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@ -31,7 +31,7 @@
<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="">2.1.1.9224</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</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">
@ -93,7 +93,7 @@
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 20 March 2025.</p>
generated on 27 March 2025.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -149,21 +149,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2025-03-20</td>
<td align="center">2025-03-27</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2025-03-20</td>
<td align="center">2025-03-27</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2025-03-20</td>
<td align="center">2025-03-27</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -288,12 +288,12 @@ taxonomic codes. Let’s check this:</p>
<span><span class="co"><span style="font-style: italic;">#&gt; dissolvens</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.565</span>)</span></span>
<span><span class="co">#&gt; <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span></span>
<span><span class="co">#&gt; "K. pneumoniae" -&gt; <span style="font-weight: bold; font-style: italic;">Klebsiella pneumoniae</span> (B_KLBSL_PNMN, <span style="color: #080808; background-color: #5FD7AF;">0.786</span>)</span></span>
<span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Klebsiella pneumoniae ozaenae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella</span></span></span>
<span><span class="co"><span style="font-style: italic;">#&gt; pneumoniae pneumoniae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.688</span>), <span style="font-style: italic;">Klebsiella pneumoniae rhinoscleromatis</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (</span><span style="color: #080808; background-color: #FFFF87;">0.658</span>), <span style="font-style: italic;">Klebsiella pasteurii</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.500</span>), <span style="font-style: italic;">Klebsiella planticola</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.500</span>),</span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Kingella potus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.400</span>), <span style="font-style: italic;">Kluyveromyces pseudotropicale</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.386</span>),</span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Kluyveromyces pseudotropicalis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.363</span>), <span style="font-style: italic;">Kosakonia pseudosacchari</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (</span><span style="color: #080808; background-color: #FFAFAF;">0.361</span>), and <span style="font-style: italic;">Kluyveromyces pseudotropicalis pseudotropicalis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.361</span>)</span></span>
<span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Klebsiella pneumoniae</span> complex<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella</span></span></span>
<span><span class="co"><span style="font-style: italic;">#&gt; pneumoniae ozaenae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella pneumoniae pneumoniae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.688</span>),</span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Klebsiella pneumoniae rhinoscleromatis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.658</span>), <span style="font-style: italic;">Klebsiella pasteurii</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (</span><span style="color: #080808; background-color: #FFAFAF;">0.500</span>), <span style="font-style: italic;">Klebsiella planticola</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.500</span>), <span style="font-style: italic;">Kingella potus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.400</span>),</span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">Kluyveromyces pseudotropicale</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.386</span>), <span style="font-style: italic;">Kluyveromyces pseudotropicalis</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (</span><span style="color: #080808; background-color: #FFAFAF;">0.363</span>), and <span style="font-style: italic;">Kosakonia pseudosacchari</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.361</span>)</span></span>
<span><span class="co">#&gt; <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span></span>
<span><span class="co">#&gt; "S. aureus" -&gt; <span style="font-weight: bold; font-style: italic;">Staphylococcus aureus</span> (B_STPHY_AURS, <span style="color: #080808; background-color: #FFFF87;">0.690</span>)</span></span>
<span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Staphylococcus aureus aureus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.643</span>), <span style="font-style: italic;">Staphylococcus</span></span></span>