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(v1.5.0.9006) major documentation update
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@ -81,7 +81,7 @@
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9005</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9006</span>
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@ -236,13 +236,13 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1509005" class="section level1">
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<h1 class="page-header" data-toc-text="1.5.0.9005">
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<a href="#amr-1509005" class="anchor"></a>AMR 1.5.0.9005<small> Unreleased </small>
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<div id="amr-1509006" class="section level1">
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<h1 class="page-header" data-toc-text="1.5.0.9006">
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<a href="#amr-1509006" class="anchor"></a>AMR 1.5.0.9006<small> Unreleased </small>
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</h1>
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<div id="last-updated-17-january-2021" class="section level2">
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<div id="last-updated-18-january-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-17-january-2021" class="anchor"></a><small>Last updated: 17 January 2021</small>
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<a href="#last-updated-18-january-2021" class="anchor"></a><small>Last updated: 18 January 2021</small>
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</h2>
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<div id="new" class="section level3">
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<h3 class="hasAnchor">
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@ -288,6 +288,13 @@
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<li>Fix for verbose output of <code><a href="../reference/mdro.html">mdro(..., verbose = TRUE)</a></code> for German guideline (3MGRN and 4MGRN) and <em>P. aeruginosa</em> in Dutch guideline (BRMO)</li>
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</ul>
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</div>
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<div id="other" class="section level3">
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<h3 class="hasAnchor">
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<a href="#other" class="anchor"></a>Other</h3>
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<ul>
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<li>Big documentation updates</li>
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</ul>
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</div>
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</div>
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</div>
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<div id="amr-150" class="section level1">
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@ -389,9 +396,9 @@
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<li><p>If <code><a href="../reference/as.mo.html">as.mo()</a></code> takes more than 30 seconds, some suggestions will be done to improve speed</p></li>
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</ul>
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</div>
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<div id="other" class="section level3">
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<div id="other-1" class="section level3">
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<h3 class="hasAnchor">
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<a href="#other" class="anchor"></a>Other</h3>
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<a href="#other-1" class="anchor"></a>Other</h3>
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<ul>
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<li>All messages and warnings thrown by this package now break sentences on whole words</li>
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<li>More extensive unit tests</li>
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@ -497,9 +504,9 @@
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<li><p>Added argument <code>excess</code> to the <code><a href="../reference/kurtosis.html">kurtosis()</a></code> function (defaults to <code>FALSE</code>), to return the <em>excess kurtosis</em>, defined as the kurtosis minus three.</p></li>
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</ul>
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</div>
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<div id="other-1" class="section level3">
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<div id="other-2" class="section level3">
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<h3 class="hasAnchor">
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<a href="#other-1" class="anchor"></a>Other</h3>
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<a href="#other-2" class="anchor"></a>Other</h3>
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<ul>
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<li>Removed functions <code>portion_R()</code>, <code>portion_S()</code> and <code>portion_I()</code> that were deprecated since version 0.9.0 (November 2019) and were replaced with <code><a href="../reference/proportion.html">proportion_R()</a></code>, <code><a href="../reference/proportion.html">proportion_S()</a></code> and <code><a href="../reference/proportion.html">proportion_I()</a></code>
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</li>
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@ -583,9 +590,9 @@
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<li><p>Fixed a bug where <code><a href="../reference/as.mic.html">as.mic()</a></code> could not handle dots without a leading zero (like <code>"<=.25</code>)</p></li>
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</ul>
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</div>
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<div id="other-2" class="section level3">
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<div id="other-3" class="section level3">
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<h3 class="hasAnchor">
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<a href="#other-2" class="anchor"></a>Other</h3>
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<a href="#other-3" class="anchor"></a>Other</h3>
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<ul>
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<li>Moved primary location of this project from GitLab to <a href="https://github.com/msberends/AMR">GitHub</a>, giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.</li>
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</ul>
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@ -645,9 +652,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<li>Added abbreviation “cfsc” for Cefoxitin and “cfav” for Ceftazidime/avibactam</li>
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</ul>
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</div>
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<div id="other-3" class="section level3">
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<div id="other-4" class="section level3">
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<h3 class="hasAnchor">
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<a href="#other-3" class="anchor"></a>Other</h3>
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<a href="#other-4" class="anchor"></a>Other</h3>
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<ul>
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<li>Removed previously deprecated function <code>p.symbol()</code> - it was replaced with <code><a href="../reference/AMR-deprecated.html">p_symbol()</a></code>
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</li>
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@ -687,9 +694,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<li>Added generic CLSI rules for R/SI interpretation using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for years 2010-2019 (thanks to Anthony Underwood)</li>
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</ul>
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</div>
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<div id="other-4" class="section level3">
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<h3 class="hasAnchor">
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<a href="#other-4" class="anchor"></a>Other</h3>
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<a href="#other-5" class="anchor"></a>Other</h3>
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<ul>
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<li>Support for the upcoming <code>dplyr</code> version 1.0.0</li>
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<li>More robust assigning for classes <code>rsi</code> and <code>mic</code>
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@ -791,9 +798,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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</li>
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</ul>
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</div>
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<h3 class="hasAnchor">
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<a href="#other-5" class="anchor"></a>Other</h3>
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<a href="#other-6" class="anchor"></a>Other</h3>
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<ul>
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<li>Add a <code>CITATION</code> file</li>
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<li>Full support for the upcoming R 4.0</li>
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</li>
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</ul>
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</div>
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<h3 class="hasAnchor">
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<a href="#other-6" class="anchor"></a>Other</h3>
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<a href="#other-7" class="anchor"></a>Other</h3>
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<ul>
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<li>Rewrote the complete documentation to markdown format, to be able to use the very latest version of the great <a href="https://roxygen2.r-lib.org/index.html">Roxygen2</a>, released in November 2019. This tremously improved the documentation quality, since the rewrite forced us to go over all texts again and make changes where needed.</li>
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<li>Change dependency on <code>clean</code> to <code>cleaner</code>, as this package was renamed accordingly upon CRAN request</li>
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</li>
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<li>Added more MIC factor levels (<code><a href="../reference/as.mic.html">as.mic()</a></code>)</li>
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</ul>
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<h4 class="hasAnchor">
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<a href="#other-7" class="anchor"></a>Other</h4>
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<a href="#other-8" class="anchor"></a>Other</h4>
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<ul>
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<li>Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors</li>
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<li>Cleaned the coding style of every single syntax line in this package with the help of the <code>lintr</code> package</li>
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</li>
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</ul>
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</div>
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<h4 class="hasAnchor">
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<a href="#other-8" class="anchor"></a>Other</h4>
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<a href="#other-9" class="anchor"></a>Other</h4>
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<ul>
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<li>Fixed a note thrown by CRAN tests</li>
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</ul>
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<li>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</li>
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</ul>
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</div>
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<a href="#other-9" class="anchor"></a>Other</h4>
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<a href="#other-10" class="anchor"></a>Other</h4>
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<ul>
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<li>Support for R 3.6.0 and later by providing support for <a href="https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html">staged install</a>
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</li>
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<li>if using different lengths of pattern and x in <code><a href="../reference/like.html">%like%</a></code>, it will now return the call</li>
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</ul>
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</div>
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<li>Updated licence text to emphasise GPL 2.0 and that this is an R package.</li>
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</ul>
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<li><p>Percentages will now will rounded more logically (e.g. in <code>freq</code> function)</p></li>
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</ul>
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</div>
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<a href="#other-11" class="anchor"></a>Other</h4>
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<li>New dependency on package <code>crayon</code>, to support formatted text in the console</li>
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<li>Dependency <code>tidyr</code> is now mandatory (went to <code>Import</code> field) since <code>portion_df</code> and <code>count_df</code> rely on it</li>
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</li>
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</ul>
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</div>
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<a href="#other-13" class="anchor"></a>Other</h4>
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<ul>
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<li>More unit tests to ensure better integrity of functions</li>
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</ul>
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<li>Other small fixes</li>
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</ul>
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</div>
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<ul>
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<li>Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
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<ul>
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<li>Functions <code>as.rsi</code> and <code>as.mic</code> now add the package name and version as attributes</li>
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</ul>
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</div>
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<li>Expanded <code>README.md</code> with more examples</li>
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<li>Added <a href="https://orcid.org">ORCID</a> of authors to DESCRIPTION file</li>
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