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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
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<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
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<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
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<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
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<h4 data-toc-skip class="date">06 October 2022</h4>
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<h4 data-toc-skip class="date">10 October 2022</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
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<div class="d-none name"><code>AMR.Rmd</code></div>
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<div class="d-none name"><code>AMR.Rmd</code></div>
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<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 06 October 2022.</p>
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<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 10 October 2022.</p>
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<div class="section level2">
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<div class="section level2">
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h2>
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</h2>
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</tr></thead>
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</tr></thead>
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<tbody>
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<tbody>
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<tr class="odd">
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<tr class="odd">
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<td align="center">2022-10-06</td>
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<td align="center">2022-10-10</td>
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<td align="center">abcd</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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</tr>
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<tr class="even">
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<tr class="even">
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<td align="center">2022-10-06</td>
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<td align="center">2022-10-10</td>
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<td align="center">abcd</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">R</td>
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</tr>
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</tr>
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<tr class="odd">
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<tr class="odd">
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<td align="center">2022-10-06</td>
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<td align="center">2022-10-10</td>
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<td align="center">efgh</td>
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<td align="center">efgh</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">R</td>
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<td align="center">R</td>
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</tr></thead>
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</tr></thead>
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<tbody>
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<tbody>
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<tr class="odd">
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<tr class="odd">
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<td align="center">2017-11-17</td>
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<td align="center">2017-08-15</td>
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<td align="center">Y8</td>
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<td align="center">V8</td>
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<td align="center">Hospital B</td>
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<td align="center">Hospital C</td>
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<td align="center">Streptococcus pneumoniae</td>
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<td align="center">Streptococcus pneumoniae</td>
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<td align="center">I</td>
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<td align="center">R</td>
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<td align="center">R</td>
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<td align="center">R</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">F</td>
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<td align="center">F</td>
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</tr>
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</tr>
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<tr class="even">
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<tr class="even">
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<td align="center">2015-02-26</td>
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<td align="center">2013-01-31</td>
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<td align="center">V8</td>
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<td align="center">L3</td>
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<td align="center">Hospital D</td>
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<td align="center">Hospital B</td>
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<td align="center">Staphylococcus aureus</td>
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<td align="center">Escherichia coli</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">M</td>
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</tr>
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<tr class="odd">
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<td align="center">2012-03-22</td>
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<td align="center">Y6</td>
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<td align="center">Hospital D</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">I</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">F</td>
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<td align="center">F</td>
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</tr>
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</tr>
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<tr class="odd">
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<tr class="even">
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<td align="center">2011-11-24</td>
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<td align="center">2012-02-11</td>
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<td align="center">I6</td>
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<td align="center">I1</td>
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<td align="center">Hospital D</td>
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<td align="center">Hospital C</td>
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<td align="center">Klebsiella pneumoniae</td>
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<td align="center">Staphylococcus aureus</td>
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<td align="center">R</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">M</td>
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<td align="center">M</td>
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</tr>
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</tr>
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<tr class="even">
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<td align="center">2013-06-23</td>
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<td align="center">O2</td>
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<td align="center">Hospital B</td>
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<td align="center">Escherichia coli</td>
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||||||
<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">F</td>
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</tr>
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<tr class="odd">
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<tr class="odd">
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<td align="center">2010-10-16</td>
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<td align="center">2012-09-29</td>
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<td align="center">X2</td>
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<td align="center">F5</td>
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||||||
<td align="center">Hospital B</td>
|
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||||||
<td align="center">Escherichia coli</td>
|
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||||||
<td align="center">I</td>
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<td align="center">I</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">F</td>
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</tr>
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<tr class="even">
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<td align="center">2012-03-22</td>
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<td align="center">U10</td>
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<td align="center">Hospital A</td>
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<td align="center">Hospital A</td>
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||||||
<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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||||||
<td align="center">R</td>
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<td align="center">S</td>
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||||||
<td align="center">I</td>
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<td align="center">S</td>
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||||||
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<td align="center">S</td>
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||||||
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<td align="center">S</td>
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||||||
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<td align="center">M</td>
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</tr>
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<tr class="even">
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<td align="center">2017-03-01</td>
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<td align="center">H10</td>
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<td align="center">Hospital B</td>
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<td align="center">Staphylococcus aureus</td>
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||||||
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<td align="center">S</td>
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||||||
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<td align="center">S</td>
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||||||
<td align="center">R</td>
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<td align="center">R</td>
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||||||
<td align="center">S</td>
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<td align="center">S</td>
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||||||
<td align="center">F</td>
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<td align="center">M</td>
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</tr>
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</tr>
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</tbody>
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</tbody>
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</table>
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</table>
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@@ -422,16 +422,16 @@ Longest: 1</p>
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<tr class="odd">
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<tr class="odd">
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<td align="left">1</td>
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<td align="left">1</td>
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<td align="left">M</td>
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<td align="left">M</td>
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<td align="right">10,375</td>
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<td align="right">10,361</td>
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<td align="right">51.88%</td>
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<td align="right">51.81%</td>
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<td align="right">10,375</td>
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<td align="right">10,361</td>
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<td align="right">51.88%</td>
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<td align="right">51.81%</td>
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</tr>
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</tr>
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<tr class="even">
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<tr class="even">
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<td align="left">2</td>
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<td align="left">2</td>
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<td align="left">F</td>
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<td align="left">F</td>
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<td align="right">9,625</td>
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<td align="right">9,639</td>
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<td align="right">48.13%</td>
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<td align="right">48.20%</td>
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<td align="right">20,000</td>
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<td align="right">20,000</td>
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<td align="right">100.00%</td>
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<td align="right">100.00%</td>
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</tr>
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</tr>
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@@ -488,9 +488,9 @@ Longest: 1</p>
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<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
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<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
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<span><span class="co"># 2</span></span>
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<span><span class="co"># 2</span></span>
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<span><span class="co"># Including isolates from ICU.</span></span>
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<span><span class="co"># Including isolates from ICU.</span></span>
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<span><span class="co"># => Found 10,694 'phenotype-based' first isolates (53.5% of total where a</span></span>
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<span><span class="co"># => Found 10,672 'phenotype-based' first isolates (53.4% of total where a</span></span>
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<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
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<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
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<p>So only 53.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
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<p>So only 53.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
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<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
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<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
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<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
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||||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
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<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
|
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@@ -499,7 +499,7 @@ Longest: 1</p>
|
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<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
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<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
|
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
|
||||||
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
|
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
|
||||||
<p>So we end up with 10,694 isolates for analysis. Now our data looks like:</p>
|
<p>So we end up with 10,672 isolates for analysis. Now our data looks like:</p>
|
||||||
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
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<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
|
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<table style="width:100%;" class="table">
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<table style="width:100%;" class="table">
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@@ -538,13 +538,13 @@ Longest: 1</p>
|
|||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">1</td>
|
<td align="left">1</td>
|
||||||
<td align="center">2017-11-17</td>
|
<td align="center">2017-08-15</td>
|
||||||
<td align="center">Y8</td>
|
<td align="center">V8</td>
|
||||||
<td align="center">Hospital B</td>
|
<td align="center">Hospital C</td>
|
||||||
<td align="center">B_STRPT_PNMN</td>
|
<td align="center">B_STRPT_PNMN</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">F</td>
|
<td align="center">F</td>
|
||||||
<td align="center">Gram-positive</td>
|
<td align="center">Gram-positive</td>
|
||||||
@@ -553,30 +553,46 @@ Longest: 1</p>
|
|||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">2</td>
|
<td align="left">3</td>
|
||||||
<td align="center">2015-02-26</td>
|
<td align="center">2012-03-22</td>
|
||||||
<td align="center">V8</td>
|
<td align="center">Y6</td>
|
||||||
<td align="center">Hospital D</td>
|
<td align="center">Hospital D</td>
|
||||||
<td align="center">B_STPHY_AURS</td>
|
<td align="center">B_ESCHR_COLI</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">F</td>
|
<td align="center">F</td>
|
||||||
|
<td align="center">Gram-negative</td>
|
||||||
|
<td align="center">Escherichia</td>
|
||||||
|
<td align="center">coli</td>
|
||||||
|
<td align="center">TRUE</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td align="left">9</td>
|
||||||
|
<td align="center">2013-06-02</td>
|
||||||
|
<td align="center">G6</td>
|
||||||
|
<td align="center">Hospital B</td>
|
||||||
|
<td align="center">B_STPHY_AURS</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">M</td>
|
||||||
<td align="center">Gram-positive</td>
|
<td align="center">Gram-positive</td>
|
||||||
<td align="center">Staphylococcus</td>
|
<td align="center">Staphylococcus</td>
|
||||||
<td align="center">aureus</td>
|
<td align="center">aureus</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="even">
|
||||||
<td align="left">3</td>
|
<td align="left">10</td>
|
||||||
<td align="center">2011-11-24</td>
|
<td align="center">2014-03-13</td>
|
||||||
<td align="center">I6</td>
|
<td align="center">C9</td>
|
||||||
<td align="center">Hospital D</td>
|
<td align="center">Hospital B</td>
|
||||||
<td align="center">B_KLBSL_PNMN</td>
|
<td align="center">B_KLBSL_PNMN</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">M</td>
|
<td align="center">M</td>
|
||||||
<td align="center">Gram-negative</td>
|
<td align="center">Gram-negative</td>
|
||||||
@@ -584,49 +600,33 @@ Longest: 1</p>
|
|||||||
<td align="center">pneumoniae</td>
|
<td align="center">pneumoniae</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
|
||||||
<td align="left">7</td>
|
|
||||||
<td align="center">2017-08-17</td>
|
|
||||||
<td align="center">U7</td>
|
|
||||||
<td align="center">Hospital B</td>
|
|
||||||
<td align="center">B_KLBSL_PNMN</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">I</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">F</td>
|
|
||||||
<td align="center">Gram-negative</td>
|
|
||||||
<td align="center">Klebsiella</td>
|
|
||||||
<td align="center">pneumoniae</td>
|
|
||||||
<td align="center">TRUE</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">8</td>
|
<td align="left">11</td>
|
||||||
<td align="center">2013-09-19</td>
|
<td align="center">2016-12-02</td>
|
||||||
<td align="center">X2</td>
|
<td align="center">S9</td>
|
||||||
<td align="center">Hospital B</td>
|
<td align="center">Hospital B</td>
|
||||||
<td align="center">B_KLBSL_PNMN</td>
|
<td align="center">B_ESCHR_COLI</td>
|
||||||
|
<td align="center">R</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">F</td>
|
<td align="center">F</td>
|
||||||
<td align="center">Gram-negative</td>
|
<td align="center">Gram-negative</td>
|
||||||
<td align="center">Klebsiella</td>
|
<td align="center">Escherichia</td>
|
||||||
<td align="center">pneumoniae</td>
|
<td align="center">coli</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">9</td>
|
<td align="left">13</td>
|
||||||
<td align="center">2012-04-26</td>
|
<td align="center">2017-06-05</td>
|
||||||
<td align="center">L7</td>
|
<td align="center">U8</td>
|
||||||
<td align="center">Hospital C</td>
|
<td align="center">Hospital A</td>
|
||||||
<td align="center">B_ESCHR_COLI</td>
|
<td align="center">B_ESCHR_COLI</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">M</td>
|
<td align="center">S</td>
|
||||||
|
<td align="center">F</td>
|
||||||
<td align="center">Gram-negative</td>
|
<td align="center">Gram-negative</td>
|
||||||
<td align="center">Escherichia</td>
|
<td align="center">Escherichia</td>
|
||||||
<td align="center">coli</td>
|
<td align="center">coli</td>
|
||||||
@@ -653,8 +653,8 @@ Longest: 1</p>
|
|||||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
|
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
|
||||||
<p><strong>Frequency table</strong></p>
|
<p><strong>Frequency table</strong></p>
|
||||||
<p>Class: character<br>
|
<p>Class: character<br>
|
||||||
Length: 10,694<br>
|
Length: 10,672<br>
|
||||||
Available: 10,694 (100.0%, NA: 0 = 0.0%)<br>
|
Available: 10,672 (100.0%, NA: 0 = 0.0%)<br>
|
||||||
Unique: 4</p>
|
Unique: 4</p>
|
||||||
<p>Shortest: 16<br>
|
<p>Shortest: 16<br>
|
||||||
Longest: 24</p>
|
Longest: 24</p>
|
||||||
@@ -671,33 +671,33 @@ Longest: 24</p>
|
|||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">1</td>
|
<td align="left">1</td>
|
||||||
<td align="left">Escherichia coli</td>
|
<td align="left">Escherichia coli</td>
|
||||||
<td align="right">4,609</td>
|
<td align="right">4,684</td>
|
||||||
<td align="right">43.10%</td>
|
<td align="right">43.89%</td>
|
||||||
<td align="right">4,609</td>
|
<td align="right">4,684</td>
|
||||||
<td align="right">43.10%</td>
|
<td align="right">43.89%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">2</td>
|
<td align="left">2</td>
|
||||||
<td align="left">Staphylococcus aureus</td>
|
<td align="left">Staphylococcus aureus</td>
|
||||||
<td align="right">2,749</td>
|
<td align="right">2,763</td>
|
||||||
<td align="right">25.71%</td>
|
<td align="right">25.89%</td>
|
||||||
<td align="right">7,358</td>
|
<td align="right">7,447</td>
|
||||||
<td align="right">68.80%</td>
|
<td align="right">69.78%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">3</td>
|
<td align="left">3</td>
|
||||||
<td align="left">Streptococcus pneumoniae</td>
|
<td align="left">Streptococcus pneumoniae</td>
|
||||||
<td align="right">2,179</td>
|
<td align="right">2,092</td>
|
||||||
<td align="right">20.38%</td>
|
<td align="right">19.60%</td>
|
||||||
<td align="right">9,537</td>
|
<td align="right">9,539</td>
|
||||||
<td align="right">89.18%</td>
|
<td align="right">89.38%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">4</td>
|
<td align="left">4</td>
|
||||||
<td align="left">Klebsiella pneumoniae</td>
|
<td align="left">Klebsiella pneumoniae</td>
|
||||||
<td align="right">1,157</td>
|
<td align="right">1,133</td>
|
||||||
<td align="right">10.82%</td>
|
<td align="right">10.62%</td>
|
||||||
<td align="right">10,694</td>
|
<td align="right">10,672</td>
|
||||||
<td align="right">100.00%</td>
|
<td align="right">100.00%</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
@@ -744,12 +744,42 @@ Longest: 24</p>
|
|||||||
</tr></thead>
|
</tr></thead>
|
||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">2017-11-17</td>
|
<td align="center">2017-08-15</td>
|
||||||
<td align="center">Y8</td>
|
<td align="center">V8</td>
|
||||||
<td align="center">Hospital B</td>
|
<td align="center">Hospital C</td>
|
||||||
<td align="center">B_STRPT_PNMN</td>
|
<td align="center">B_STRPT_PNMN</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">F</td>
|
||||||
|
<td align="center">Gram-positive</td>
|
||||||
|
<td align="center">Streptococcus</td>
|
||||||
|
<td align="center">pneumoniae</td>
|
||||||
|
<td align="center">TRUE</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td align="center">2010-05-16</td>
|
||||||
|
<td align="center">G10</td>
|
||||||
|
<td align="center">Hospital D</td>
|
||||||
|
<td align="center">B_STRPT_PNMN</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">M</td>
|
||||||
|
<td align="center">Gram-positive</td>
|
||||||
|
<td align="center">Streptococcus</td>
|
||||||
|
<td align="center">pneumoniae</td>
|
||||||
|
<td align="center">TRUE</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td align="center">2017-11-18</td>
|
||||||
|
<td align="center">Z3</td>
|
||||||
|
<td align="center">Hospital C</td>
|
||||||
|
<td align="center">B_STRPT_PNMN</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">F</td>
|
<td align="center">F</td>
|
||||||
@@ -759,80 +789,50 @@ Longest: 24</p>
|
|||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">2017-08-17</td>
|
<td align="center">2010-06-25</td>
|
||||||
<td align="center">U7</td>
|
<td align="center">W9</td>
|
||||||
|
<td align="center">Hospital D</td>
|
||||||
|
<td align="center">B_STRPT_PNMN</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">F</td>
|
||||||
|
<td align="center">Gram-positive</td>
|
||||||
|
<td align="center">Streptococcus</td>
|
||||||
|
<td align="center">pneumoniae</td>
|
||||||
|
<td align="center">TRUE</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td align="center">2014-12-03</td>
|
||||||
|
<td align="center">A1</td>
|
||||||
<td align="center">Hospital B</td>
|
<td align="center">Hospital B</td>
|
||||||
|
<td align="center">B_ESCHR_COLI</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">M</td>
|
||||||
|
<td align="center">Gram-negative</td>
|
||||||
|
<td align="center">Escherichia</td>
|
||||||
|
<td align="center">coli</td>
|
||||||
|
<td align="center">TRUE</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td align="center">2014-11-26</td>
|
||||||
|
<td align="center">A3</td>
|
||||||
|
<td align="center">Hospital A</td>
|
||||||
<td align="center">B_KLBSL_PNMN</td>
|
<td align="center">B_KLBSL_PNMN</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">I</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">F</td>
|
<td align="center">M</td>
|
||||||
<td align="center">Gram-negative</td>
|
<td align="center">Gram-negative</td>
|
||||||
<td align="center">Klebsiella</td>
|
<td align="center">Klebsiella</td>
|
||||||
<td align="center">pneumoniae</td>
|
<td align="center">pneumoniae</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
|
||||||
<td align="center">2016-01-02</td>
|
|
||||||
<td align="center">E9</td>
|
|
||||||
<td align="center">Hospital C</td>
|
|
||||||
<td align="center">B_STRPT_PNMN</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">M</td>
|
|
||||||
<td align="center">Gram-positive</td>
|
|
||||||
<td align="center">Streptococcus</td>
|
|
||||||
<td align="center">pneumoniae</td>
|
|
||||||
<td align="center">TRUE</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="even">
|
|
||||||
<td align="center">2015-02-13</td>
|
|
||||||
<td align="center">D10</td>
|
|
||||||
<td align="center">Hospital A</td>
|
|
||||||
<td align="center">B_STRPT_PNMN</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">M</td>
|
|
||||||
<td align="center">Gram-positive</td>
|
|
||||||
<td align="center">Streptococcus</td>
|
|
||||||
<td align="center">pneumoniae</td>
|
|
||||||
<td align="center">TRUE</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="odd">
|
|
||||||
<td align="center">2016-05-02</td>
|
|
||||||
<td align="center">E2</td>
|
|
||||||
<td align="center">Hospital C</td>
|
|
||||||
<td align="center">B_STRPT_PNMN</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">M</td>
|
|
||||||
<td align="center">Gram-positive</td>
|
|
||||||
<td align="center">Streptococcus</td>
|
|
||||||
<td align="center">pneumoniae</td>
|
|
||||||
<td align="center">TRUE</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="even">
|
|
||||||
<td align="center">2014-04-15</td>
|
|
||||||
<td align="center">W8</td>
|
|
||||||
<td align="center">Hospital B</td>
|
|
||||||
<td align="center">B_STRPT_PNMN</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">F</td>
|
|
||||||
<td align="center">Gram-positive</td>
|
|
||||||
<td align="center">Streptococcus</td>
|
|
||||||
<td align="center">pneumoniae</td>
|
|
||||||
<td align="center">TRUE</td>
|
|
||||||
</tr>
|
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
<p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
|
<p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
|
||||||
@@ -854,50 +854,50 @@ Longest: 24</p>
|
|||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">E. coli</td>
|
<td align="center">E. coli</td>
|
||||||
<td align="center">AMX</td>
|
<td align="center">AMX</td>
|
||||||
<td align="center">2165</td>
|
<td align="center">2201</td>
|
||||||
<td align="center">105</td>
|
<td align="center">138</td>
|
||||||
<td align="center">2339</td>
|
<td align="center">2345</td>
|
||||||
<td align="center">4609</td>
|
<td align="center">4684</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">E. coli</td>
|
<td align="center">E. coli</td>
|
||||||
<td align="center">AMC</td>
|
<td align="center">AMC</td>
|
||||||
<td align="center">3396</td>
|
<td align="center">3471</td>
|
||||||
<td align="center">157</td>
|
<td align="center">156</td>
|
||||||
<td align="center">1056</td>
|
<td align="center">1057</td>
|
||||||
<td align="center">4609</td>
|
<td align="center">4684</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">E. coli</td>
|
<td align="center">E. coli</td>
|
||||||
<td align="center">CIP</td>
|
<td align="center">CIP</td>
|
||||||
<td align="center">3357</td>
|
<td align="center">3422</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">1252</td>
|
<td align="center">1262</td>
|
||||||
<td align="center">4609</td>
|
<td align="center">4684</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">E. coli</td>
|
<td align="center">E. coli</td>
|
||||||
<td align="center">GEN</td>
|
<td align="center">GEN</td>
|
||||||
<td align="center">4052</td>
|
<td align="center">4073</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">557</td>
|
<td align="center">611</td>
|
||||||
<td align="center">4609</td>
|
<td align="center">4684</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">K. pneumoniae</td>
|
<td align="center">K. pneumoniae</td>
|
||||||
<td align="center">AMX</td>
|
<td align="center">AMX</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">1157</td>
|
<td align="center">1133</td>
|
||||||
<td align="center">1157</td>
|
<td align="center">1133</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">K. pneumoniae</td>
|
<td align="center">K. pneumoniae</td>
|
||||||
<td align="center">AMC</td>
|
<td align="center">AMC</td>
|
||||||
<td align="center">899</td>
|
<td align="center">898</td>
|
||||||
<td align="center">49</td>
|
<td align="center">43</td>
|
||||||
<td align="center">209</td>
|
<td align="center">192</td>
|
||||||
<td align="center">1157</td>
|
<td align="center">1133</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
@@ -920,34 +920,34 @@ Longest: 24</p>
|
|||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">E. coli</td>
|
<td align="center">E. coli</td>
|
||||||
<td align="center">GEN</td>
|
<td align="center">GEN</td>
|
||||||
<td align="center">4052</td>
|
<td align="center">4073</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">557</td>
|
<td align="center">611</td>
|
||||||
<td align="center">4609</td>
|
<td align="center">4684</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">K. pneumoniae</td>
|
<td align="center">K. pneumoniae</td>
|
||||||
<td align="center">GEN</td>
|
<td align="center">GEN</td>
|
||||||
<td align="center">1054</td>
|
<td align="center">1009</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">103</td>
|
<td align="center">124</td>
|
||||||
<td align="center">1157</td>
|
<td align="center">1133</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">S. aureus</td>
|
<td align="center">S. aureus</td>
|
||||||
<td align="center">GEN</td>
|
<td align="center">GEN</td>
|
||||||
<td align="center">2418</td>
|
<td align="center">2462</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">331</td>
|
<td align="center">301</td>
|
||||||
<td align="center">2749</td>
|
<td align="center">2763</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">S. pneumoniae</td>
|
<td align="center">S. pneumoniae</td>
|
||||||
<td align="center">GEN</td>
|
<td align="center">GEN</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">0</td>
|
<td align="center">0</td>
|
||||||
<td align="center">2179</td>
|
<td align="center">2092</td>
|
||||||
<td align="center">2179</td>
|
<td align="center">2092</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
@@ -961,7 +961,7 @@ Longest: 24</p>
|
|||||||
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
|
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
|
||||||
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
|
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
|
||||||
<span><span class="co"># [1] 0.5487189</span></span></code></pre></div>
|
<span><span class="co"># [1] 0.5403861</span></span></code></pre></div>
|
||||||
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||||
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||||
@@ -975,19 +975,19 @@ Longest: 24</p>
|
|||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Hospital A</td>
|
<td align="center">Hospital A</td>
|
||||||
<td align="center">0.5417823</td>
|
<td align="center">0.5367144</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Hospital B</td>
|
<td align="center">Hospital B</td>
|
||||||
<td align="center">0.5486465</td>
|
<td align="center">0.5420436</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Hospital C</td>
|
<td align="center">Hospital C</td>
|
||||||
<td align="center">0.5634971</td>
|
<td align="center">0.5339252</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Hospital D</td>
|
<td align="center">Hospital D</td>
|
||||||
<td align="center">0.5485369</td>
|
<td align="center">0.5478097</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
@@ -1008,23 +1008,23 @@ Longest: 24</p>
|
|||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Hospital A</td>
|
<td align="center">Hospital A</td>
|
||||||
<td align="center">0.5417823</td>
|
<td align="center">0.5367144</td>
|
||||||
<td align="center">3243</td>
|
<td align="center">3214</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Hospital B</td>
|
<td align="center">Hospital B</td>
|
||||||
<td align="center">0.5486465</td>
|
<td align="center">0.5420436</td>
|
||||||
<td align="center">3731</td>
|
<td align="center">3758</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Hospital C</td>
|
<td align="center">Hospital C</td>
|
||||||
<td align="center">0.5634971</td>
|
<td align="center">0.5339252</td>
|
||||||
<td align="center">1567</td>
|
<td align="center">1577</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Hospital D</td>
|
<td align="center">Hospital D</td>
|
||||||
<td align="center">0.5485369</td>
|
<td align="center">0.5478097</td>
|
||||||
<td align="center">2153</td>
|
<td align="center">2123</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
@@ -1047,27 +1047,27 @@ Longest: 24</p>
|
|||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Escherichia</td>
|
<td align="center">Escherichia</td>
|
||||||
<td align="center">0.7708831</td>
|
<td align="center">0.7743382</td>
|
||||||
<td align="center">0.8791495</td>
|
<td align="center">0.8695559</td>
|
||||||
<td align="center">0.9791712</td>
|
<td align="center">0.9739539</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Klebsiella</td>
|
<td align="center">Klebsiella</td>
|
||||||
<td align="center">0.8193604</td>
|
<td align="center">0.8305384</td>
|
||||||
<td align="center">0.9109767</td>
|
<td align="center">0.8905560</td>
|
||||||
<td align="center">0.9783924</td>
|
<td align="center">0.9841130</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Staphylococcus</td>
|
<td align="center">Staphylococcus</td>
|
||||||
<td align="center">0.7871953</td>
|
<td align="center">0.7853782</td>
|
||||||
<td align="center">0.8795926</td>
|
<td align="center">0.8910604</td>
|
||||||
<td align="center">0.9770826</td>
|
<td align="center">0.9768368</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Streptococcus</td>
|
<td align="center">Streptococcus</td>
|
||||||
<td align="center">0.5268472</td>
|
<td align="center">0.5363289</td>
|
||||||
<td align="center">0.0000000</td>
|
<td align="center">0.0000000</td>
|
||||||
<td align="center">0.5268472</td>
|
<td align="center">0.5363289</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
@@ -1092,22 +1092,22 @@ Longest: 24</p>
|
|||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">Hospital A</td>
|
<td align="left">Hospital A</td>
|
||||||
<td align="right">54.2%</td>
|
<td align="right">53.7%</td>
|
||||||
<td align="right">26.2%</td>
|
<td align="right">26.5%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">Hospital B</td>
|
<td align="left">Hospital B</td>
|
||||||
<td align="right">54.9%</td>
|
<td align="right">54.2%</td>
|
||||||
<td align="right">27.0%</td>
|
<td align="right">26.3%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">Hospital C</td>
|
<td align="left">Hospital C</td>
|
||||||
<td align="right">56.3%</td>
|
<td align="right">53.4%</td>
|
||||||
<td align="right">28.1%</td>
|
<td align="right">25.1%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">Hospital D</td>
|
<td align="left">Hospital D</td>
|
||||||
<td align="right">54.9%</td>
|
<td align="right">54.8%</td>
|
||||||
<td align="right">27.1%</td>
|
<td align="right">27.1%</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
@@ -1206,16 +1206,16 @@ Longest: 24</p>
|
|||||||
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
|
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
|
||||||
<span><span class="va">mic_values</span></span>
|
<span><span class="va">mic_values</span></span>
|
||||||
<span><span class="co"># Class <mic></span></span>
|
<span><span class="co"># Class <mic></span></span>
|
||||||
<span><span class="co"># [1] 2 0.0625 0.25 128 64 256 0.01 0.01 0.0625 0.5 </span></span>
|
<span><span class="co"># [1] 0.125 64 256 0.005 0.001 0.025 2 256 16 256 </span></span>
|
||||||
<span><span class="co"># [11] 0.002 0.001 0.125 0.025 128 0.002 0.01 256 1 1 </span></span>
|
<span><span class="co"># [11] 0.002 0.25 0.002 4 64 256 16 0.01 0.025 0.025 </span></span>
|
||||||
<span><span class="co"># [21] 0.025 32 0.125 1 0.0625 1 2 1 0.25 32 </span></span>
|
<span><span class="co"># [21] 8 8 4 0.005 32 1 0.0625 0.125 0.125 0.025 </span></span>
|
||||||
<span><span class="co"># [31] 0.0625 0.5 0.002 0.25 0.001 0.002 0.025 0.01 32 0.5 </span></span>
|
<span><span class="co"># [31] 4 0.025 0.005 16 0.001 256 8 0.002 0.0625 0.0625</span></span>
|
||||||
<span><span class="co"># [41] 128 16 16 0.0625 4 256 256 16 64 0.125 </span></span>
|
<span><span class="co"># [41] 256 0.25 4 0.005 0.5 16 64 0.002 0.125 4 </span></span>
|
||||||
<span><span class="co"># [51] 0.01 0.01 8 0.01 2 256 64 1 0.5 32 </span></span>
|
<span><span class="co"># [51] 128 32 8 0.125 0.005 128 0.01 0.5 128 0.025 </span></span>
|
||||||
<span><span class="co"># [61] 0.025 2 16 0.005 0.025 16 2 64 8 4 </span></span>
|
<span><span class="co"># [61] 0.125 0.002 64 0.005 0.001 0.01 64 0.01 0.01 16 </span></span>
|
||||||
<span><span class="co"># [71] 16 0.5 0.01 16 8 0.0625 0.01 128 128 0.005 </span></span>
|
<span><span class="co"># [71] 32 64 16 1 64 0.002 8 0.0625 0.125 0.01 </span></span>
|
||||||
<span><span class="co"># [81] 64 0.25 0.25 0.001 0.001 256 8 0.0625 0.125 0.01 </span></span>
|
<span><span class="co"># [81] 32 2 0.125 8 128 0.005 0.01 0.002 0.5 0.25 </span></span>
|
||||||
<span><span class="co"># [91] 0.5 8 64 0.5 0.002 0.002 32 128 4 128</span></span></code></pre></div>
|
<span><span class="co"># [91] 0.01 1 64 0.025 0.25 2 256 0.0625 0.001 0.002</span></span></code></pre></div>
|
||||||
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
|
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
|
||||||
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
|
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
|
||||||
@@ -1242,10 +1242,10 @@ Longest: 24</p>
|
|||||||
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
|
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
|
||||||
<span><span class="va">disk_values</span></span>
|
<span><span class="va">disk_values</span></span>
|
||||||
<span><span class="co"># Class <disk></span></span>
|
<span><span class="co"># Class <disk></span></span>
|
||||||
<span><span class="co"># [1] 18 31 31 29 22 20 28 21 23 17 27 23 24 21 23 28 27 27 28 29 23 20 30 17 31</span></span>
|
<span><span class="co"># [1] 26 20 31 29 17 23 21 22 28 21 30 24 28 29 31 26 21 29 27 18 18 24 18 20 26</span></span>
|
||||||
<span><span class="co"># [26] 21 25 21 30 31 31 26 26 19 31 23 26 18 23 24 29 27 23 23 20 29 23 24 26 18</span></span>
|
<span><span class="co"># [26] 19 23 21 29 25 25 18 21 22 28 29 30 20 20 23 23 30 23 26 23 30 31 30 29 25</span></span>
|
||||||
<span><span class="co"># [51] 21 25 31 22 31 22 30 25 31 21 27 28 26 29 28 17 18 31 27 27 20 26 23 27 18</span></span>
|
<span><span class="co"># [51] 19 25 31 18 30 31 25 27 28 29 27 22 26 29 23 18 24 20 20 17 21 19 21 23 28</span></span>
|
||||||
<span><span class="co"># [76] 28 20 29 30 27 23 26 24 22 27 26 20 22 29 21 19 26 22 24 23 29 22 20 27 24</span></span></code></pre></div>
|
<span><span class="co"># [76] 21 30 23 31 17 19 17 31 17 29 17 26 17 23 26 27 18 21 24 19 22 20 22 31 18</span></span></code></pre></div>
|
||||||
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
|
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
|
||||||
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>
|
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>
|
||||||
|
|||||||
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@@ -38,7 +38,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
+29
-29
@@ -38,7 +38,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -314,19 +314,19 @@ Unique: 2</p>
|
|||||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
|
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
|
||||||
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
|
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
|
||||||
<span><span class="co"># 1 S I S S I R</span></span>
|
<span><span class="co"># 1 R R R I R R</span></span>
|
||||||
<span><span class="co"># 2 S R S S R S</span></span>
|
<span><span class="co"># 2 R R S R I R</span></span>
|
||||||
<span><span class="co"># 3 I I S R I I</span></span>
|
<span><span class="co"># 3 I R S S R S</span></span>
|
||||||
<span><span class="co"># 4 R R R I R R</span></span>
|
<span><span class="co"># 4 I I S R R S</span></span>
|
||||||
<span><span class="co"># 5 R I S I R S</span></span>
|
<span><span class="co"># 5 I R I I R I</span></span>
|
||||||
<span><span class="co"># 6 S S S S S I</span></span>
|
<span><span class="co"># 6 S R I R R R</span></span>
|
||||||
<span><span class="co"># kanamycin</span></span>
|
<span><span class="co"># kanamycin</span></span>
|
||||||
<span><span class="co"># 1 R</span></span>
|
<span><span class="co"># 1 R</span></span>
|
||||||
<span><span class="co"># 2 R</span></span>
|
<span><span class="co"># 2 S</span></span>
|
||||||
<span><span class="co"># 3 I</span></span>
|
<span><span class="co"># 3 I</span></span>
|
||||||
<span><span class="co"># 4 R</span></span>
|
<span><span class="co"># 4 S</span></span>
|
||||||
<span><span class="co"># 5 I</span></span>
|
<span><span class="co"># 5 R</span></span>
|
||||||
<span><span class="co"># 6 I</span></span></code></pre></div>
|
<span><span class="co"># 6 S</span></span></code></pre></div>
|
||||||
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
||||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
|
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
|
||||||
@@ -357,40 +357,40 @@ Unique: 5</p>
|
|||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">1</td>
|
<td align="left">1</td>
|
||||||
<td align="left">Mono-resistant</td>
|
<td align="left">Mono-resistant</td>
|
||||||
<td align="right">3196</td>
|
<td align="right">3199</td>
|
||||||
<td align="right">63.92%</td>
|
<td align="right">63.98%</td>
|
||||||
<td align="right">3196</td>
|
<td align="right">3199</td>
|
||||||
<td align="right">63.92%</td>
|
<td align="right">63.98%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">2</td>
|
<td align="left">2</td>
|
||||||
<td align="left">Negative</td>
|
<td align="left">Negative</td>
|
||||||
<td align="right">1003</td>
|
<td align="right">1012</td>
|
||||||
<td align="right">20.06%</td>
|
<td align="right">20.24%</td>
|
||||||
<td align="right">4199</td>
|
<td align="right">4211</td>
|
||||||
<td align="right">83.98%</td>
|
<td align="right">84.22%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">3</td>
|
<td align="left">3</td>
|
||||||
<td align="left">Multi-drug-resistant</td>
|
<td align="left">Multi-drug-resistant</td>
|
||||||
<td align="right">473</td>
|
<td align="right">428</td>
|
||||||
<td align="right">9.46%</td>
|
<td align="right">8.56%</td>
|
||||||
<td align="right">4672</td>
|
<td align="right">4639</td>
|
||||||
<td align="right">93.44%</td>
|
<td align="right">92.78%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">4</td>
|
<td align="left">4</td>
|
||||||
<td align="left">Poly-resistant</td>
|
<td align="left">Poly-resistant</td>
|
||||||
<td align="right">224</td>
|
<td align="right">252</td>
|
||||||
<td align="right">4.48%</td>
|
<td align="right">5.04%</td>
|
||||||
<td align="right">4896</td>
|
<td align="right">4891</td>
|
||||||
<td align="right">97.92%</td>
|
<td align="right">97.82%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">5</td>
|
<td align="left">5</td>
|
||||||
<td align="left">Extensively drug-resistant</td>
|
<td align="left">Extensively drug-resistant</td>
|
||||||
<td align="right">104</td>
|
<td align="right">109</td>
|
||||||
<td align="right">2.08%</td>
|
<td align="right">2.18%</td>
|
||||||
<td align="right">5000</td>
|
<td align="right">5000</td>
|
||||||
<td align="right">100.00%</td>
|
<td align="right">100.00%</td>
|
||||||
</tr>
|
</tr>
|
||||||
|
|||||||
+1
-1
@@ -38,7 +38,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
+3
-3
@@ -38,7 +38,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -162,7 +162,7 @@
|
|||||||
<img src="../logo.svg" class="logo" alt=""><h1>How to import data from SPSS / SAS / Stata</h1>
|
<img src="../logo.svg" class="logo" alt=""><h1>How to import data from SPSS / SAS / Stata</h1>
|
||||||
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
|
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
|
||||||
|
|
||||||
<h4 data-toc-skip class="date">06 October 2022</h4>
|
<h4 data-toc-skip class="date">10 October 2022</h4>
|
||||||
|
|
||||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
|
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
|
||||||
<div class="d-none name"><code>SPSS.Rmd</code></div>
|
<div class="d-none name"><code>SPSS.Rmd</code></div>
|
||||||
@@ -196,7 +196,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<p><strong>R has a huge community.</strong></p>
|
<p><strong>R has a huge community.</strong></p>
|
||||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">465,095 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
|
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">466,054 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
|
<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
|
||||||
|
|||||||
@@ -38,7 +38,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
+10
-10
@@ -38,7 +38,7 @@
|
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<main id="main" class="col-md-9"><div class="page-header">
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
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<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
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<h4 data-toc-skip class="date">06 October 2022</h4>
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<h4 data-toc-skip class="date">10 October 2022</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
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<div class="d-none name"><code>datasets.Rmd</code></div>
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<div class="d-none name"><code>datasets.Rmd</code></div>
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</h2>
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</h2>
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<p>A data set with 48,787 rows and 22 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>source</em>, <em>lpsn</em>, <em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>, <em>gbif_parent</em>, <em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
|
<p>A data set with 48,787 rows and 22 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>source</em>, <em>lpsn</em>, <em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>, <em>gbif_parent</em>, <em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
|
||||||
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
|
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
|
||||||
<p>It was last updated on 6 October 2022 10:20:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
|
<p>It was last updated on 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
|
||||||
<p><strong>Direct download links:</strong></p>
|
<p><strong>Direct download links:</strong></p>
|
||||||
<ul>
|
<ul>
|
||||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.1 MB)<br>
|
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.1 MB)<br>
|
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</h2>
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</h2>
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<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
|
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
|
||||||
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
|
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
|
||||||
<p>It was last updated on 6 October 2022 10:20:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
<p>It was last updated on 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||||
<p><strong>Direct download links:</strong></p>
|
<p><strong>Direct download links:</strong></p>
|
||||||
<ul>
|
<ul>
|
||||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
|
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
|
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</h2>
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</h2>
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<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
|
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
|
||||||
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
|
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
|
||||||
<p>It was last updated on 6 October 2022 10:20:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
<p>It was last updated on 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||||
<p><strong>Direct download links:</strong></p>
|
<p><strong>Direct download links:</strong></p>
|
||||||
<ul>
|
<ul>
|
||||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
|
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
|
||||||
@@ -754,7 +754,7 @@
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</h2>
|
</h2>
|
||||||
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
|
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
|
||||||
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
|
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
|
||||||
<p>It was last updated on 6 October 2022 10:20:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
<p>It was last updated on 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||||
<p><strong>Direct download links:</strong></p>
|
<p><strong>Direct download links:</strong></p>
|
||||||
<ul>
|
<ul>
|
||||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
|
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
|
||||||
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|||||||
</h2>
|
</h2>
|
||||||
<p>A data set with 134,659 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
|
<p>A data set with 134,659 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
|
||||||
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
|
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
|
||||||
<p>It was last updated on 6 October 2022 10:20:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
|
<p>It was last updated on 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
|
||||||
<p><strong>Direct download links:</strong></p>
|
<p><strong>Direct download links:</strong></p>
|
||||||
<ul>
|
<ul>
|
||||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original R Data Structure (RDS) file</a> (78 kB)<br>
|
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original R Data Structure (RDS) file</a> (78 kB)<br>
|
||||||
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</h2>
|
</h2>
|
||||||
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
|
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
|
||||||
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
|
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
|
||||||
<p>It was last updated on 6 October 2022 10:20:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
|
<p>It was last updated on 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
|
||||||
<p><strong>Direct download links:</strong></p>
|
<p><strong>Direct download links:</strong></p>
|
||||||
<ul>
|
<ul>
|
||||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
|
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
|
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</h2>
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</h2>
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<p>A data set with 2,000 rows and 46 columns, containing the following column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>, <em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>, <em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>, <em>FEP</em>, <em>CXM</em>, <em>FOX</em>, <em>CTX</em>, <em>CAZ</em>, <em>CRO</em>, <em>GEN</em>, <em>TOB</em>, <em>AMK</em>, <em>KAN</em>, <em>TMP</em>, <em>SXT</em>, <em>NIT</em>, <em>FOS</em>, <em>LNZ</em>, <em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>, <em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>, <em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>, <em>MUP</em> and <em>RIF</em>.</p>
|
<p>A data set with 2,000 rows and 46 columns, containing the following column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>, <em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>, <em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>, <em>FEP</em>, <em>CXM</em>, <em>FOX</em>, <em>CTX</em>, <em>CAZ</em>, <em>CRO</em>, <em>GEN</em>, <em>TOB</em>, <em>AMK</em>, <em>KAN</em>, <em>TMP</em>, <em>SXT</em>, <em>NIT</em>, <em>FOS</em>, <em>LNZ</em>, <em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>, <em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>, <em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>, <em>MUP</em> and <em>RIF</em>.</p>
|
||||||
<p>This data set is in R available as <code>example_isolates</code>, after you load the <code>AMR</code> package.</p>
|
<p>This data set is in R available as <code>example_isolates</code>, after you load the <code>AMR</code> package.</p>
|
||||||
<p>It was last updated on 6 October 2022 10:20:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
|
<p>It was last updated on 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
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<div class="section level3">
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<div class="section level3">
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<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
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<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
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</h2>
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<p>A data set with 3,000 rows and 8 columns, containing the following column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>, <em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and <em>GEN</em>.</p>
|
<p>A data set with 3,000 rows and 8 columns, containing the following column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>, <em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and <em>GEN</em>.</p>
|
||||||
<p>This data set is in R available as <code>example_isolates_unclean</code>, after you load the <code>AMR</code> package.</p>
|
<p>This data set is in R available as <code>example_isolates_unclean</code>, after you load the <code>AMR</code> package.</p>
|
||||||
<p>It was last updated on 6 October 2022 10:20:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
|
<p>It was last updated on 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
|
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<div class="section level3">
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<div class="section level3">
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<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
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<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
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</h3>
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</h3>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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||||||
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
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</div>
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<div class="section level2">
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<h2 class="pkg-version" data-toc-text="1.8.2.9007" id="amr-1829007">AMR 1.8.2.9007<a class="anchor" aria-label="anchor" href="#amr-1829007"></a></h2>
|
<h2 class="pkg-version" data-toc-text="1.8.2.9008" id="amr-1829008">AMR 1.8.2.9008<a class="anchor" aria-label="anchor" href="#amr-1829008"></a></h2>
|
||||||
<p>This version will eventually become v2.0! We’re happy to reach a new major milestone soon!</p>
|
<p>This version will eventually become v2.0! We’re happy to reach a new major milestone soon!</p>
|
||||||
<div class="section level4">
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<div class="section level4">
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<h4 id="breaking-1-8-2-9007">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9007"></a></h4>
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<h4 id="breaking-1-8-2-9008">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9008"></a></h4>
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<ul><li>Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons:<ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li>
|
<ul><li>Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons:<ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li>
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||||||
<li>Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package</li>
|
<li>Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package</li>
|
||||||
<li>Chromista are almost never clinically relevant, thus lacking the secondary scope of this package</li>
|
<li>Chromista are almost never clinically relevant, thus lacking the secondary scope of this package</li>
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@@ -140,7 +140,7 @@
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<li>The <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> now count deletions and substitutions as 2 instead of 1, which impacts the outcome of <code><a href="../reference/as.mo.html">as.mo()</a></code> and any <code>mo_*()</code> function</li>
|
<li>The <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> now count deletions and substitutions as 2 instead of 1, which impacts the outcome of <code><a href="../reference/as.mo.html">as.mo()</a></code> and any <code>mo_*()</code> function</li>
|
||||||
</ul></div>
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<div class="section level4">
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<h4 id="new-1-8-2-9007">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9007"></a></h4>
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<h4 id="new-1-8-2-9008">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9008"></a></h4>
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||||||
<ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
|
<ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
|
||||||
<li>All new algorithm for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and thus internally all <code>mo_*()</code> functions) while still following our original set-up as described in our paper (DOI 10.18637/jss.v104.i03).<ul><li>A new argument <code>keep_synonyms</code> allows to <em>not</em> correct for updated taxonomy, in favour of the now deleted argument <code>allow_uncertain</code>
|
<li>All new algorithm for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and thus internally all <code>mo_*()</code> functions) while still following our original set-up as described in our paper (DOI 10.18637/jss.v104.i03).<ul><li>A new argument <code>keep_synonyms</code> allows to <em>not</em> correct for updated taxonomy, in favour of the now deleted argument <code>allow_uncertain</code>
|
||||||
</li>
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</li>
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||||||
@@ -149,13 +149,14 @@
|
|||||||
</ul></li>
|
</ul></li>
|
||||||
<li>Function <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code> to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.</li>
|
<li>Function <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code> to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.</li>
|
||||||
<li>Function <code><a href="../reference/as.rsi.html">rsi_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which <code><a href="../reference/as.rsi.html">as.rsi()</a></code> was run.</li>
|
<li>Function <code><a href="../reference/as.rsi.html">rsi_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which <code><a href="../reference/as.rsi.html">as.rsi()</a></code> was run.</li>
|
||||||
|
<li>Function <code><a href="../reference/mo_property.html">mo_current()</a></code> to get the currently valid taxonomic name of a microorganism</li>
|
||||||
<li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://rdrr.io/pkg/janitor/man/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code>tsibble::tsibble</code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li>
|
<li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://rdrr.io/pkg/janitor/man/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code>tsibble::tsibble</code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li>
|
||||||
<li>All data sets in this package are now exported as <code>tibble</code>, instead of base R <code>data.frame</code>s. Older R versions are still supported.</li>
|
<li>All data sets in this package are now exported as <code>tibble</code>, instead of base R <code>data.frame</code>s. Older R versions are still supported.</li>
|
||||||
<li>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages.</li>
|
<li>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages.</li>
|
||||||
<li>Our data sets are now also continually exported to Apache Feather and Apache Parquet formats. You can find more info <a href="https://msberends.github.io/AMR/articles/datasets.html">in this article on our website</a>.</li>
|
<li>Our data sets are now also continually exported to Apache Feather and Apache Parquet formats. You can find more info <a href="https://msberends.github.io/AMR/articles/datasets.html">in this article on our website</a>.</li>
|
||||||
</ul></div>
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|
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<div class="section level4">
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||||||
<h4 id="changed-1-8-2-9007">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9007"></a></h4>
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<h4 id="changed-1-8-2-9008">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9008"></a></h4>
|
||||||
<ul><li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
|
<ul><li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
|
||||||
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
|
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
|
||||||
<li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
|
<li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
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@@ -180,7 +181,7 @@
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|||||||
<code><a href="../reference/mo_property.html">mo_snomed()</a></code> now returns class <code>character</code>, not <code>numeric</code> anymore (to make long SNOMED codes readable)</li>
|
<code><a href="../reference/mo_property.html">mo_snomed()</a></code> now returns class <code>character</code>, not <code>numeric</code> anymore (to make long SNOMED codes readable)</li>
|
||||||
</ul></div>
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<div class="section level4">
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<h4 id="other-1-8-2-9007">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9007"></a></h4>
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<h4 id="other-1-8-2-9008">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9008"></a></h4>
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||||||
<ul><li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
|
<ul><li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
|
||||||
<li>Added Peter Dutey-Magni, Dmytro Mykhailenko and Anton Mymrikov as contributors, to thank them for their valuable input</li>
|
<li>Added Peter Dutey-Magni, Dmytro Mykhailenko and Anton Mymrikov as contributors, to thank them for their valuable input</li>
|
||||||
<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>
|
<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>
|
||||||
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datasets: datasets.html
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datasets: datasets.html
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||||||
resistance_predict: resistance_predict.html
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resistance_predict: resistance_predict.html
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||||||
welcome_to_AMR: welcome_to_AMR.html
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welcome_to_AMR: welcome_to_AMR.html
|
||||||
last_built: 2022-10-06T10:23Z
|
last_built: 2022-10-10T08:15Z
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||||||
urls:
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urls:
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||||||
reference: https://msberends.github.io/AMR/reference
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reference: https://msberends.github.io/AMR/reference
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article: https://msberends.github.io/AMR/articles
|
article: https://msberends.github.io/AMR/articles
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|
||||||
@@ -190,16 +190,16 @@
|
|||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 1 1966-12-05 55 55.83562 33</span>
|
<span class="r-out co"><span class="r-pr">#></span> 1 1943-01-25 79 79.70685 56</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 2 1982-12-29 39 39.76986 17</span>
|
<span class="r-out co"><span class="r-pr">#></span> 2 1995-08-08 27 27.17260 4</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 3 1970-08-17 52 52.13699 29</span>
|
<span class="r-out co"><span class="r-pr">#></span> 3 1984-05-25 38 38.37808 15</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 4 1957-08-07 65 65.16438 42</span>
|
<span class="r-out co"><span class="r-pr">#></span> 4 1961-04-13 61 61.49315 38</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 5 1939-05-23 83 83.37260 60</span>
|
<span class="r-out co"><span class="r-pr">#></span> 5 1975-12-08 46 46.83836 24</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 6 1943-07-30 79 79.18630 56</span>
|
<span class="r-out co"><span class="r-pr">#></span> 6 1994-09-30 28 28.02740 5</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 7 1965-11-29 56 56.85205 34</span>
|
<span class="r-out co"><span class="r-pr">#></span> 7 1998-12-17 23 23.81370 1</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 8 1996-07-03 26 26.26027 3</span>
|
<span class="r-out co"><span class="r-pr">#></span> 8 1977-02-03 45 45.68219 22</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 9 1976-06-23 46 46.28767 23</span>
|
<span class="r-out co"><span class="r-pr">#></span> 9 1951-12-10 70 70.83288 48</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 10 1964-05-29 58 58.35616 35</span>
|
<span class="r-out co"><span class="r-pr">#></span> 10 1949-05-23 73 73.38356 50</span>
|
||||||
</code></pre></div>
|
</code></pre></div>
|
||||||
</div>
|
</div>
|
||||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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|||||||
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
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+11
-11
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|||||||
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|
||||||
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|
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|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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||||||
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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||||||
@@ -484,16 +484,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
|||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 50 × 13</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 50 × 13</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_input ab_consid…¹ mo_in…² mo_conside…³ guide…⁴</span>
|
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_input ab_consid…¹ mo_in…² mo_conside…³ guide…⁴</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2022-10-06 <span style="color: #949494;">10:23:18</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2022-10-10 <span style="color: #949494;">08:15:37</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2022-10-06 <span style="color: #949494;">10:23:18</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2022-10-10 <span style="color: #949494;">08:15:37</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2022-10-06 <span style="color: #949494;">10:23:18</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2022-10-10 <span style="color: #949494;">08:15:37</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2022-10-06 <span style="color: #949494;">10:23:19</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2022-10-10 <span style="color: #949494;">08:15:37</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2022-10-06 <span style="color: #949494;">10:23:19</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2022-10-10 <span style="color: #949494;">08:15:37</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2022-10-06 <span style="color: #949494;">10:23:19</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2022-10-10 <span style="color: #949494;">08:15:38</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2022-10-06 <span style="color: #949494;">10:23:19</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2022-10-10 <span style="color: #949494;">08:15:38</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2022-10-06 <span style="color: #949494;">10:23:19</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2022-10-10 <span style="color: #949494;">08:15:38</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2022-10-06 <span style="color: #949494;">10:23:19</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2022-10-10 <span style="color: #949494;">08:15:38</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2022-10-06 <span style="color: #949494;">10:23:19</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2022-10-10 <span style="color: #949494;">08:15:38</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 40 more rows, 6 more variables: ref_table <chr>, method <chr>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 40 more rows, 6 more variables: ref_table <chr>, method <chr>,</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S <dbl>, breakpoint_R <dbl>, input <dbl>, interpretation <rsi>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S <dbl>, breakpoint_R <dbl>, input <dbl>, interpretation <rsi>,</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># and abbreviated variable names ¹ab_considered, ²mo_input, ³mo_considered,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># and abbreviated variable names ¹ab_considered, ²mo_input, ³mo_considered,</span></span>
|
||||||
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||||||
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||||||
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||||||
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@@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
|||||||
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
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||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -10,7 +10,7 @@
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|||||||
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|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
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||||||
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||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
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@@ -12,7 +12,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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||||||
|
|||||||
+65
-65
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -177,40 +177,40 @@
|
|||||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
|
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2 1 52 9 1 5 52 4 4 33 43 5 44 22 9 19 6 17 1 56 4 15 44 46 49</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 49 45 39 34 32 25 14 10 65 5 28 63 26 42 9 56 25 35 9 5 24 67 19 40 1</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [26] 2 49 37 26 31 48 11 25 33 5 7 9 42 56 10 35 2 51 47 40 21 50 59 50 39</span>
|
<span class="r-out co"><span class="r-pr">#></span> [26] 53 31 61 38 67 8 42 28 40 45 33 4 1 50 5 44 49 26 40 22 64 29 51 58 4</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [51] 40 24 29 57 2 14 12 31 54 18 8 53 39 58 21 54 1 38 2 12 20 52 42 41 5</span>
|
<span class="r-out co"><span class="r-pr">#></span> [51] 57 31 7 44 53 13 5 64 10 7 11 23 30 59 20 11 5 37 67 60 32 60 59 10 7</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [76] 8 15 26 32 44 21 43 5 25 50 23 22 10 43 48 11 45 12 52 26 28 23 34 8 27</span>
|
<span class="r-out co"><span class="r-pr">#></span> [76] 44 61 49 55 20 3 12 62 20 27 41 46 24 56 13 19 34 47 52 12 11 59 5 54 12</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [101] 53 46 53 23 61 16 29 11 25 46 39 3 46 57 21 45 38 43 54 33 16 4 56 38 7</span>
|
<span class="r-out co"><span class="r-pr">#></span> [101] 17 30 26 43 25 25 56 17 47 18 67 40 27 25 45 23 64 43 8 46 60 8 15 25 6</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [126] 42 7 14 31 60 3 59 59 9 56 7 38 25 4 42 33 7 49 19 14 46 24 49 47 29</span>
|
<span class="r-out co"><span class="r-pr">#></span> [126] 67 11 2 9 50 4 46 60 59 46 49 14 7 28 9 36 36 50 60 2 12 11 66 48 21</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [151] 49 6 56 59 51 45 12 60 4 53 22 17 55 59 57 30 24 58 10 48 36 6 37 32 10</span>
|
<span class="r-out co"><span class="r-pr">#></span> [151] 31 65 66 12 54 42 62 3 64 42 61 2 7 9 25 1 16 41 63 37 38 39 51 60 24</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [176] 18 57 60 37 50 58 36 9 29 33 56 58 29 37 21 57 10 9 30 13 24 34 22 6 18</span>
|
<span class="r-out co"><span class="r-pr">#></span> [176] 59 17 62 41 55 62 59 45 25 33 21 50 62 35 57 57 15 52 40 13 48 33 67 63 33</span>
|
||||||
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
|
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [37] TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [37] TRUE FALSE TRUE TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE TRUE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE TRUE FALSE TRUE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [85] TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE FALSE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [97] TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [109] FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [109] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [121] TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [145] TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE TRUE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [145] FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [157] TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE TRUE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [181] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [181] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE</span>
|
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
|
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
|
||||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-09-08 B8CB09 60 F Outpatie… B_STPHY_CONS S NA S NA </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-06-23 798871 82 M Clinical B_ENTRC_FCLS NA NA NA NA </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-11-04 304347 62 M Clinical B_STRPT_PNMN S NA NA S </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-07-21 955940 82 F Clinical B_PSDMN_AERG R NA NA R </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>,</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>,</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>,</span></span>
|
||||||
@@ -246,16 +246,16 @@
|
|||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: condition [3]</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: condition [3]</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> patient date condition new_episode</span>
|
<span class="r-out co"><span class="r-pr">#></span> patient date condition new_episode</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 833842 2002-05-04 B FALSE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 545388 2013-07-29 A FALSE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 858515 2002-01-17 B TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 107DD1 2012-09-03 B FALSE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> A84726 2015-08-14 C FALSE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 829641 2011-01-03 A FALSE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 570937 2004-02-18 B FALSE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B54813 2009-10-15 B FALSE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 614772 2002-02-27 B FALSE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 942999 2009-02-17 C FALSE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 6BC362 2003-04-25 C FALSE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 0E2483 2007-08-10 A FALSE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> D43214 2015-06-16 B FALSE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 871360 2004-12-13 B FALSE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 384360 2003-01-09 C FALSE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> C58921 2004-01-01 A FALSE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 89B405 2003-01-04 B FALSE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 468282 2017-05-31 C TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 4F6830 2010-03-12 B FALSE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 762305 2002-11-16 A FALSE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
||||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||||
@@ -267,19 +267,19 @@
|
|||||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [183]</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [178]</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> ICU 2002-05-04 833842 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2013-07-29 545388 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU 2002-01-17 858515 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2012-09-03 107DD1 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2015-08-14 A84726 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2011-01-03 829641 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2004-02-18 570937 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ICU 2009-10-15 B54813 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2002-02-27 614772 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2009-02-17 942999 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU 2003-04-25 6BC362 1 FALSE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU 2007-08-10 0E2483 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2015-06-16 D43214 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2004-12-13 871360 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical 2003-01-09 384360 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical 2004-01-01 C58921 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2003-01-04 89B405 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2017-05-31 468282 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2010-03-12 4F6830 1 TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2002-11-16 762305 1 TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
||||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||||
@@ -294,9 +294,9 @@
|
|||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
|
<span class="r-out co"><span class="r-pr">#></span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 118 15 50 75</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 111 15 55 72</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 51 12 32 40</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 55 13 37 44</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 14 8 14 14</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 12 8 12 12</span>
|
||||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span> <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
|
<span class="r-in"><span> <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
|
||||||
@@ -326,19 +326,19 @@
|
|||||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
|
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
|
||||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [195]</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [191]</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 833842 B_STPHY_AURS ICU TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 545388 B_KLBSL_PNMN Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 858515 B_STPHY_EPDR ICU TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 107DD1 B_STPHY_CONS Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> A84726 B_STPHY_EPDR Clinical TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 829641 B_ESCHR_COLI Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 570937 B_KLBSL_PNMN Clinical TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B54813 B_ENTRC ICU TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 614772 B_STPHY_HMNS Clinical TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 942999 B_STRPT_PNMN Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 6BC362 B_CRYNB ICU TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 0E2483 B_ENTRC_FACM ICU TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> D43214 B_STPHY_HMNS Clinical TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 871360 B_KLBSL_PNMN Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 384360 B_STPHY_CONS Clinical TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> C58921 B_ESCHR_COLI Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 89B405 B_STRPT_PNMN Clinical TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 468282 B_STPHY_AURS Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 4F6830 B_ESCHR_COLI Clinical TRUE </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 762305 B_PROTS_MRBL Clinical TRUE </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
||||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||||
</code></pre></div>
|
</code></pre></div>
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -143,7 +143,7 @@
|
|||||||
<dd>Transform Input to a Microorganism Code</dd>
|
<dd>Transform Input to a Microorganism Code</dd>
|
||||||
</dl><dl><dt>
|
</dl><dl><dt>
|
||||||
|
|
||||||
<code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_domain()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_status()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_is_gram_negative()</a></code> <code><a href="mo_property.html">mo_is_gram_positive()</a></code> <code><a href="mo_property.html">mo_is_yeast()</a></code> <code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code> <code><a href="mo_property.html">mo_snomed()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_lpsn()</a></code> <code><a href="mo_property.html">mo_gbif()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code>
|
<code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_domain()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_status()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_is_gram_negative()</a></code> <code><a href="mo_property.html">mo_is_gram_positive()</a></code> <code><a href="mo_property.html">mo_is_yeast()</a></code> <code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code> <code><a href="mo_property.html">mo_snomed()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_lpsn()</a></code> <code><a href="mo_property.html">mo_gbif()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_current()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code>
|
||||||
</dt>
|
</dt>
|
||||||
<dd>Get Properties of a Microorganism</dd>
|
<dd>Get Properties of a Microorganism</dd>
|
||||||
</dl><dl><dt>
|
</dl><dl><dt>
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
+1
-1
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -167,9 +167,9 @@
|
|||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
|
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2.989759</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 3.029181</span>
|
||||||
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.06909556</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] -0.01584586</span>
|
||||||
</code></pre></div>
|
</code></pre></div>
|
||||||
</div>
|
</div>
|
||||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||||
|
|||||||
+1
-1
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
+1
-1
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -195,11 +195,10 @@
|
|||||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||||
<span class="r-in"><span><span class="va">x</span></span></span>
|
<span class="r-in"><span><span class="va">x</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 32 8 0.01 0.01 >=256 0.01 8 0.005 <=0.001</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 0.001 0.125 1 >=128 0.005 >=128 0.001 0.0625 0.005 0.005 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [10] 0.125 </span>
|
|
||||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.1315344 0.8152036 -0.7101208 -0.7101208 1.6060306 -0.7101208</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] -0.99724839 0.09165344 0.56061793 1.65486841 -0.63428112 1.65486841</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.8152036 -0.8682862 -1.2355349 -0.1337888</span>
|
<span class="r-out co"><span class="r-pr">#></span> [7] -0.99724839 -0.06466806 -0.63428112 -0.63428112</span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="va">y</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
<span class="r-in"><span><span class="va">y</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||||
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
|
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
|
||||||
@@ -209,38 +208,38 @@
|
|||||||
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
|
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
|
||||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||||
<span class="r-in"><span><span class="va">y</span></span></span>
|
<span class="r-in"><span><span class="va">y</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 8 >=1 1 <=1</span>
|
<span class="r-out co"><span class="r-pr">#></span> 1 A 8 0.5 <=0.5 >=8</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 2 B <=2 0.0625 8 <=1</span>
|
<span class="r-out co"><span class="r-pr">#></span> 2 B 1 <=0.0625 2 >=8</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 3 C >=64 0.5 8 4</span>
|
<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.25 4 >=8</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.125 >=16 <=1</span>
|
<span class="r-out co"><span class="r-pr">#></span> 4 D 8 <=0.0625 <=0.5 4</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.5 8 2</span>
|
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.0625 4 >=8</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 16 0.5 2 4</span>
|
<span class="r-out co"><span class="r-pr">#></span> 6 F 2 0.25 4 >=8</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 16 0.125 2 2</span>
|
<span class="r-out co"><span class="r-pr">#></span> 7 G 4 1 1 <=2</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 32 0.5 1 2</span>
|
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 1 4 >=8</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.5 1 8</span>
|
<span class="r-out co"><span class="r-pr">#></span> 9 I 4 <=0.0625 2 >=8</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 10 J <=2 0.5 2 4</span>
|
<span class="r-out co"><span class="r-pr">#></span> 10 J 1 1 1 <=2</span>
|
||||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> "id" and "tobr"</span>
|
<span class="r-msg co"><span class="r-pr">#></span> "id" and "tobr"</span>
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.30066368 -0.89674084 0.93947445 -0.07754651 0.09008074 0.30370274</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 0.14820813 -0.44647774 0.81311070 -0.56450282 0.14549038 0.23021697</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.33364342 0.04742155 0.37971141 -0.15179644</span>
|
<span class="r-out co"><span class="r-pr">#></span> [7] -0.29155363 0.70353938 -0.05788192 -0.68014945</span>
|
||||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
|
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 2 B <=2 0.0625 8 <=1 -0.89674084</span>
|
<span class="r-out co"><span class="r-pr">#></span> 10 J 1 1 1 <=2 -0.68014945</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 16 0.125 2 2 -0.33364342</span>
|
<span class="r-out co"><span class="r-pr">#></span> 4 D 8 <=0.0625 <=0.5 4 -0.56450282</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 8 >=1 1 <=1 -0.30066368</span>
|
<span class="r-out co"><span class="r-pr">#></span> 2 B 1 <=0.0625 2 >=8 -0.44647774</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 10 J <=2 0.5 2 4 -0.15179644</span>
|
<span class="r-out co"><span class="r-pr">#></span> 7 G 4 1 1 <=2 -0.29155363</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.125 >=16 <=1 -0.07754651</span>
|
<span class="r-out co"><span class="r-pr">#></span> 9 I 4 <=0.0625 2 >=8 -0.05788192</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 32 0.5 1 2 0.04742155</span>
|
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.0625 4 >=8 0.14549038</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.5 8 2 0.09008074</span>
|
<span class="r-out co"><span class="r-pr">#></span> 1 A 8 0.5 <=0.5 >=8 0.14820813</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 16 0.5 2 4 0.30370274</span>
|
<span class="r-out co"><span class="r-pr">#></span> 6 F 2 0.25 4 >=8 0.23021697</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.5 1 8 0.37971141</span>
|
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 1 4 >=8 0.70353938</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 3 C >=64 0.5 8 4 0.93947445</span>
|
<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.25 4 >=8 0.81311070</span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||||
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||||
@@ -252,17 +251,17 @@
|
|||||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 1 C >=64 0.5 8 4 0.93947445 0.0000000</span>
|
<span class="r-out co"><span class="r-pr">#></span> 1 C 16 0.25 4 >=8 0.81311070 0.0000000</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 2 I 16 0.5 1 8 0.37971141 0.5597630</span>
|
<span class="r-out co"><span class="r-pr">#></span> 2 H 4 1 4 >=8 0.70353938 0.1095713</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 3 F 16 0.5 2 4 0.30370274 0.6357717</span>
|
<span class="r-out co"><span class="r-pr">#></span> 3 F 2 0.25 4 >=8 0.23021697 0.5828937</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 4 E 4 0.5 8 2 0.09008074 0.8493937</span>
|
<span class="r-out co"><span class="r-pr">#></span> 4 A 8 0.5 <=0.5 >=8 0.14820813 0.6649026</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 5 H 32 0.5 1 2 0.04742155 0.8920529</span>
|
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.0625 4 >=8 0.14549038 0.6676203</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 6 D 16 0.125 >=16 <=1 -0.07754651 1.0170210</span>
|
<span class="r-out co"><span class="r-pr">#></span> 6 I 4 <=0.0625 2 >=8 -0.05788192 0.8709926</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 7 J <=2 0.5 2 4 -0.15179644 1.0912709</span>
|
<span class="r-out co"><span class="r-pr">#></span> 7 G 4 1 1 <=2 -0.29155363 1.1046643</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 8 A 8 >=1 1 <=1 -0.30066368 1.2401381</span>
|
<span class="r-out co"><span class="r-pr">#></span> 8 B 1 <=0.0625 2 >=8 -0.44647774 1.2595884</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 9 G 16 0.125 2 2 -0.33364342 1.2731179</span>
|
<span class="r-out co"><span class="r-pr">#></span> 9 D 8 <=0.0625 <=0.5 4 -0.56450282 1.3776135</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 10 B <=2 0.0625 8 <=1 -0.89674084 1.8362153</span>
|
<span class="r-out co"><span class="r-pr">#></span> 10 J 1 1 1 <=2 -0.68014945 1.4932602</span>
|
||||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||||
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
|
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
|
||||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -330,6 +330,8 @@
|
|||||||
<span> <span class="va">...</span></span>
|
<span> <span class="va">...</span></span>
|
||||||
<span><span class="op">)</span></span>
|
<span><span class="op">)</span></span>
|
||||||
<span></span>
|
<span></span>
|
||||||
|
<span><span class="fu">mo_current</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||||
|
<span></span>
|
||||||
<span><span class="fu">mo_info</span><span class="op">(</span></span>
|
<span><span class="fu">mo_info</span><span class="op">(</span></span>
|
||||||
<span> <span class="va">x</span>,</span>
|
<span> <span class="va">x</span>,</span>
|
||||||
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
|
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
|
||||||
@@ -389,7 +391,7 @@
|
|||||||
|
|
||||||
|
|
||||||
<ul><li><p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> in case of <code>mo_year()</code></p></li>
|
<ul><li><p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> in case of <code>mo_year()</code></p></li>
|
||||||
<li><p>A <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a> in case of <code>mo_taxonomy()</code> and <code>mo_info()</code></p></li>
|
<li><p>A <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a> in case of <code>mo_taxonomy()</code>, <code>mo_synonyms()</code> and <code>mo_info()</code></p></li>
|
||||||
<li><p>A named <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> in case of <code>mo_url()</code></p></li>
|
<li><p>A named <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> in case of <code>mo_url()</code></p></li>
|
||||||
<li><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> in case of <code>mo_snomed()</code></p></li>
|
<li><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> in case of <code>mo_snomed()</code></p></li>
|
||||||
<li><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> in all other cases</p></li>
|
<li><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> in all other cases</p></li>
|
||||||
@@ -407,6 +409,7 @@
|
|||||||
<p>All output <a href="translate.html">will be translated</a> where possible.</p>
|
<p>All output <a href="translate.html">will be translated</a> where possible.</p>
|
||||||
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
|
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
|
||||||
<p>SNOMED codes - <code>mo_snomed()</code> - are from the version of 1 July, 2021. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
|
<p>SNOMED codes - <code>mo_snomed()</code> - are from the version of 1 July, 2021. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
|
||||||
|
<p>Old taxonomic names (so-called 'synonyms') can be retrieved with <code>mo_synonyms()</code>, the current taxonomic name can be retrieved with <code>mo_current()</code>. Both functions return full names.</p>
|
||||||
</div>
|
</div>
|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 id="matching-score-for-microorganisms">Matching Score for Microorganisms<a class="anchor" aria-label="anchor" href="#matching-score-for-microorganisms"></a></h2>
|
<h2 id="matching-score-for-microorganisms">Matching Score for Microorganisms<a class="anchor" aria-label="anchor" href="#matching-score-for-microorganisms"></a></h2>
|
||||||
|
|||||||
@@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
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||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
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@@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
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||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
+18
-17
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -178,42 +178,43 @@
|
|||||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.01 1 0.025 4 2 256 0.125 0.005 0.0625 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2 0.5 32 0.01 1 0.5 <=0.002 0.005 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [10] 4 0.005 64 1 16 0.5 <=0.002 0.5 0.005 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [10] 0.01 32 >=256 0.01 4 0.125 0.025 32 >=256 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [19] 0.005 16 16 128 0.01 16 <=0.002</span>
|
<span class="r-out co"><span class="r-pr">#></span> [19] 1 1 4 0.025 4 64 0.0625 </span>
|
||||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 49 25 17 40 42 40 37 45 6 46 13 6 48 38 38 28 46 14 40 9 19 41 41 40 43</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 46 43 39 46 43 42 23 46 47 47 49 43 50 47 45 32 40 43 37 43 40 48 21 12 49</span>
|
||||||
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] S S R R R R I S I I S R I S S R I S S R S R I R S</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] R S S I S R I I I R S R R R S R R S R I I I S S I</span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||||
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
|
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
|
||||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
|
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 32 4 4 0.002 8 2 0.025 <=0.001</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 32 0.5 0.001 16 0.001 2 0.0625 0.0625 16 0.125 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [10] 0.25 128 0.002 16 32 0.125 16 0.5 4 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [11] 0.025 32 0.5 0.005 16 0.125 0.0625 0.125 0.002 64 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [19] 256 16 0.0625 <=0.001 0.5 256 32 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [21] 0.01 32 8 16 0.0625</span>
|
||||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
|
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 8 >=16 >=16 >=16 >=16 2 <=1 8 8 4 8 <=1 4 <=1 <=1 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 2 >=32 16 4 4 16 2 16 4 2 >=32 2 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [16] >=16 >=16 <=1 <=1 8 8 4 2 4 8 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [13] 2 <=0.5 <=0.5 4 8 8 1 16 16 >=32 8 <=0.5</span>
|
||||||
|
<span class="r-out co"><span class="r-pr">#></span> [25] 2 </span>
|
||||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
|
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 4 0.5 0.0625 4 >=16 1 0.5 0.5 0.0625 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 1 >=16 2 0.25 0.125 8 0.25 >=16 1 1 8 0.5 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [10] 4 0.25 0.25 0.0625 8 4 8 0.25 8 </span>
|
<span class="r-out co"><span class="r-pr">#></span> [13] 8 0.5 >=16 0.25 1 0.5 >=16 1 4 0.125 8 2 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [19] 0.25 4 1 >=16 <=0.025 4 <=0.025</span>
|
<span class="r-out co"><span class="r-pr">#></span> [25] 8 </span>
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
|
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 21 37 33 13 16 25 34 10 46 40 48 31 42 13 33 30 9 24 15 41 20 22 43 45 42</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 28 44 33 10 35 18 23 48 50 33 44 27 41 19 40 45 44 42 18 42 38 29 47 47 48</span>
|
||||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
|
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 13 17 15 16 16 11 16 14 15 13 12 13 13 14 14 16 13 16 14 17 13 15 11 17 14</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 12 17 15 17 14 16 17 13 14 16 16 16 12 13 12 12 14 12 16 17 17 12 15 13 14</span>
|
||||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
|
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] 18 20 17 22 27 15 22 15 18 25 20 19 22 19 15 23 15 19 27 17 23 15 16 15 21</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] 24 22 25 27 24 26 18 22 17 20 24 18 17 20 23 26 15 22 22 21 19 17 16 17 16</span>
|
||||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||||
</code></pre></div>
|
</code></pre></div>
|
||||||
</div>
|
</div>
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.02820659</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.001386368</span>
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</code></pre></div>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame( patient_id = patients, gender = c( rep(\"M\", 135), rep(\"F\", 125) ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c( \"Escherichia coli\", \"Staphylococcus aureus\", \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated
|
[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame( patient_id = patients, gender = c( rep(\"M\", 135), rep(\"F\", 125) ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c( \"Escherichia coli\", \"Staphylococcus aureus\", \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated
|
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