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Built site for AMR: 2.0.0.9015@5f9769a

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2023-05-12 08:43:14 +00:00
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@ -38,7 +38,7 @@
<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="">2.0.0.9014</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</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">
@ -187,7 +187,7 @@
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 08 May 2023.</p>
generated on 12 May 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -243,21 +243,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-05-08</td>
<td align="center">2023-05-12</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">2023-05-08</td>
<td align="center">2023-05-12</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">2023-05-08</td>
<td align="center">2023-05-12</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -371,7 +371,6 @@ taxonomic codes. Let’s check this:</p>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "E. coli" -&gt; Escherichia coli (B_ESCHR_COLI, 0.688)</span></span>
<span><span class="co">#&gt; Based on input "E coli"</span></span>
<span><span class="co">#&gt; Also matched: Enterobacter cowanii (0.600), Eubacterium combesii</span></span>
<span><span class="co">#&gt; (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi</span></span>
<span><span class="co">#&gt; (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides</span></span>
@ -380,7 +379,6 @@ taxonomic codes. Let’s check this:</p>
<span><span class="co">#&gt; dissolvens (0.565)</span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "K. pneumoniae" -&gt; Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span></span>
<span><span class="co">#&gt; Based on input "K pneumoniae"</span></span>
<span><span class="co">#&gt; Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span></span>
<span><span class="co">#&gt; pneumoniae pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis</span></span>
<span><span class="co">#&gt; (0.658), Klebsiella pasteurii (0.500), Klebsiella planticola (0.500),</span></span>
@ -389,7 +387,6 @@ taxonomic codes. Let’s check this:</p>
<span><span class="co">#&gt; (0.333)</span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "S. aureus" -&gt; Staphylococcus aureus (B_STPHY_AURS, 0.690)</span></span>
<span><span class="co">#&gt; Based on input "S aureus"</span></span>
<span><span class="co">#&gt; Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus</span></span>
<span><span class="co">#&gt; argenteus (0.625), Staphylococcus aureus anaerobius (0.625),</span></span>
<span><span class="co">#&gt; Streptomyces argenteolus (0.483), Streptomyces aureus (0.474),</span></span>
@ -398,7 +395,6 @@ taxonomic codes. Let’s check this:</p>
<span><span class="co">#&gt; Streptomyces aureocirculatus (0.429)</span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "S. pneumoniae" -&gt; Streptococcus pneumoniae (B_STRPT_PNMN, 0.750)</span></span>
<span><span class="co">#&gt; Based on input "S pneumoniae"</span></span>
<span><span class="co">#&gt; Also matched: Streptococcus pseudopneumoniae (0.700), Serratia</span></span>
<span><span class="co">#&gt; proteamaculans quinovora (0.545), Streptococcus pseudoporcinus (0.536),</span></span>
<span><span class="co">#&gt; Staphylococcus pseudintermedius (0.532), Serratia proteamaculans</span></span>