetPartial,</span>
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1286
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="diff"> final double branchPrecision) {</span>
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1287
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F P0 = wrap(partialNodeBuffer, offsetPartial + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj P0 = wrap(partialNodeBuffer, offsetPartial + dimTrait, dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="diff"> final int missingCount = countFiniteDiagonals(P0);</span>
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1291
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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="diff"> </span>
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1292
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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="diff"> if (missingCount == 0) { // Completely observed</span>
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<pre style="margin: 0;">+<span id="LC1293" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -167,26 +167,26 @@</span></span>
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<pre style="margin: 0;">+<span id="LC1294" class="line" lang="diff"> final int[] observed = indices.getComplement();</span>
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<pre style="margin: 0;">+<span id="LC1295" class="line" lang="diff"> final int[] missing = indices.getArray();</span>
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<pre style="margin: 0;">+<span id="LC1296" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F V1 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.scale(1.0 / branchPrecision, Vd, V1);</span></span>
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<pre style="margin: 0;">+<span id="LC1299" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj V1 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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1300
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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.scale(1.0 / branchPrecision, Vd, V1);</span></span>
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1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="diff"> </span>
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1302
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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="diff"> ConditionalVarianceAndTransform2 transform =</span>
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1303
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<pre style="margin: 0;">+<span id="LC1303" class="line" lang="diff"> new ConditionalVarianceAndTransform2(</span>
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1304
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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="diff"> V1, missing, observed</span>
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1305
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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="diff"> ); // TODO Cache (via delegated function)</span>
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1306
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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="diff"> </span>
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1307
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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F cP0 = new DenseMatrix64F(missing.length, missing.length);</span></span>
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1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj cP0 = new DMatrixRMaj(missing.length, missing.length);</span></span>
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1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="diff"> gatherRowsAndColumns(P0, cP0, missing, missing);</span>
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1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="diff"> </span>
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1311
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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="diff"> final WrappedVector cM2 = transform.getConditionalMean(</span>
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1312
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<pre style="margin: 0;">+<span id="LC1312" class="line" lang="diff"> partialNodeBuffer, offsetPartial, // Tip value</span>
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1313
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<pre style="margin: 0;">+<span id="LC1313" class="line" lang="diff"> sample, offsetParent); // Parent value</span>
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1314
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<pre style="margin: 0;">+<span id="LC1314" class="line" lang="diff"> </span>
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1315
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<pre style="margin: 0;">+<span id="LC1315" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F cP1 = transform.getConditionalPrecision();</span></span>
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1316
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<pre style="margin: 0;">+<span id="LC1316" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj cP1 = transform.getConditionalPrecision();</span></span>
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1317
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<pre style="margin: 0;">+<span id="LC1317" class="line" lang="diff"> </span>
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1318
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F cP2 = new DenseMatrix64F(missing.length, missing.length);</span></span>
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1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F cV2 = new DenseMatrix64F(missing.length, missing.length);</span></span>
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1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(cP0, cP1, cP2);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1321" 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">
1321
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj cP2 = new DMatrixRMaj(missing.length, missing.length);</span></span>
</pre>
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1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj cV2 = new DMatrixRMaj(missing.length, missing.length);</span></span>
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1323
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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(cP0, cP1, cP2);</span></span>
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<pre style="margin: 0;">+<span id="LC1324" class="line" lang="diff"> </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="diff"> safeInvert(cP2, cV2, false);</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="diff"> double[][] cC2 = getCholeskyOfVariance(cV2.getData(), missing.length);</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="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -205,8 +205,8 @@</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="diff"> final WrappedVector M0 = new WrappedVector.Raw(partialNodeBuffer, offsetPartial, dimTrait);</span>
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1329
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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="diff"> </span>
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1330
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="diff"> final WrappedVector M1 = new WrappedVector.Raw(sample, offsetParent, dimTrait);</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="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F P1 = new DenseMatrix64F(dimTrait, dimTrait);</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="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.scale(branchPrecision, Pd, P1);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1333" 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">
1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj P1 = new DMatrixRMaj(dimTrait, dimTrait);</span></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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.scale(branchPrecision, Pd, P1);</span></span>
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1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="diff"> </span>
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1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="diff"> final WrappedVector newSample = new WrappedVector.Raw(sample, offsetSample, dimTrait);</span>
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1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -246,25 +246,25 @@</span></span>
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="diff"> if (!Double.isInfinite(branchPrecision)) {</span>
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="diff"> </span>
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1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="diff"> final WrappedVector M0 = new WrappedVector.Raw(partialNodeBuffer, offsetPartial, dimTrait);</span>
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1342
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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F P0 = wrap(partialNodeBuffer, offsetPartial + dimTrait, dimTrait, dimTrait);</span></span>
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1343
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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj P0 = wrap(partialNodeBuffer, offsetPartial + dimTrait, dimTrait, dimTrait);</span></span>
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1344
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<pre style="margin: 0;">+<span id="LC1344" class="line" lang="diff"> </span>
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1345
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="diff"> final WrappedVector M1;</span>
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<td class="diff-line-num new new_line" data-linenumber="1346" 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">
1346
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F P1;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1347" 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">
1347
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<pre style="margin: 0;">+<span id="LC1347" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj P1;</span></span>
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1348
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<pre style="margin: 0;">+<span id="LC1348" class="line" lang="diff"> </span>
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1349
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="diff"> if (hasNoDrift) {</span>
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1350
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<pre style="margin: 0;">+<span id="LC1350" class="line" lang="diff"> M1 = new WrappedVector.Raw(sample, offsetParent, dimTrait);</span>
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1351
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<pre style="margin: 0;">+<span id="LC1351" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- P1 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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1352
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<pre style="margin: 0;">+<span id="LC1352" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.scale(branchPrecision, Pd, P1);</span></span>
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1353
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<pre style="margin: 0;">+<span id="LC1353" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ P1 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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1354
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<pre style="margin: 0;">+<span id="LC1354" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.scale(branchPrecision, Pd, P1);</span></span>
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1355
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<pre style="margin: 0;">+<span id="LC1355" class="line" lang="diff"> } else {</span>
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1356
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<pre style="margin: 0;">+<span id="LC1356" class="line" lang="diff"> M1 = getMeanWithDrift(sample, offsetParent, displacementBuffer, dimTrait);</span>
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1357
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<pre style="margin: 0;">+<span id="LC1357" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- P1 = DenseMatrix64F.wrap(dimTrait, dimTrait, precisionBuffer);</span></span>
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1358
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<pre style="margin: 0;">+<span id="LC1358" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ P1 = DMatrixRMaj.wrap(dimTrait, dimTrait, precisionBuffer);</span></span>
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1359
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<pre style="margin: 0;">+<span id="LC1359" class="line" lang="diff"> }</span>
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1360
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<pre style="margin: 0;">+<span id="LC1360" class="line" lang="diff"> </span>
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1361
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<pre style="margin: 0;">+<span id="LC1361" class="line" lang="diff"> // boolean DEBUG_PRECISION = false;</span>
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1362
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<pre style="margin: 0;">+<span id="LC1362" class="line" lang="diff"> //</span>
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1363
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<pre style="margin: 0;">+<span id="LC1363" class="line" lang="diff"> // if (DEBUG_PRECISION) {</span>
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1364
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<pre style="margin: 0;">+<span id="LC1364" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// DenseMatrix64F tP1 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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1365
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<pre style="margin: 0;">+<span id="LC1365" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// CommonOps.scale(branchPrecision, Pd, tP1);</span></span>
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1366
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<pre style="margin: 0;">+<span id="LC1366" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// DMatrixRMaj tP1 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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1367
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<pre style="margin: 0;">+<span id="LC1367" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// CommonOps_DDRM.scale(branchPrecision, Pd, tP1);</span></span>
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1368
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<pre style="margin: 0;">+<span id="LC1368" class="line" lang="diff"> //</span>
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1369
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<pre style="margin: 0;">+<span id="LC1369" class="line" lang="diff"> // for (int i = 0; i < dimTrait; ++i) {</span>
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1370
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<pre style="margin: 0;">+<span id="LC1370" class="line" lang="diff"> // for (int j = 0; j < dimTrait; ++j) {</span>
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1371
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<pre style="margin: 0;">+<span id="LC1371" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -277,10 +277,10 @@</span></span>
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1372
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<pre style="margin: 0;">+<span id="LC1372" class="line" lang="diff"> // }</span>
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<pre style="margin: 0;">+<span id="LC1373" class="line" lang="diff"> </span>
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1374
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="diff"> final WrappedVector M2 = new WrappedVector.Raw(tmpMean, 0, dimTrait);</span>
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1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F P2 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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1376
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F V2 = new DenseMatrix64F(dimTrait, dimTrait);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1377" 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">
1377
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<pre style="margin: 0;">+<span id="LC1377" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj P2 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1378" 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">
1378
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<pre style="margin: 0;">+<span id="LC1378" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj V2 = new DMatrixRMaj(dimTrait, dimTrait);</span></span>
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1379
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<pre style="margin: 0;">+<span id="LC1379" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1380" 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">
1380
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<pre style="margin: 0;">+<span id="LC1380" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.add(P0, P1, P2);</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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.add(P0, P1, P2);</span></span>
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1382
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<pre style="margin: 0;">+<span id="LC1382" class="line" lang="diff"> safeInvert(P2, V2, false);</span>
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1383
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<pre style="margin: 0;">+<span id="LC1383" class="line" lang="diff"> weightedAverage(M0, P0, M1, P1, M2, V2, dimTrait);</span>
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1384
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<pre style="margin: 0;">+<span id="LC1384" class="line" lang="diff"> </span>
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1385
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<pre style="margin: 0;">+<span id="LC1385" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/dr/evomodel/treedatalikelihood/preorder/ProcessSimulationDelegate.java</span></span>
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<pre style="margin: 0;">+<span id="LC1386" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/dr/evomodel/treedatalikelihood/preorder/ProcessSimulationDelegate.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1387" 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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<pre style="margin: 0;">+<span id="LC1387" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -35,7 +35,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC1388" class="line" lang="diff"> import dr.inference.model.Model;</span>
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<pre style="margin: 0;">+<span id="LC1389" class="line" lang="diff"> import dr.inference.model.ModelListener;</span>
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1390
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<pre style="margin: 0;">+<span id="LC1390" class="line" lang="diff"> import dr.math.matrixAlgebra.*;</span>
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1391
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<pre style="margin: 0;">+<span id="LC1391" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.data.DenseMatrix64F;</span></span>
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1392
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<pre style="margin: 0;">+<span id="LC1392" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.data.DMatrixRMaj;</span></span>
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<pre style="margin: 0;">+<span id="LC1393" class="line" lang="diff"> </span>
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1394
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<pre style="margin: 0;">+<span id="LC1394" class="line" lang="diff"> import java.util.List;</span>
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1395
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<pre style="margin: 0;">+<span id="LC1395" class="line" lang="diff"> import java.util.Map;</span>
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<pre style="margin: 0;">+<span id="LC1396" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -161,8 +161,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC1397" class="line" lang="diff"> final ContinuousDataLikelihoodDelegate likelihoodDelegate;</span>
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1398
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<pre style="margin: 0;">+<span id="LC1398" class="line" lang="diff"> </span>
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1399
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<pre style="margin: 0;">+<span id="LC1399" class="line" lang="diff"> double[] diffusionVariance;</span>
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1400
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<pre style="margin: 0;">+<span id="LC1400" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F Vd;</span></span>
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1401
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<pre style="margin: 0;">+<span id="LC1401" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DenseMatrix64F Pd;</span></span>
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1402
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<pre style="margin: 0;">+<span id="LC1402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj Vd;</span></span>
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1403
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<pre style="margin: 0;">+<span id="LC1403" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DMatrixRMaj Pd;</span></span>
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1404
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<pre style="margin: 0;">+<span id="LC1404" class="line" lang="diff"> </span>
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1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="diff"> double[][] cholesky;</span>
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1406
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<pre style="margin: 0;">+<span id="LC1406" class="line" lang="diff"> Map<PartiallyMissingInformation.HashedIntArray,</span>
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<pre style="margin: 0;">+<span id="LC1407" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -221,7 +221,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="diff"> double[][] diffusionPrecision = diffusionModel.getPrecisionmatrix();</span>
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="diff"> diffusionVariance = getVectorizedVarianceFromPrecision(diffusionPrecision);</span>
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="diff"> Vd = wrap(diffusionVariance, 0, dimTrait, dimTrait);</span>
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Pd = new DenseMatrix64F(diffusionPrecision);</span></span>
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<pre style="margin: 0;">+<span id="LC1412" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Pd = new DMatrixRMaj(diffusionPrecision);</span></span>
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC1414" class="line" lang="diff"> if (cholesky == null) {</span>
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<pre style="margin: 0;">+<span id="LC1415" class="line" lang="diff"> cholesky = getCholeskyOfVariance(diffusionVariance, dimTrait);</span>
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1416
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<pre style="margin: 0;">+<span id="LC1416" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/dr/inferencexml/operators/EllipticalSliceOperatorParser.java</span></span>
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/dr/inferencexml/operators/EllipticalSliceOperatorParser.java</span></span>
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<pre style="margin: 0;">+<span id="LC1418" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -35,7 +35,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC1419" class="line" lang="diff"> import dr.math.distributions.GaussianProcessRandomGenerator;</span>
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<pre style="margin: 0;">+<span id="LC1420" class="line" lang="diff"> import dr.math.distributions.MultivariateNormalDistribution;</span>
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<pre style="margin: 0;">+<span id="LC1421" class="line" lang="diff"> import dr.xml.*;</span>
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<pre style="margin: 0;">+<span id="LC1422" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.ops.CommonOps;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1423" 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">
1423
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<pre style="margin: 0;">+<span id="LC1423" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.dense.row.CommonOps_DDRM;</span></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="1424" 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">
1424
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<pre style="margin: 0;">+<span id="LC1424" class="line" lang="diff"> </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="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="diff"> /**</span>
</pre>
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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="diff"> */</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="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="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/dr/math/matrixAlgebra/missingData/MissingOps.java</span></span>
</pre>
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</td>
<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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/dr/math/matrixAlgebra/missingData/MissingOps.java</span></span>
</pre>
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</td>
<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="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -3,17 +3,17 @@</span></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="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="diff"> import dr.math.matrixAlgebra.Vector;</span>
</pre>
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</td>
<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="diff"> import dr.math.matrixAlgebra.WrappedVector;</span>
</pre>
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</td>
<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="diff"> import dr.util.Transform;</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="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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.alg.dense.decomposition.lu.LUDecompositionAlt_D64;</span></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="1434" 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">
1434
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<pre style="margin: 0;">+<span id="LC1434" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.alg.dense.decomposition.qr.QRColPivDecompositionHouseholderColumn_D64;</span></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="1435" 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">
1435
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<pre style="margin: 0;">+<span id="LC1435" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.alg.dense.linsol.lu.LinearSolverLu_D64;</span></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="1436" 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">
1436
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<pre style="margin: 0;">+<span id="LC1436" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.alg.dense.misc.UnrolledDeterminantFromMinor;</span></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="1437" 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">
1437
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<pre style="margin: 0;">+<span id="LC1437" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.alg.dense.misc.UnrolledInverseFromMinor;</span></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="1438" 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">
1438
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<pre style="margin: 0;">+<span id="LC1438" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.data.DenseMatrix64F;</span></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="1439" 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">
1439
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<pre style="margin: 0;">+<span id="LC1439" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.factory.LinearSolverFactory;</span></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="1440" 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">
1440
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<pre style="margin: 0;">+<span id="LC1440" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.interfaces.decomposition.QRPDecomposition;</span></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="1441" 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">
1441
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<pre style="margin: 0;">+<span id="LC1441" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.interfaces.decomposition.SingularValueDecomposition;</span></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="1442" 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">
1442
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<pre style="margin: 0;">+<span id="LC1442" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.dense.row.decomposition.lu.LUDecompositionAlt_DDRM;</span></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="1443" 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">
1443
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<pre style="margin: 0;">+<span id="LC1443" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.dense.row.decomposition.qr.QRColPivDecompositionHouseholderColumn_DDRM;</span></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="1444" 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">
1444
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<pre style="margin: 0;">+<span id="LC1444" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.dense.row.linsol.lu.LinearSolverLu_DDRM;</span></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="1445" 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">
1445
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<pre style="margin: 0;">+<span id="LC1445" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.dense.row.misc.UnrolledDeterminantFromMinor_DDRM;</span></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="1446" 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">
1446
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<pre style="margin: 0;">+<span id="LC1446" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.dense.row.misc.UnrolledInverseFromMinor_DDRM;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1447" 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">
1447
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<pre style="margin: 0;">+<span id="LC1447" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.data.DMatrixRMaj;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1448" 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">
1448
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<pre style="margin: 0;">+<span id="LC1448" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.dense.row.factory.LinearSolverFactory_DDRM;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1449" 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">
1449
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<pre style="margin: 0;">+<span id="LC1449" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.interfaces.decomposition.QRPDecomposition_F64;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1450" 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">
1450
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<pre style="margin: 0;">+<span id="LC1450" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.interfaces.decomposition.SingularValueDecomposition_F64;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1451" 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">
1451
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<pre style="margin: 0;">+<span id="LC1451" class="line" lang="diff"> import org.ejml.interfaces.linsol.LinearSolver;</span>
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<td class="diff-line-num new new_line" data-linenumber="1452" 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">
1452
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<pre style="margin: 0;">+<span id="LC1452" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.ejml.ops.CommonOps;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1453" 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">
1453
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<pre style="margin: 0;">+<span id="LC1453" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.ejml.dense.row.CommonOps_DDRM;</span></span>
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1454
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<pre style="margin: 0;">+<span id="LC1454" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1455" 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">
1455
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<pre style="margin: 0;">+<span id="LC1455" class="line" lang="diff"> import java.util.Arrays;</span>
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<td class="diff-line-num new new_line" data-linenumber="1456" 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">
1456
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<pre style="margin: 0;">+<span id="LC1456" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1457" 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">
1457
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<pre style="margin: 0;">+<span id="LC1457" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -26,21 +26,21 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1458" 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">
1458
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<pre style="margin: 0;">+<span id="LC1458" class="line" lang="diff"> */</span>
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<td class="diff-line-num new new_line" data-linenumber="1459" 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">
1459
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<pre style="margin: 0;">+<span id="LC1459" class="line" lang="diff"> public class MissingOps {</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="1460" 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">
1460
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<pre style="margin: 0;">+<span id="LC1460" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1461" 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">
1461
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<pre style="margin: 0;">+<span id="LC1461" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static DenseMatrix64F wrap(final double[] source, final int offset,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1462" 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">
1462
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<pre style="margin: 0;">+<span id="LC1462" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static DMatrixRMaj wrap(final double[] source, final int offset,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1463" 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">
1463
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<pre style="margin: 0;">+<span id="LC1463" class="line" lang="diff"> final int numRows, final int numCols) {</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="1464" 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">
1464
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<pre style="margin: 0;">+<span id="LC1464" class="line" lang="diff"> double[] buffer = new double[numRows * numCols];</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1465" 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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<pre style="margin: 0;">+<span id="LC1465" class="line" lang="diff"> return wrap(source, offset, numRows, numCols, buffer);</span>
</pre>
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<pre style="margin: 0;">+<span id="LC1466" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="1467" 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">
1467
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<pre style="margin: 0;">+<span id="LC1467" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1468" 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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<pre style="margin: 0;">+<span id="LC1468" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static DenseMatrix64F wrap(final double[] source, final int offset,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1469" 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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<pre style="margin: 0;">+<span id="LC1469" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static DMatrixRMaj wrap(final double[] source, final int offset,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1470" 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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<pre style="margin: 0;">+<span id="LC1470" class="line" lang="diff"> final int numRows, final int numCols,</span>
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<td class="diff-line-num new new_line" data-linenumber="1471" 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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<pre style="margin: 0;">+<span id="LC1471" class="line" lang="diff"> final double[] buffer) {</span>
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1472
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<pre style="margin: 0;">+<span id="LC1472" class="line" lang="diff"> System.arraycopy(source, offset, buffer, 0, numRows * numCols);</span>
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<td class="diff-line-num new new_line" data-linenumber="1473" 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">
1473
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<pre style="margin: 0;">+<span id="LC1473" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return DenseMatrix64F.wrap(numRows, numCols, buffer);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1474" 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">
1474
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<pre style="margin: 0;">+<span id="LC1474" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return DMatrixRMaj.wrap(numRows, numCols, buffer);</span></span>
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1475
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<pre style="margin: 0;">+<span id="LC1475" class="line" lang="diff"> }</span>
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1476
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<pre style="margin: 0;">+<span id="LC1476" class="line" lang="diff"> </span>
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1477
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<pre style="margin: 0;">+<span id="LC1477" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1478" 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">
1478
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<pre style="margin: 0;">+<span id="LC1478" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static void gatherRowsAndColumns(final DenseMatrix64F source, final DenseMatrix64F destination,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1479" 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">
1479
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<pre style="margin: 0;">+<span id="LC1479" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static void gatherRowsAndColumns(final DMatrixRMaj source, final DMatrixRMaj destination,</span></span>
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<pre style="margin: 0;">+<span id="LC1480" class="line" lang="diff"> final int[] rowIndices, final int[] colIndices) {</span>
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1481
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<pre style="margin: 0;">+<span id="LC1481" class="line" lang="diff"> </span>
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1482
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<pre style="margin: 0;">+<span id="LC1482" class="line" lang="diff"> final int rowLength = rowIndices.length;</span>
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1483
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<pre style="margin: 0;">+<span id="LC1483" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -57,7 +57,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC1484" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC1485" class="line" lang="diff"> }</span>
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1486
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<pre style="margin: 0;">+<span id="LC1486" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1487" 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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<pre style="margin: 0;">+<span id="LC1487" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static void scatterRowsAndColumns(final DenseMatrix64F source, final DenseMatrix64F destination,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1488" 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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<pre style="margin: 0;">+<span id="LC1488" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static void scatterRowsAndColumns(final DMatrixRMaj source, final DMatrixRMaj destination,</span></span>
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<pre style="margin: 0;">+<span id="LC1489" class="line" lang="diff"> final int[] rowIdices, final int[] colIndices, final boolean clear) {</span>
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<pre style="margin: 0;">+<span id="LC1490" class="line" lang="diff"> if (clear) {</span>
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1491
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<pre style="margin: 0;">+<span id="LC1491" class="line" lang="diff"> Arrays.fill(destination.getData(), 0.0);</span>
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<pre style="margin: 0;">+<span id="LC1492" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -77,11 +77,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC1493" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC1494" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC1495" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1496" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static void unwrap(final DenseMatrix64F source, final double[] destination, final int offset) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1497" 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">
1497
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<pre style="margin: 0;">+<span id="LC1497" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static void unwrap(final DMatrixRMaj source, final double[] destination, final int offset) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1498" 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">
1498
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<pre style="margin: 0;">+<span id="LC1498" class="line" lang="diff"> System.arraycopy(source.getData(), 0, destination, offset, source.getNumElements());</span>
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1499
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<pre style="margin: 0;">+<span id="LC1499" class="line" lang="diff"> }</span>
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1500
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<pre style="margin: 0;">+<span id="LC1500" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1501" 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">
1501
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<pre style="margin: 0;">+<span id="LC1501" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static boolean anyDiagonalInfinities(DenseMatrix64F source) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1502" 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">
1502
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<pre style="margin: 0;">+<span id="LC1502" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static boolean anyDiagonalInfinities(DMatrixRMaj source) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1503" 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">
1503
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<pre style="margin: 0;">+<span id="LC1503" class="line" lang="diff"> boolean anyInfinities = false;</span>
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<td class="diff-line-num new new_line" data-linenumber="1504" 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">
1504
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<pre style="margin: 0;">+<span id="LC1504" class="line" lang="diff"> for (int i = 0; i < source.getNumCols() && !anyInfinities; ++i) {</span>
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<td class="diff-line-num new new_line" data-linenumber="1505" 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">
1505
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<pre style="margin: 0;">+<span id="LC1505" class="line" lang="diff"> if (Double.isInfinite(source.unsafe_get(i, i))) {</span>
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<td class="diff-line-num new new_line" data-linenumber="1506" 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">
1506
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<pre style="margin: 0;">+<span id="LC1506" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -91,7 +91,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1507" 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">
1507
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<pre style="margin: 0;">+<span id="LC1507" class="line" lang="diff"> return anyInfinities;</span>
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1508
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<pre style="margin: 0;">+<span id="LC1508" class="line" lang="diff"> }</span>
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1509
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<pre style="margin: 0;">+<span id="LC1509" class="line" lang="diff"> </span>
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1510
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<pre style="margin: 0;">+<span id="LC1510" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static boolean allFiniteDiagonals(DenseMatrix64F source) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1511" 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">
1511
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<pre style="margin: 0;">+<span id="LC1511" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static boolean allFiniteDiagonals(DMatrixRMaj source) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1512" 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">
1512
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<pre style="margin: 0;">+<span id="LC1512" class="line" lang="diff"> boolean allFinite = true;</span>
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1513
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<pre style="margin: 0;">+<span id="LC1513" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1514" 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">
1514
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<pre style="margin: 0;">+<span id="LC1514" class="line" lang="diff"> final int length = source.getNumCols();</span>
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<td class="diff-line-num new new_line" data-linenumber="1515" 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">
1515
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<pre style="margin: 0;">+<span id="LC1515" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -101,7 +101,7 @@</span></span>
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1516
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<pre style="margin: 0;">+<span id="LC1516" class="line" lang="diff"> return allFinite;</span>
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1517
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<pre style="margin: 0;">+<span id="LC1517" class="line" lang="diff"> }</span>
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1518
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<pre style="margin: 0;">+<span id="LC1518" class="line" lang="diff"> </span>
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1519
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<pre style="margin: 0;">+<span id="LC1519" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static int countFiniteDiagonals(DenseMatrix64F source) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1520" 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">
1520
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<pre style="margin: 0;">+<span id="LC1520" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static int countFiniteDiagonals(DMatrixRMaj source) {</span></span>
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<pre style="margin: 0;">+<span id="LC1521" class="line" lang="diff"> final int length = source.getNumCols();</span>
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1522
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<pre style="margin: 0;">+<span id="LC1522" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1523" 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">
1523
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<pre style="margin: 0;">+<span id="LC1523" class="line" lang="diff"> int count = 0;</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="1524" 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">
1524
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<pre style="margin: 0;">+<span id="LC1524" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -114,7 +114,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1525" 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">
1525
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<pre style="margin: 0;">+<span id="LC1525" class="line" lang="diff"> return count;</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="1526" 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">
1526
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<pre style="margin: 0;">+<span id="LC1526" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="1527" 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">
1527
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<pre style="margin: 0;">+<span id="LC1527" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1528" 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">
1528
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<pre style="margin: 0;">+<span id="LC1528" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static int countZeroDiagonals(DenseMatrix64F source) {</span></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="1529" 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">
1529
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<pre style="margin: 0;">+<span id="LC1529" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static int countZeroDiagonals(DMatrixRMaj source) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1530" 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">
1530
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<pre style="margin: 0;">+<span id="LC1530" class="line" lang="diff"> final int length = source.getNumCols();</span>
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<td class="diff-line-num new new_line" data-linenumber="1531" 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">
1531
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<pre style="margin: 0;">+<span id="LC1531" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1532" 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">
1532
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<pre style="margin: 0;">+<span id="LC1532" class="line" lang="diff"> int count = 0;</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="1533" 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">
1533
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<pre style="margin: 0;">+<span id="LC1533" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -127,7 +127,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1534" 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">
1534
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<pre style="margin: 0;">+<span id="LC1534" class="line" lang="diff"> return count;</span>
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<td class="diff-line-num new new_line" data-linenumber="1535" 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">
1535
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<pre style="margin: 0;">+<span id="LC1535" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="1536" 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">
1536
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1537" 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">
1537
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<pre style="margin: 0;">+<span id="LC1537" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static void getFiniteDiagonalIndices(final DenseMatrix64F source, final int[] indices) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1538" 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">
1538
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<pre style="margin: 0;">+<span id="LC1538" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static void getFiniteDiagonalIndices(final DMatrixRMaj source, final int[] indices) {</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1539" 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">
1539
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<pre style="margin: 0;">+<span id="LC1539" class="line" lang="diff"> final int length = source.getNumCols();</span>
</pre>
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1540
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<pre style="margin: 0;">+<span id="LC1540" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1541" 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">
1541
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<pre style="margin: 0;">+<span id="LC1541" class="line" lang="diff"> int index = 0;</span>
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<td class="diff-line-num new new_line" data-linenumber="1542" 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">
1542
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<pre style="margin: 0;">+<span id="LC1542" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -140,7 +140,7 @@</span></span>
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1543
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<pre style="margin: 0;">+<span id="LC1543" class="line" lang="diff"> }</span>
</pre>
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1544
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<pre style="margin: 0;">+<span id="LC1544" class="line" lang="diff"> }</span>
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1545
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<pre style="margin: 0;">+<span id="LC1545" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1546" 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">
1546
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<pre style="margin: 0;">+<span id="LC1546" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static int countFiniteNonZeroDiagonals(DenseMatrix64F source) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1547" 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">
1547
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<pre style="margin: 0;">+<span id="LC1547" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static int countFiniteNonZeroDiagonals(DMatrixRMaj source) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1548" 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">
1548
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<pre style="margin: 0;">+<span id="LC1548" class="line" lang="diff"> final int length = source.getNumCols();</span>
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1549
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<pre style="margin: 0;">+<span id="LC1549" class="line" lang="diff"> </span>
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1550
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<pre style="margin: 0;">+<span id="LC1550" class="line" lang="diff"> int count = 0;</span>
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<td class="diff-line-num new new_line" data-linenumber="1551" 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">
1551
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<pre style="margin: 0;">+<span id="LC1551" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -153,7 +153,7 @@</span></span>
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1552
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<pre style="margin: 0;">+<span id="LC1552" class="line" lang="diff"> return count;</span>
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1553
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<pre style="margin: 0;">+<span id="LC1553" class="line" lang="diff"> }</span>
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1554
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<pre style="margin: 0;">+<span id="LC1554" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1555" 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">
1555
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<pre style="margin: 0;">+<span id="LC1555" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static void getFiniteNonZeroDiagonalIndices(final DenseMatrix64F source, final int[] indices) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1556" 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">
1556
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<pre style="margin: 0;">+<span id="LC1556" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static void getFiniteNonZeroDiagonalIndices(final DMatrixRMaj source, final int[] indices) {</span></span>
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1557
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<pre style="margin: 0;">+<span id="LC1557" class="line" lang="diff"> final int length = source.getNumCols();</span>
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1558
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<pre style="margin: 0;">+<span id="LC1558" class="line" lang="diff"> </span>
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1559
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<pre style="margin: 0;">+<span id="LC1559" class="line" lang="diff"> int index = 0;</span>
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1560
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<pre style="margin: 0;">+<span id="LC1560" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -166,22 +166,22 @@</span></span>
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1561
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<pre style="margin: 0;">+<span id="LC1561" class="line" lang="diff"> }</span>
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1562
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<pre style="margin: 0;">+<span id="LC1562" class="line" lang="diff"> }</span>
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1563
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<pre style="margin: 0;">+<span id="LC1563" class="line" lang="diff"> </span>
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1564
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<pre style="margin: 0;">+<span id="LC1564" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static void addToDiagonal(DenseMatrix64F source, double increment) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1565" 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">
1565
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<pre style="margin: 0;">+<span id="LC1565" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static void addToDiagonal(DMatrixRMaj source, double increment) {</span></span>
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1566
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<pre style="margin: 0;">+<span id="LC1566" class="line" lang="diff"> final int width = source.getNumRows();</span>
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1567
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<pre style="margin: 0;">+<span id="LC1567" class="line" lang="diff"> for (int i = 0; i < width; ++i) {</span>
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1568
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<pre style="margin: 0;">+<span id="LC1568" class="line" lang="diff"> source.unsafe_set(i,i, source.unsafe_get(i, i) + increment);</span>
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1569
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<pre style="margin: 0;">+<span id="LC1569" class="line" lang="diff"> }</span>
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1570
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<pre style="margin: 0;">+<span id="LC1570" class="line" lang="diff"> }</span>
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1571
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<pre style="margin: 0;">+<span id="LC1571" class="line" lang="diff"> </span>
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1572
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<pre style="margin: 0;">+<span id="LC1572" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static double det(DenseMatrix64F mat) {</span></span>
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1573
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<pre style="margin: 0;">+<span id="LC1573" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static double det(DMatrixRMaj mat) {</span></span>
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1574
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<pre style="margin: 0;">+<span id="LC1574" class="line" lang="diff"> int numCol = mat.getNumCols();</span>
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1575
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<pre style="margin: 0;">+<span id="LC1575" class="line" lang="diff"> int numRow = mat.getNumRows();</span>
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1576
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<pre style="margin: 0;">+<span id="LC1576" class="line" lang="diff"> if(numCol != numRow) {</span>
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1577
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<pre style="margin: 0;">+<span id="LC1577" class="line" lang="diff"> throw new IllegalArgumentException("Must be a square matrix.");</span>
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1578
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<pre style="margin: 0;">+<span id="LC1578" class="line" lang="diff"> } else if(numCol <= 6) {</span>
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<td class="diff-line-num new new_line" data-linenumber="1579" 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">
1579
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<pre style="margin: 0;">+<span id="LC1579" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return numCol >= 2? UnrolledDeterminantFromMinor.det(mat):mat.get(0);</span></span>
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1580
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<pre style="margin: 0;">+<span id="LC1580" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return numCol >= 2? UnrolledDeterminantFromMinor_DDRM.det(mat):mat.get(0);</span></span>
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1581
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<pre style="margin: 0;">+<span id="LC1581" class="line" lang="diff"> } else {</span>
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1582
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<pre style="margin: 0;">+<span id="LC1582" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- LUDecompositionAlt_D64 alg = new LUDecompositionAlt_D64();</span></span>
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1583
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<pre style="margin: 0;">+<span id="LC1583" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ LUDecompositionAlt_DDRM alg = new LUDecompositionAlt_DDRM();</span></span>
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1584
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<pre style="margin: 0;">+<span id="LC1584" class="line" lang="diff"> if(alg.inputModified()) {</span>
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1585
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<pre style="margin: 0;">+<span id="LC1585" class="line" lang="diff"> mat = mat.copy();</span>
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1586
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<pre style="margin: 0;">+<span id="LC1586" class="line" lang="diff"> }</span>
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1587
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<pre style="margin: 0;">+<span id="LC1587" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -190,7 +190,7 @@</span></span>
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1588
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<pre style="margin: 0;">+<span id="LC1588" class="line" lang="diff"> }</span>
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1589
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<pre style="margin: 0;">+<span id="LC1589" class="line" lang="diff"> }</span>
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1590
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<pre style="margin: 0;">+<span id="LC1590" class="line" lang="diff"> </span>
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1591
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<pre style="margin: 0;">+<span id="LC1591" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static double invertAndGetDeterminant(DenseMatrix64F mat, DenseMatrix64F result) {</span></span>
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1592
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<pre style="margin: 0;">+<span id="LC1592" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static double invertAndGetDeterminant(DMatrixRMaj mat, DMatrixRMaj result) {</span></span>
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1593
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<pre style="margin: 0;">+<span id="LC1593" class="line" lang="diff"> </span>
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1594
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<pre style="margin: 0;">+<span id="LC1594" class="line" lang="diff"> final int numCol = mat.getNumCols();</span>
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1595
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<pre style="margin: 0;">+<span id="LC1595" class="line" lang="diff"> final int numRow = mat.getNumRows();</span>
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<pre style="margin: 0;">+<span id="LC1596" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -201,18 +201,18 @@</span></span>
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1597
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<pre style="margin: 0;">+<span id="LC1597" class="line" lang="diff"> if (numCol <= 5) {</span>
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1598
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<pre style="margin: 0;">+<span id="LC1598" class="line" lang="diff"> </span>
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1599
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<pre style="margin: 0;">+<span id="LC1599" class="line" lang="diff"> if (numCol >= 2) {</span>
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1600
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<pre style="margin: 0;">+<span id="LC1600" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- UnrolledInverseFromMinor.inv(mat, result);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1601" 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">
1601
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<pre style="margin: 0;">+<span id="LC1601" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ UnrolledInverseFromMinor_DDRM.inv(mat, result);</span></span>
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1602
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<pre style="margin: 0;">+<span id="LC1602" class="line" lang="diff"> } else {</span>
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<td class="diff-line-num new new_line" data-linenumber="1603" 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">
1603
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<pre style="margin: 0;">+<span id="LC1603" class="line" lang="diff"> result.set(0, 1.0D / mat.get(0));</span>
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1604
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<pre style="margin: 0;">+<span id="LC1604" class="line" lang="diff"> }</span>
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1605
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<pre style="margin: 0;">+<span id="LC1605" class="line" lang="diff"> </span>
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1606
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<pre style="margin: 0;">+<span id="LC1606" class="line" lang="diff"> return numCol >= 2 ?</span>
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1607
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<pre style="margin: 0;">+<span id="LC1607" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- UnrolledDeterminantFromMinor.det(mat) :</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1608" 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">
1608
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<pre style="margin: 0;">+<span id="LC1608" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ UnrolledDeterminantFromMinor_DDRM.det(mat) :</span></span>
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1609
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<pre style="margin: 0;">+<span id="LC1609" class="line" lang="diff"> mat.get(0);</span>
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1610
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<pre style="margin: 0;">+<span id="LC1610" class="line" lang="diff"> } else {</span>
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1611
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<pre style="margin: 0;">+<span id="LC1611" class="line" lang="diff"> </span>
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1612
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<pre style="margin: 0;">+<span id="LC1612" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- LUDecompositionAlt_D64 alg = new LUDecompositionAlt_D64();</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1613" 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">
1613
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<pre style="margin: 0;">+<span id="LC1613" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- LinearSolverLu_D64 solver = new LinearSolverLu_D64(alg);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1614" 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">
1614
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<pre style="margin: 0;">+<span id="LC1614" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ LUDecompositionAlt_DDRM alg = new LUDecompositionAlt_DDRM();</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1615" 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">
1615
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<pre style="margin: 0;">+<span id="LC1615" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ LinearSolverLu_DDRM solver = new LinearSolverLu_DDRM(alg);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1616" 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">
1616
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<pre style="margin: 0;">+<span id="LC1616" class="line" lang="diff"> if (solver.modifiesA()) {</span>
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1617
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<pre style="margin: 0;">+<span id="LC1617" class="line" lang="diff"> mat = mat.copy();</span>
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1618
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<pre style="margin: 0;">+<span id="LC1618" class="line" lang="diff"> }</span>
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1619
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<pre style="margin: 0;">+<span id="LC1619" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -228,7 +228,7 @@</span></span>
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1620
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<pre style="margin: 0;">+<span id="LC1620" class="line" lang="diff"> }</span>
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1621
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<pre style="margin: 0;">+<span id="LC1621" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC1622" class="line" lang="diff"> </span>
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1623
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<pre style="margin: 0;">+<span id="LC1623" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static InversionResult safeDeterminant(DenseMatrix64F source, boolean invert) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1624" 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">
1624
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<pre style="margin: 0;">+<span id="LC1624" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static InversionResult safeDeterminant(DMatrixRMaj source, boolean invert) {</span></span>
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1625
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<pre style="margin: 0;">+<span id="LC1625" class="line" lang="diff"> final int finiteCount = countFiniteNonZeroDiagonals(source);</span>
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1626
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<pre style="margin: 0;">+<span id="LC1626" class="line" lang="diff"> </span>
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1627
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<pre style="margin: 0;">+<span id="LC1627" class="line" lang="diff"> InversionResult result;</span>
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<td class="diff-line-num new new_line" data-linenumber="1628" 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">
1628
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<pre style="margin: 0;">+<span id="LC1628" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -236,10 +236,10 @@</span></span>
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1629
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<pre style="margin: 0;">+<span id="LC1629" class="line" lang="diff"> if (finiteCount == 0) {</span>
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<pre style="margin: 0;">+<span id="LC1630" class="line" lang="diff"> result = new InversionResult(NOT_OBSERVED, 0, 0);</span>
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1631
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<pre style="margin: 0;">+<span id="LC1631" class="line" lang="diff"> } else {</span>
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1632
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<pre style="margin: 0;">+<span id="LC1632" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- LinearSolver<DenseMatrix64F> solver = LinearSolverFactory.pseudoInverse(true);</span></span>
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1633
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<pre style="margin: 0;">+<span id="LC1633" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ LinearSolver<DMatrixRMaj, DMatrixRMaj> solver = LinearSolverFactory_DDRM.pseudoInverse(true);</span></span>
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1634
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<pre style="margin: 0;">+<span id="LC1634" class="line" lang="diff"> solver.setA(source);</span>
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1635
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<pre style="margin: 0;">+<span id="LC1635" class="line" lang="diff"> </span>
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1636
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<pre style="margin: 0;">+<span id="LC1636" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SingularValueDecomposition<DenseMatrix64F> svd = solver.getDecomposition();</span></span>
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1637
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<pre style="margin: 0;">+<span id="LC1637" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SingularValueDecomposition_F64<DMatrixRMaj> svd = solver.getDecomposition();</span></span>
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1638
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<pre style="margin: 0;">+<span id="LC1638" class="line" lang="diff"> double[] values = svd.getSingularValues();</span>
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1639
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<pre style="margin: 0;">+<span id="LC1639" class="line" lang="diff"> </span>
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1640
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<pre style="margin: 0;">+<span id="LC1640" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1641" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -267,7 +267,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC1642" class="line" lang="diff"> return result;</span>
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1643
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<pre style="margin: 0;">+<span id="LC1643" class="line" lang="diff"> }</span>
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1644
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<pre style="margin: 0;">+<span id="LC1644" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1645" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static InversionResult safeSolve(DenseMatrix64F A,</span></span>
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1646
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<pre style="margin: 0;">+<span id="LC1646" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static InversionResult safeSolve(DMatrixRMaj A,</span></span>
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1647
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<pre style="margin: 0;">+<span id="LC1647" class="line" lang="diff"> WrappedVector b,</span>
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1648
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<pre style="margin: 0;">+<span id="LC1648" class="line" lang="diff"> WrappedVector x,</span>
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1649
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<pre style="margin: 0;">+<span id="LC1649" class="line" lang="diff"> boolean getDeterminat) {</span>
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1650
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<pre style="margin: 0;">+<span id="LC1650" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -275,8 +275,8 @@</span></span>
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1651
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<pre style="margin: 0;">+<span id="LC1651" class="line" lang="diff"> </span>
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1652
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<pre style="margin: 0;">+<span id="LC1652" class="line" lang="diff"> assert(A.getNumRows() == dim && A.getNumCols() == dim);</span>
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1653
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<pre style="margin: 0;">+<span id="LC1653" class="line" lang="diff"> </span>
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1654
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<pre style="margin: 0;">+<span id="LC1654" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F B = wrap(b.getBuffer(), b.getOffset(), dim, 1);</span></span>
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1655
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<pre style="margin: 0;">+<span id="LC1655" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F X = new DenseMatrix64F(dim, 1);</span></span>
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1656
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<pre style="margin: 0;">+<span id="LC1656" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj B = wrap(b.getBuffer(), b.getOffset(), dim, 1);</span></span>
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1657
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<pre style="margin: 0;">+<span id="LC1657" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj X = new DMatrixRMaj(dim, 1);</span></span>
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1658
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<pre style="margin: 0;">+<span id="LC1658" class="line" lang="diff"> </span>
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1659
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<pre style="margin: 0;">+<span id="LC1659" class="line" lang="diff"> InversionResult ir = safeSolve(A, B, X, getDeterminat);</span>
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1660
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<pre style="margin: 0;">+<span id="LC1660" class="line" lang="diff"> </span>
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1661
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<pre style="margin: 0;">+<span id="LC1661" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -288,7 +288,7 @@</span></span>
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1662
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<pre style="margin: 0;">+<span id="LC1662" class="line" lang="diff"> return ir;</span>
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1663
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<pre style="margin: 0;">+<span id="LC1663" class="line" lang="diff"> }</span>
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1664
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<pre style="margin: 0;">+<span id="LC1664" class="line" lang="diff"> </span>
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1665
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<pre style="margin: 0;">+<span id="LC1665" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static InversionResult safeSolve(DenseMatrix64F A, DenseMatrix64F B, DenseMatrix64F X, boolean getDeterminant) {</span></span>
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1666
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<pre style="margin: 0;">+<span id="LC1666" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static InversionResult safeSolve(DMatrixRMaj A, DMatrixRMaj B, DMatrixRMaj X, boolean getDeterminant) {</span></span>
</pre>
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1667
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<pre style="margin: 0;">+<span id="LC1667" class="line" lang="diff"> </span>
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1668
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<pre style="margin: 0;">+<span id="LC1668" class="line" lang="diff"> final int finiteCount = countFiniteNonZeroDiagonals(A);</span>
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1669
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<pre style="margin: 0;">+<span id="LC1669" class="line" lang="diff"> </span>
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1670
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<pre style="margin: 0;">+<span id="LC1670" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -298,7 +298,7 @@</span></span>
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1671
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<pre style="margin: 0;">+<span id="LC1671" class="line" lang="diff"> result = new InversionResult(NOT_OBSERVED, 0, 0);</span>
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<pre style="margin: 0;">+<span id="LC1672" class="line" lang="diff"> } else {</span>
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1673
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<pre style="margin: 0;">+<span id="LC1673" class="line" lang="diff"> </span>
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1674
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<pre style="margin: 0;">+<span id="LC1674" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- LinearSolver<DenseMatrix64F> solver = LinearSolverFactory.pseudoInverse(true);</span></span>
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1675
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<pre style="margin: 0;">+<span id="LC1675" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ LinearSolver<DMatrixRMaj, DMatrixRMaj> solver = LinearSolverFactory_DDRM.pseudoInverse(true);</span></span>
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1676
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<pre style="margin: 0;">+<span id="LC1676" class="line" lang="diff"> solver.setA(A);</span>
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1677
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<pre style="margin: 0;">+<span id="LC1677" class="line" lang="diff"> solver.solve(B, X);</span>
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1678
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<pre style="margin: 0;">+<span id="LC1678" class="line" lang="diff"> </span>
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1679
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<pre style="margin: 0;">+<span id="LC1679" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -306,7 +306,7 @@</span></span>
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1680
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<pre style="margin: 0;">+<span id="LC1680" class="line" lang="diff"> double det = 1;</span>
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1681
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<pre style="margin: 0;">+<span id="LC1681" class="line" lang="diff"> </span>
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1682
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<pre style="margin: 0;">+<span id="LC1682" class="line" lang="diff"> if (getDeterminant) {</span>
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1683
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<pre style="margin: 0;">+<span id="LC1683" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SingularValueDecomposition<DenseMatrix64F> svd = solver.getDecomposition();</span></span>
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1684
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<pre style="margin: 0;">+<span id="LC1684" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SingularValueDecomposition_F64<DMatrixRMaj> svd = solver.getDecomposition();</span></span>
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<pre style="margin: 0;">+<span id="LC1685" class="line" lang="diff"> double[] values = svd.getSingularValues();</span>
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1686
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<pre style="margin: 0;">+<span id="LC1686" class="line" lang="diff"> </span>
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1687
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<pre style="margin: 0;">+<span id="LC1687" class="line" lang="diff"> for (int i = 0; i < values.length; ++i) {</span>
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<pre style="margin: 0;">+<span id="LC1688" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -325,7 +325,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC1689" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC1690" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1691" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1692" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public static InversionResult safeInvert(DenseMatrix64F source, DenseMatrix64F destination, boolean getDeterminant) {</span></span>
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<pre style="margin: 0;">+<span id="LC1693" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static InversionResult safeInvert(DMatrixRMaj source, DMatrixRMaj destination, boolean getDeterminant) {</span></span>
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<pre style="margin: 0;">+<span id="LC1694" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1695" class="line" lang="diff"> final int dim = source.getNumCols();</span>
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<pre style="margin: 0;">+<span id="LC1696" class="line" lang="diff"> final int finiteCount = countFiniteNonZeroDiagonals(source);</span>
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<td class="diff-line-num new new_line" data-linenumber="1697" 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">
1697
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<pre style="margin: 0;">+<span id="LC1697" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -335,7 +335,7 @@</span></span>
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1698
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<pre style="margin: 0;">+<span id="LC1698" class="line" lang="diff"> if (getDeterminant) {</span>
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<td class="diff-line-num new new_line" data-linenumber="1699" 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">
1699
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<pre style="margin: 0;">+<span id="LC1699" class="line" lang="diff"> det = invertAndGetDeterminant(source, destination);</span>
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1700
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<pre style="margin: 0;">+<span id="LC1700" class="line" lang="diff"> } else {</span>
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<td class="diff-line-num new new_line" data-linenumber="1701" 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">
1701
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<pre style="margin: 0;">+<span id="LC1701" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.invert(source, destination);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1702" 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">
1702
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<pre style="margin: 0;">+<span id="LC1702" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.invert(source, destination);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1703" 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">
1703
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<pre style="margin: 0;">+<span id="LC1703" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="1704" 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">
1704
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<pre style="margin: 0;">+<span id="LC1704" class="line" lang="diff"> return new InversionResult(FULLY_OBSERVED, dim, det);</span>
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<td class="diff-line-num new new_line" data-linenumber="1705" 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">
1705
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<pre style="margin: 0;">+<span id="LC1705" class="line" lang="diff"> } else {</span>
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<td class="diff-line-num new new_line" data-linenumber="1706" 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">
1706
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<pre style="margin: 0;">+<span id="LC1706" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -346,14 +346,14 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1707" 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">
1707
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<pre style="margin: 0;">+<span id="LC1707" class="line" lang="diff"> final int[] finiteIndices = new int[finiteCount];</span>
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<td class="diff-line-num new new_line" data-linenumber="1708" 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">
1708
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<pre style="margin: 0;">+<span id="LC1708" class="line" lang="diff"> getFiniteNonZeroDiagonalIndices(source, finiteIndices);</span>
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<td class="diff-line-num new new_line" data-linenumber="1709" 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">
1709
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<pre style="margin: 0;">+<span id="LC1709" class="line" lang="diff"> </span>
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1710
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<pre style="margin: 0;">+<span id="LC1710" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F subSource = new DenseMatrix64F(finiteCount, finiteCount);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1711" 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">
1711
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<pre style="margin: 0;">+<span id="LC1711" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj subSource = new DMatrixRMaj(finiteCount, finiteCount);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1712" 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">
1712
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<pre style="margin: 0;">+<span id="LC1712" class="line" lang="diff"> gatherRowsAndColumns(source, subSource, finiteIndices, finiteIndices);</span>
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1713
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<pre style="margin: 0;">+<span id="LC1713" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1714" 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">
1714
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<pre style="margin: 0;">+<span id="LC1714" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F inverseSubSource = new DenseMatrix64F(finiteCount, finiteCount);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1715" 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">
1715
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<pre style="margin: 0;">+<span id="LC1715" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj inverseSubSource = new DMatrixRMaj(finiteCount, finiteCount);</span></span>
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1716
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<pre style="margin: 0;">+<span id="LC1716" class="line" lang="diff"> if (getDeterminant) {</span>
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1717
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<pre style="margin: 0;">+<span id="LC1717" class="line" lang="diff"> det = invertAndGetDeterminant(subSource, inverseSubSource);</span>
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<td class="diff-line-num new new_line" data-linenumber="1718" 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">
1718
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<pre style="margin: 0;">+<span id="LC1718" class="line" lang="diff"> } else {</span>
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<td class="diff-line-num new new_line" data-linenumber="1719" 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">
1719
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<pre style="margin: 0;">+<span id="LC1719" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CommonOps.invert(subSource, inverseSubSource);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1720" 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">
1720
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<pre style="margin: 0;">+<span id="LC1720" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommonOps_DDRM.invert(subSource, inverseSubSource);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1721" 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">
1721
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<pre style="margin: 0;">+<span id="LC1721" class="line" lang="diff"> }</span>
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1722
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<pre style="margin: 0;">+<span id="LC1722" class="line" lang="diff"> </span>
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1723
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<pre style="margin: 0;">+<span id="LC1723" class="line" lang="diff"> scatterRowsAndColumns(inverseSubSource, destination, finiteIndices, finiteIndices, true);</span>
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1724
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<pre style="margin: 0;">+<span id="LC1724" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -364,11 +364,11 @@</span></span>
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1725
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<pre style="margin: 0;">+<span id="LC1725" class="line" lang="diff"> }</span>
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1726
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<pre style="margin: 0;">+<span id="LC1726" class="line" lang="diff"> </span>
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1727
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<pre style="margin: 0;">+<span id="LC1727" class="line" lang="diff"> public static void weightedAverage(final WrappedVector mi,</span>
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1728
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<pre style="margin: 0;">+<span id="LC1728" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pi,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1729" 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">
1729
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<pre style="margin: 0;">+<span id="LC1729" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pi,</span></span>
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1730
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<pre style="margin: 0;">+<span id="LC1730" class="line" lang="diff"> final WrappedVector mj,</span>
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1731
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<pre style="margin: 0;">+<span id="LC1731" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pj,</span></span>
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1732
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<pre style="margin: 0;">+<span id="LC1732" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pj,</span></span>
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1733
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<pre style="margin: 0;">+<span id="LC1733" class="line" lang="diff"> final WrappedVector mk,</span>
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1734
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<pre style="margin: 0;">+<span id="LC1734" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vk,</span></span>
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1735
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<pre style="margin: 0;">+<span id="LC1735" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vk,</span></span>
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1736
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<pre style="margin: 0;">+<span id="LC1736" class="line" lang="diff"> final int dimTrait) {</span>
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1737
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<pre style="margin: 0;">+<span id="LC1737" class="line" lang="diff"> final double[] tmp = new double[dimTrait];</span>
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1738
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<pre style="margin: 0;">+<span id="LC1738" class="line" lang="diff"> for (int g = 0; g < dimTrait; ++g) {</span>
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1739
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<pre style="margin: 0;">+<span id="LC1739" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -390,13 +390,13 @@</span></span>
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1740
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<pre style="margin: 0;">+<span id="LC1740" class="line" lang="diff"> </span>
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1741
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<pre style="margin: 0;">+<span id="LC1741" class="line" lang="diff"> public static void weightedAverage(final double[] ipartial,</span>
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1742
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<pre style="margin: 0;">+<span id="LC1742" class="line" lang="diff"> final int ibo,</span>
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1743
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<pre style="margin: 0;">+<span id="LC1743" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pi,</span></span>
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1744
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<pre style="margin: 0;">+<span id="LC1744" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pi,</span></span>
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1745
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<pre style="margin: 0;">+<span id="LC1745" class="line" lang="diff"> final double[] jpartial,</span>
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1746
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<pre style="margin: 0;">+<span id="LC1746" class="line" lang="diff"> final int jbo,</span>
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<td class="diff-line-num new new_line" data-linenumber="1747" 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">
1747
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<pre style="margin: 0;">+<span id="LC1747" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Pj,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1748" 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">
1748
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<pre style="margin: 0;">+<span id="LC1748" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Pj,</span></span>
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1749
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<pre style="margin: 0;">+<span id="LC1749" class="line" lang="diff"> final double[] kpartial,</span>
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1750
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<pre style="margin: 0;">+<span id="LC1750" class="line" lang="diff"> final int kbo,</span>
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1751
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<pre style="margin: 0;">+<span id="LC1751" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final DenseMatrix64F Vk,</span></span>
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1752
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<pre style="margin: 0;">+<span id="LC1752" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final DMatrixRMaj Vk,</span></span>
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1753
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<pre style="margin: 0;">+<span id="LC1753" class="line" lang="diff"> final int dimTrait) {</span>
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1754
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<pre style="margin: 0;">+<span id="LC1754" class="line" lang="diff"> final double[] tmp = new double[dimTrait];</span>
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1755
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<pre style="margin: 0;">+<span id="LC1755" class="line" lang="diff"> for (int g = 0; g < dimTrait; ++g) {</span></pre>
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