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Built site for AMR@2.1.1.9092: c588902

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2024-10-06 14:35:11 +00:00
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@@ -29,7 +29,7 @@
<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="">2.1.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</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">
@@ -87,7 +87,7 @@
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 02 October 2024.</p>
generated on 06 October 2024.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -143,21 +143,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2024-10-02</td>
<td align="center">2024-10-06</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">2024-10-02</td>
<td align="center">2024-10-06</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">2024-10-02</td>
<td align="center">2024-10-06</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -272,10 +272,11 @@ taxonomic codes. Let’s check this:</p>
<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; Also matched: Enterococcus crotali (0.650), Escherichia coli coli</span></span>
<span><span class="co">#&gt; (0.643), Escherichia coli expressing (0.611), Enterococcus columbae</span></span>
<span><span class="co">#&gt; (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus</span></span>
<span><span class="co">#&gt; (0.577), Enterococcus canis (0.556), Enterococcus cecorum (0.550),</span></span>
<span><span class="co">#&gt; Enterococcus canintestini (0.540), and Enterobacter cowanii (0.522)</span></span>
<span><span class="co">#&gt; (0.643), Escherichia coli expressing (0.611), Enterobacter cowanii</span></span>
<span><span class="co">#&gt; (0.600), Enterococcus columbae (0.595), Enterococcus camelliae (0.591),</span></span>
<span><span class="co">#&gt; Enterococcus casseliflavus (0.577), Enterobacter cloacae cloacae</span></span>
<span><span class="co">#&gt; (0.571), Enterobacter cloacae complex (0.571), and Enterobacter cloacae</span></span>
<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; Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span></span>
@@ -295,11 +296,12 @@ taxonomic codes. Let’s check this:</p>
<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; Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus</span></span>
<span><span class="co">#&gt; phocae salmonis (0.552), Streptococcus pseudoporcinus (0.536),</span></span>
<span><span class="co">#&gt; Staphylococcus piscifermentans (0.533), Staphylococcus pseudintermedius</span></span>
<span><span class="co">#&gt; (0.532), Streptococcus gallolyticus pasteurianus (0.526), Salmonella</span></span>
<span><span class="co">#&gt; Portanigra (0.524), Streptococcus periodonticum (0.519), Streptococcus</span></span>
<span><span class="co">#&gt; phocae phocae (0.519), and Streptococcus pluranimalium (0.519)</span></span>
<span><span class="co">#&gt; phocae salmonis (0.552), Serratia proteamaculans quinovora (0.545),</span></span>
<span><span class="co">#&gt; Streptococcus pseudoporcinus (0.536), Staphylococcus piscifermentans</span></span>
<span><span class="co">#&gt; (0.533), Staphylococcus pseudintermedius (0.532), Serratia</span></span>
<span><span class="co">#&gt; proteamaculans proteamaculans (0.526), Streptococcus gallolyticus</span></span>
<span><span class="co">#&gt; pasteurianus (0.526), Salmonella Portanigra (0.524), and Streptococcus</span></span>
<span><span class="co">#&gt; periodonticum (0.519)</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Only the first 10 other matches of each record are shown. Run</span></span>
<span><span class="co">#&gt; print(mo_uncertainties(), n = ...) to view more entries, or save</span></span>