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@@ -30,7 +30,7 @@
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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="">3.0.1.9035</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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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@@ -91,7 +91,7 @@
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website update since they are based on randomly created values and the
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page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
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Markdown</a>. However, the methodology remains unchanged. This page was
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generated on 18 March 2026.</p>
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generated on 20 March 2026.</p>
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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>
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@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
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</tr></thead>
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<tbody>
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<tr class="odd">
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<td align="center">2026-03-18</td>
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<td align="center">2026-03-20</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">S</td>
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<td align="center">S</td>
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</tr>
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<tr class="even">
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<td align="center">2026-03-18</td>
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<td align="center">2026-03-20</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">S</td>
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<td align="center">R</td>
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</tr>
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<tr class="odd">
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<td align="center">2026-03-18</td>
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<td align="center">2026-03-20</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">R</td>
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@@ -263,56 +263,54 @@ user input can be used:</p>
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<p>Now we can thus clean our data:</p>
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<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span> <span class="op"><-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
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<span><span class="co">#> <span style="color: #0000BB;">ℹ Retrieved values from the `microorganisms.codes` data set for "ESCCOL",</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> "KLEPNE", "STAAUR", and "STRPNE".</span></span></span>
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<span><span class="co">#> <span style="color: #0000BB;">ℹ Microorganism translation was uncertain for four microorganisms. Run</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> `mo_uncertainties()` to review these uncertainties, or use</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> `add_custom_microorganisms()` to add custom entries.</span></span></span></code></pre></div>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Retrieved values from the `microorganisms.codes` data set for "ESCCOL",</span></span>
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<span><span class="co">#> "KLEPNE", "STAAUR", and "STRPNE".</span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Microorganism translation was uncertain for four microorganisms. Run</span></span>
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<span><span class="co">#> `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to review these</span></span>
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<span><span class="co">#> uncertainties, or use `add_custom_microorganisms()`</span></span>
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<span><span class="co">#> (`?AMR::add_custom_microorganisms()`) to add custom entries.</span></span></code></pre></div>
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<p>Apparently, there was some uncertainty about the translation to
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taxonomic codes. Let’s check this:</p>
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<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span>
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<span><span class="co">#> <span style="color: #0000BB;">Matching scores are based on the resemblance between the input and the full</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.</span></span></span>
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<span><span class="co">#> <span style="color: #0000BB;">Colour keys: </span><span style="color: #080808; background-color: #FF5F5F;"> 0.000-0.549 </span><span style="color: #080808; background-color: #FFD787;"> 0.550-0.649 </span><span style="color: #080808; background-color: #FFFF87;"> 0.650-0.749 </span><span style="color: #080808; background-color: #5FD7AF;"> 0.750-1.000 </span></span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span></span>
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<span><span class="co">#> "E. coli" -> <span style="font-weight: bold; font-style: italic;">Escherichia coli</span> (B_ESCHR_COLI, <span style="color: #080808; background-color: #FFFF87;">0.688</span>)</span></span>
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<span><span class="co">#> Also matched: <span style="font-style: italic;">Enterococcus crotali</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.650</span>), <span style="font-style: italic;">Escherichia coli coli</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> (</span><span style="color: #080808; background-color: #FFD787;">0.643</span>), <span style="font-style: italic;">Escherichia coli expressing</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.611</span>), <span style="font-style: italic;">Enterobacter cowanii</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> (</span><span style="color: #080808; background-color: #FFD787;">0.600</span>), <span style="font-style: italic;">Enterococcus columbae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.595</span>), <span style="font-style: italic;">Enterococcus camelliae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.591</span>),</span></span>
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<span><span class="co">#> <span style="font-style: italic;">Enterococcus casseliflavus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.577</span>), <span style="font-style: italic;">Enterobacter cloacae cloacae</span></span></span>
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||||
<span><span class="co"><span style="color: #0000BB;">#> (</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), <span style="font-style: italic;">Enterobacter cloacae</span> complex<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), and <span style="font-style: italic;">Enterobacter cloacae</span></span></span>
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<span><span class="co"><span style="font-style: italic;">#> dissolvens</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.565</span>)</span></span>
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<span><span class="co">#> <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span></span>
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<span><span class="co">#> "K. pneumoniae" -> <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>
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||||
<span><span class="co">#> 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>
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||||
<span><span class="co"><span style="font-style: italic;">#> 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>
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||||
<span><span class="co">#> <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>
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||||
<span><span class="co"><span style="color: #0000BB;">#> (</span><span style="color: #080808; background-color: #FF5F5F;">0.500</span>), <span style="font-style: italic;">Klebsiella planticola</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.500</span>), <span style="font-style: italic;">Kingella potus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.400</span>),</span></span>
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||||
<span><span class="co">#> <span style="font-style: italic;">Kluyveromyces pseudotropicale</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.386</span>), <span style="font-style: italic;">Kluyveromyces pseudotropicalis</span></span></span>
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||||
<span><span class="co"><span style="color: #0000BB;">#> (</span><span style="color: #080808; background-color: #FF5F5F;">0.363</span>), and <span style="font-style: italic;">Kosakonia pseudosacchari</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.361</span>)</span></span>
|
||||
<span><span class="co">#> <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span></span>
|
||||
<span><span class="co">#> "S. aureus" -> <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">#> 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>
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||||
<span><span class="co"><span style="font-style: italic;">#> argenteus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.625</span>), <span style="font-style: italic;">Staphylococcus aureus anaerobius</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.625</span>),</span></span>
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||||
<span><span class="co">#> <span style="font-style: italic;">Staphylococcus auricularis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.615</span>), <span style="font-style: italic;">Salmonella</span> Aurelianis<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.595</span>),</span></span>
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||||
<span><span class="co">#> <span style="font-style: italic;">Salmonella</span> Aarhus<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.588</span>), <span style="font-style: italic;">Salmonella</span> Amounderness<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.587</span>),</span></span>
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||||
<span><span class="co">#> <span style="font-style: italic;">Staphylococcus argensis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.587</span>), <span style="font-style: italic;">Streptococcus australis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.587</span>), and</span></span>
|
||||
<span><span class="co">#> <span style="font-style: italic;">Salmonella choleraesuis arizonae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.562</span>)</span></span>
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||||
<span><span class="co">#> <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span></span>
|
||||
<span><span class="co">#> "S. pneumoniae" -> <span style="font-weight: bold; font-style: italic;">Streptococcus pneumoniae</span> (B_STRPT_PNMN, <span style="color: #080808; background-color: #5FD7AF;">0.750</span>)</span></span>
|
||||
<span><span class="co">#> Also matched: <span style="font-style: italic;">Streptococcus pseudopneumoniae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.700</span>), <span style="font-style: italic;">Streptococcus</span></span></span>
|
||||
<span><span class="co"><span style="font-style: italic;">#> phocae salmonis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.552</span>), <span style="font-style: italic;">Serratia proteamaculans quinovora</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.545</span>),</span></span>
|
||||
<span><span class="co">#> <span style="font-style: italic;">Streptococcus pseudoporcinus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.536</span>), <span style="font-style: italic;">Staphylococcus piscifermentans</span></span></span>
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||||
<span><span class="co"><span style="color: #0000BB;">#> (</span><span style="color: #080808; background-color: #FF5F5F;">0.533</span>), <span style="font-style: italic;">Staphylococcus pseudintermedius</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.532</span>), <span style="font-style: italic;">Serratia</span></span></span>
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<span><span class="co"><span style="font-style: italic;">#> proteamaculans proteamaculans</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.526</span>), <span style="font-style: italic;">Streptococcus gallolyticus</span></span></span>
|
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<span><span class="co"><span style="font-style: italic;">#> pasteurianus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.526</span>), <span style="font-style: italic;">Salmonella</span> Portanigra<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.524</span>), and <span style="font-style: italic;">Streptococcus</span></span></span>
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<span><span class="co"><span style="font-style: italic;">#> periodonticum</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.519</span>)</span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co"><span style="color: #0000BB;">#> Only the first 10 other matches of each record are shown. Run</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> `print(mo_uncertainties(), n = ...)` to view more entries, or save</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> `mo_uncertainties()` to an object.</span></span></span></code></pre></div>
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<span><span class="co">#> Matching scores are based on the resemblance between the input and the full</span></span>
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<span><span class="co">#> taxonomic name, and the pathogenicity in humans. See `mo_matching_score()`</span></span>
|
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<span><span class="co">#> (`?AMR::mo_matching_score()`).</span></span>
|
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<span><span class="co">#> Colour keys: <span style="color: #080808; background-color: #FF5F5F;"> 0.000-0.549 </span><span style="color: #080808; background-color: #FFD787;"> 0.550-0.649 </span><span style="color: #080808; background-color: #FFFF87;"> 0.650-0.749 </span><span style="color: #080808; background-color: #5FD7AF;"> 0.750-1.000 </span></span></span>
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<span><span class="co">#> <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
|
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<span><span class="co">#> <span style="color: #0000BB;">"E. coli"</span> -> <span style="font-weight: bold; font-style: italic;">Escherichia coli</span> (B_ESCHR_COLI, <span style="color: #080808; background-color: #FFFF87;">0.688</span>)</span></span>
|
||||
<span><span class="co">#> Also matched: <span style="font-style: italic;">Enterococcus crotali</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.650</span>), <span style="font-style: italic;">Escherichia coli coli</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.643</span>),</span></span>
|
||||
<span><span class="co">#> <span style="font-style: italic;">Escherichia coli expressing</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.611</span>), <span style="font-style: italic;">Enterobacter cowanii</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.600</span>), <span style="font-style: italic;">Enterococcus</span></span></span>
|
||||
<span><span class="co">#> <span style="font-style: italic;">columbae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.595</span>), <span style="font-style: italic;">Enterococcus camelliae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.591</span>), <span style="font-style: italic;">Enterococcus casseliflavus</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.577</span>), <span style="font-style: italic;">Enterobacter cloacae cloacae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), <span style="font-style: italic;">Enterobacter cloacae</span> complex</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), and <span style="font-style: italic;">Enterobacter cloacae dissolvens</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.565</span>)</span></span>
|
||||
<span><span class="co">#> <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">"K. pneumoniae"</span> -> <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">#> 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 pneumoniae</span></span></span>
|
||||
<span><span class="co">#> <span style="font-style: italic;">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 style="font-style: italic;">Klebsiella</span></span></span>
|
||||
<span><span class="co">#> <span style="font-style: italic;">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 style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.500</span>), <span style="font-style: italic;">Klebsiella</span></span></span>
|
||||
<span><span class="co">#> <span style="font-style: italic;">planticola</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.500</span>), <span style="font-style: italic;">Kingella potus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.400</span>), <span style="font-style: italic;">Kluyveromyces pseudotropicale</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FF5F5F;">0.386</span>), <span style="font-style: italic;">Kluyveromyces pseudotropicalis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.363</span>), and <span style="font-style: italic;">Kosakonia pseudosacchari</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FF5F5F;">0.361</span>)</span></span>
|
||||
<span><span class="co">#> <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">"S. aureus"</span> -> <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">#> 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 argenteus</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.625</span>), <span style="font-style: italic;">Staphylococcus aureus anaerobius</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.625</span>), <span style="font-style: italic;">Staphylococcus auricularis</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.615</span>), <span style="font-style: italic;">Salmonella</span> Aurelianis<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.595</span>), <span style="font-style: italic;">Salmonella</span> Aarhus<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.588</span>), <span style="font-style: italic;">Salmonella</span></span></span>
|
||||
<span><span class="co">#> Amounderness<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.587</span>), <span style="font-style: italic;">Staphylococcus argensis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.587</span>), <span style="font-style: italic;">Streptococcus australis</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.587</span>), and <span style="font-style: italic;">Salmonella choleraesuis arizonae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.562</span>)</span></span>
|
||||
<span><span class="co">#> <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">"S. pneumoniae"</span> -> <span style="font-weight: bold; font-style: italic;">Streptococcus pneumoniae</span> (B_STRPT_PNMN, <span style="color: #080808; background-color: #5FD7AF;">0.750</span>)</span></span>
|
||||
<span><span class="co">#> Also matched: <span style="font-style: italic;">Streptococcus pseudopneumoniae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.700</span>), <span style="font-style: italic;">Streptococcus phocae</span></span></span>
|
||||
<span><span class="co">#> <span style="font-style: italic;">salmonis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.552</span>), <span style="font-style: italic;">Serratia proteamaculans quinovora</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.545</span>), <span style="font-style: italic;">Streptococcus</span></span></span>
|
||||
<span><span class="co">#> <span style="font-style: italic;">pseudoporcinus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.536</span>), <span style="font-style: italic;">Staphylococcus piscifermentans</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.533</span>), <span style="font-style: italic;">Staphylococcus</span></span></span>
|
||||
<span><span class="co">#> <span style="font-style: italic;">pseudintermedius</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.532</span>), <span style="font-style: italic;">Serratia proteamaculans proteamaculans</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.526</span>),</span></span>
|
||||
<span><span class="co">#> <span style="font-style: italic;">Streptococcus gallolyticus pasteurianus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.526</span>), <span style="font-style: italic;">Salmonella</span> Portanigra<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.524</span>),</span></span>
|
||||
<span><span class="co">#> and <span style="font-style: italic;">Streptococcus periodonticum</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.519</span>)</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Only the first 10 other matches of each record are shown. Run</span></span>
|
||||
<span><span class="co">#> `print(mo_uncertainties(), n = ...)` (`?AMR::mo_uncertainties()`) to view</span></span>
|
||||
<span><span class="co">#> more entries, or save `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to an</span></span>
|
||||
<span><span class="co">#> object.</span></span></code></pre></div>
|
||||
<p>That’s all good.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
@@ -399,16 +397,15 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #BB0000;">ℹ Determining first isolates using an episode length of </span><span style="color: #BB0000; font-weight: bold;">365 days</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">' as input for `col_mo`.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">first</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> it seems to be cefozopran (ZOP)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">date</span><span style="color: #0000BB;">' as input for `col_date`.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">patient_id</span><span style="color: #0000BB;">' as input for `col_patient_id`.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span></span>
|
||||
<span><span class="co"><span style="color: #BB0000;">#> of 2</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BBBBBB;">=> Found </span><span style="color: #BBBBBB; font-weight: bold;">2,724 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (90.8% of total where a</span></span></span>
|
||||
<span><span class="co"><span style="color: #BBBBBB;">#> microbial ID was available)</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Determining first isolates using an episode length of <span style="font-weight: bold;">365 days</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">bacteria</span>' as input for `col_mo`.</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Column '<span style="font-weight: bold;">first</span>' is SIR eligible (despite only having empty values), since it</span></span>
|
||||
<span><span class="co">#> seems to be cefozopran (ZOP)</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">date</span>' as input for `col_date`.</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">patient_id</span>' as input for `col_patient_id`.</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Basing inclusion on all antimicrobial results, using a points threshold of 2</span></span>
|
||||
<span><span class="co">#> => Found <span style="font-weight: bold;">2,724 'phenotype-based' first isolates</span> (90.8% of total where a</span></span>
|
||||
<span><span class="co">#> microbial ID was available)</span></span></code></pre></div>
|
||||
<p>So only 91% 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>
|
||||
@@ -525,7 +522,7 @@ in:</p>
|
||||
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<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="va">date</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For `aminoglycosides()` using column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using column '<span style="font-weight: bold;">GEN</span>' (gentamicin)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 2</span></span></span>
|
||||
<span><span class="co">#> date GEN </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||||
@@ -543,8 +540,8 @@ in:</p>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<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="va">bacteria</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For `betalactams()` using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (amoxicillin/clavulanic acid)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">AMX</span>' (amoxicillin) and '<span style="font-weight: bold;">AMC</span>'</span></span>
|
||||
<span><span class="co">#> (amoxicillin/clavulanic acid)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 3</span></span></span>
|
||||
<span><span class="co">#> bacteria AMX AMC </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||||
@@ -580,7 +577,7 @@ in:</p>
|
||||
<span><span class="co"># filtering using AB selectors is also possible:</span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<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="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For `aminoglycosides()` using column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using column '<span style="font-weight: bold;">GEN</span>' (gentamicin)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 981 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <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;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
@@ -598,8 +595,8 @@ in:</p>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<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="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For `betalactams()` using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (amoxicillin/clavulanic acid)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">AMX</span>' (amoxicillin) and '<span style="font-weight: bold;">AMC</span>'</span></span>
|
||||
<span><span class="co">#> (amoxicillin/clavulanic acid)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <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;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
@@ -617,8 +614,8 @@ in:</p>
|
||||
<span></span>
|
||||
<span><span class="co"># even works in base R (since R 3.0):</span></span>
|
||||
<span><span class="va">our_data_1st</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For `betalactams()` using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (amoxicillin/clavulanic acid)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">AMX</span>' (amoxicillin) and '<span style="font-weight: bold;">AMC</span>'</span></span>
|
||||
<span><span class="co">#> (amoxicillin/clavulanic acid)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <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;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
@@ -699,9 +696,9 @@ previously mentioned antibiotic class selectors:</p>
|
||||
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||||
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
|
||||
<span><span class="co">#> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="12%">
|
||||
@@ -830,8 +827,8 @@ language to be Spanish using the <code>language</code> argument:</p>
|
||||
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
|
||||
<span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
|
||||
<span> language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
|
||||
<span><span class="co">#> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="15%">
|
||||
@@ -956,9 +953,9 @@ argument must be used. This can be any column in the data, or e.g. an
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||||
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
|
||||
<span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For `carbapenems()` using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
|
||||
<span><span class="co">#> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns '<span style="font-weight: bold;">IPM</span>' (imipenem) and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="10%">
|
||||
@@ -1285,10 +1282,11 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
|
||||
own:</p>
|
||||
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_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">#> <span style="color: #0000BB;">ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span></span>
|
||||
<span><span class="co">#> considers the 'I' category susceptible. Set the `guideline` argument or the</span></span>
|
||||
<span><span class="co">#> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
|
||||
<span><span class="co">#> (`?AMR::AMR-options`).</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
|
||||
<span><span class="co">#> [1] 0.4203377</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>
|
||||
|
||||
108
articles/AMR.md
108
articles/AMR.md
@@ -3,7 +3,7 @@
|
||||
**Note:** values on this page will change with every website update
|
||||
since they are based on randomly created values and the page was written
|
||||
in [R Markdown](https://rmarkdown.rstudio.com/). However, the
|
||||
methodology remains unchanged. This page was generated on 18 March 2026.
|
||||
methodology remains unchanged. This page was generated on 20 March 2026.
|
||||
|
||||
## Introduction
|
||||
|
||||
@@ -51,9 +51,9 @@ structure of your data generally look like this:
|
||||
|
||||
| date | patient_id | mo | AMX | CIP |
|
||||
|:----------:|:----------:|:----------------:|:---:|:---:|
|
||||
| 2026-03-18 | abcd | Escherichia coli | S | S |
|
||||
| 2026-03-18 | abcd | Escherichia coli | S | R |
|
||||
| 2026-03-18 | efgh | Escherichia coli | R | S |
|
||||
| 2026-03-20 | abcd | Escherichia coli | S | S |
|
||||
| 2026-03-20 | abcd | Escherichia coli | S | R |
|
||||
| 2026-03-20 | efgh | Escherichia coli | R | S |
|
||||
|
||||
### Needed R packages
|
||||
|
||||
@@ -169,8 +169,9 @@ our_data$bacteria <- as.mo(our_data$bacteria, info = TRUE)
|
||||
#> ℹ Retrieved values from the `microorganisms.codes` data set for "ESCCOL",
|
||||
#> "KLEPNE", "STAAUR", and "STRPNE".
|
||||
#> ℹ Microorganism translation was uncertain for four microorganisms. Run
|
||||
#> `mo_uncertainties()` to review these uncertainties, or use
|
||||
#> `add_custom_microorganisms()` to add custom entries.
|
||||
#> `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to review these
|
||||
#> uncertainties, or use `add_custom_microorganisms()`
|
||||
#> (`?AMR::add_custom_microorganisms()`) to add custom entries.
|
||||
```
|
||||
|
||||
Apparently, there was some uncertainty about the translation to
|
||||
@@ -179,46 +180,43 @@ taxonomic codes. Let’s check this:
|
||||
``` r
|
||||
mo_uncertainties()
|
||||
#> Matching scores are based on the resemblance between the input and the full
|
||||
#> taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.
|
||||
#> taxonomic name, and the pathogenicity in humans. See `mo_matching_score()`
|
||||
#> (`?AMR::mo_matching_score()`).
|
||||
#> Colour keys: 0.000-0.549 0.550-0.649 0.650-0.749 0.750-1.000
|
||||
#>
|
||||
#> --------------------------------------------------------------------------------
|
||||
#> -------------------------------------------------------------------------------
|
||||
#> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)
|
||||
#> Also matched: Enterococcus crotali (0.650), Escherichia coli coli
|
||||
#> (0.643), Escherichia coli expressing (0.611), Enterobacter cowanii
|
||||
#> (0.600), Enterococcus columbae (0.595), Enterococcus camelliae (0.591),
|
||||
#> Enterococcus casseliflavus (0.577), Enterobacter cloacae cloacae
|
||||
#> (0.571), Enterobacter cloacae complex (0.571), and Enterobacter cloacae
|
||||
#> dissolvens (0.565)
|
||||
#> --------------------------------------------------------------------------------
|
||||
#> Also matched: Enterococcus crotali (0.650), Escherichia coli coli (0.643),
|
||||
#> Escherichia coli expressing (0.611), Enterobacter cowanii (0.600), Enterococcus
|
||||
#> columbae (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus
|
||||
#> (0.577), Enterobacter cloacae cloacae (0.571), Enterobacter cloacae complex
|
||||
#> (0.571), and Enterobacter cloacae dissolvens (0.565)
|
||||
#> -------------------------------------------------------------------------------
|
||||
#> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)
|
||||
#> Also matched: Klebsiella pneumoniae complex (0.707), Klebsiella
|
||||
#> pneumoniae ozaenae (0.707), Klebsiella pneumoniae pneumoniae (0.688),
|
||||
#> Klebsiella pneumoniae rhinoscleromatis (0.658), Klebsiella pasteurii
|
||||
#> (0.500), Klebsiella planticola (0.500), Kingella potus (0.400),
|
||||
#> Kluyveromyces pseudotropicale (0.386), Kluyveromyces pseudotropicalis
|
||||
#> (0.363), and Kosakonia pseudosacchari (0.361)
|
||||
#> --------------------------------------------------------------------------------
|
||||
#> Also matched: Klebsiella pneumoniae complex (0.707), Klebsiella pneumoniae
|
||||
#> ozaenae (0.707), Klebsiella pneumoniae pneumoniae (0.688), Klebsiella
|
||||
#> pneumoniae rhinoscleromatis (0.658), Klebsiella pasteurii (0.500), Klebsiella
|
||||
#> planticola (0.500), Kingella potus (0.400), Kluyveromyces pseudotropicale
|
||||
#> (0.386), Kluyveromyces pseudotropicalis (0.363), and Kosakonia pseudosacchari
|
||||
#> (0.361)
|
||||
#> -------------------------------------------------------------------------------
|
||||
#> "S. aureus" -> Staphylococcus aureus (B_STPHY_AURS, 0.690)
|
||||
#> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus
|
||||
#> argenteus (0.625), Staphylococcus aureus anaerobius (0.625),
|
||||
#> Staphylococcus auricularis (0.615), Salmonella Aurelianis (0.595),
|
||||
#> Salmonella Aarhus (0.588), Salmonella Amounderness (0.587),
|
||||
#> Staphylococcus argensis (0.587), Streptococcus australis (0.587), and
|
||||
#> Salmonella choleraesuis arizonae (0.562)
|
||||
#> --------------------------------------------------------------------------------
|
||||
#> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus argenteus
|
||||
#> (0.625), Staphylococcus aureus anaerobius (0.625), Staphylococcus auricularis
|
||||
#> (0.615), Salmonella Aurelianis (0.595), Salmonella Aarhus (0.588), Salmonella
|
||||
#> Amounderness (0.587), Staphylococcus argensis (0.587), Streptococcus australis
|
||||
#> (0.587), and Salmonella choleraesuis arizonae (0.562)
|
||||
#> -------------------------------------------------------------------------------
|
||||
#> "S. pneumoniae" -> Streptococcus pneumoniae (B_STRPT_PNMN, 0.750)
|
||||
#> Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus
|
||||
#> phocae salmonis (0.552), Serratia proteamaculans quinovora (0.545),
|
||||
#> Streptococcus pseudoporcinus (0.536), Staphylococcus piscifermentans
|
||||
#> (0.533), Staphylococcus pseudintermedius (0.532), Serratia
|
||||
#> proteamaculans proteamaculans (0.526), Streptococcus gallolyticus
|
||||
#> pasteurianus (0.526), Salmonella Portanigra (0.524), and Streptococcus
|
||||
#> periodonticum (0.519)
|
||||
#>
|
||||
#> Only the first 10 other matches of each record are shown. Run
|
||||
#> `print(mo_uncertainties(), n = ...)` to view more entries, or save
|
||||
#> `mo_uncertainties()` to an object.
|
||||
#> Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus phocae
|
||||
#> salmonis (0.552), Serratia proteamaculans quinovora (0.545), Streptococcus
|
||||
#> pseudoporcinus (0.536), Staphylococcus piscifermentans (0.533), Staphylococcus
|
||||
#> pseudintermedius (0.532), Serratia proteamaculans proteamaculans (0.526),
|
||||
#> Streptococcus gallolyticus pasteurianus (0.526), Salmonella Portanigra (0.524),
|
||||
#> and Streptococcus periodonticum (0.519)
|
||||
#> ℹ Only the first 10 other matches of each record are shown. Run
|
||||
#> `print(mo_uncertainties(), n = ...)` (`?AMR::mo_uncertainties()`) to view
|
||||
#> more entries, or save `mo_uncertainties()` (`?AMR::mo_uncertainties()`) to an
|
||||
#> object.
|
||||
```
|
||||
|
||||
That’s all good.
|
||||
@@ -317,14 +315,13 @@ our_data <- our_data %>%
|
||||
mutate(first = first_isolate(info = TRUE))
|
||||
#> ℹ Determining first isolates using an episode length of 365 days
|
||||
#> ℹ Using column 'bacteria' as input for `col_mo`.
|
||||
#> ℹ Column 'first' is SIR eligible (despite only having empty values), since
|
||||
#> it seems to be cefozopran (ZOP)
|
||||
#> ℹ Column 'first' is SIR eligible (despite only having empty values), since it
|
||||
#> seems to be cefozopran (ZOP)
|
||||
#> ℹ Using column 'date' as input for `col_date`.
|
||||
#> ℹ Using column 'patient_id' as input for `col_patient_id`.
|
||||
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold
|
||||
#> of 2
|
||||
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
|
||||
#> => Found 2,724 'phenotype-based' first isolates (90.8% of total where a
|
||||
#> microbial ID was available)
|
||||
#> microbial ID was available)
|
||||
```
|
||||
|
||||
So only 91% is suitable for resistance analysis! We can now filter on it
|
||||
@@ -628,8 +625,8 @@ antibiotic class selectors:
|
||||
``` r
|
||||
antibiogram(example_isolates,
|
||||
antibiotics = c(aminoglycosides(), carbapenems()))
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
```
|
||||
|
||||
@@ -667,8 +664,8 @@ antibiogram(example_isolates,
|
||||
antibiotics = aminoglycosides(),
|
||||
ab_transform = "name",
|
||||
language = "es")
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
```
|
||||
|
||||
| Patógeno | Amikacina | Gentamicina | Kanamicina | Tobramicina |
|
||||
@@ -711,8 +708,8 @@ on certain columns:
|
||||
antibiogram(example_isolates,
|
||||
antibiotics = c(aminoglycosides(), carbapenems()),
|
||||
syndromic_group = "ward")
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
```
|
||||
|
||||
@@ -844,9 +841,10 @@ These functions can be used on their own:
|
||||
|
||||
``` r
|
||||
our_data_1st %>% resistance(AMX)
|
||||
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
|
||||
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
|
||||
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
|
||||
#> ℹ `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus
|
||||
#> considers the 'I' category susceptible. Set the `guideline` argument or the
|
||||
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
|
||||
#> (`?AMR::AMR-options`).
|
||||
#> ℹ This message will be shown once per session.
|
||||
#> [1] 0.4203377
|
||||
```
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<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="">3.0.1.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<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="">3.0.1.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
|
||||
@@ -179,14 +179,14 @@ package.</p>
|
||||
<span> mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="co"># drop NAs - the ones without a Gramstain (fungi, etc.)</span></span>
|
||||
<span> <span class="fu">drop_na</span><span class="op">(</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For `betalactams()` using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (piperacillin/tazobactam), '</span><span style="color: #0000BB; font-weight: bold;">CZO</span><span style="color: #0000BB;">' (cefazolin), '</span><span style="color: #0000BB; font-weight: bold;">FEP</span><span style="color: #0000BB;">' (cefepime), '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (cefuroxime), '</span><span style="color: #0000BB; font-weight: bold;">FOX</span><span style="color: #0000BB;">' (cefoxitin), '</span><span style="color: #0000BB; font-weight: bold;">CTX</span><span style="color: #0000BB;">' (cefotaxime), '</span><span style="color: #0000BB; font-weight: bold;">CAZ</span><span style="color: #0000BB;">' (ceftazidime),</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> '</span><span style="color: #0000BB; font-weight: bold;">CRO</span><span style="color: #0000BB;">' (ceftriaxone), '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem), and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
|
||||
<span><span class="co">#> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">PEN</span>' (benzylpenicillin), '<span style="font-weight: bold;">OXA</span>'</span></span>
|
||||
<span><span class="co">#> (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span></span>
|
||||
<span><span class="co">#> (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">TZP</span>'</span></span>
|
||||
<span><span class="co">#> (piperacillin/tazobactam), '<span style="font-weight: bold;">CZO</span>' (cefazolin), '<span style="font-weight: bold;">FEP</span>' (cefepime), '<span style="font-weight: bold;">CXM</span>'</span></span>
|
||||
<span><span class="co">#> (cefuroxime), '<span style="font-weight: bold;">FOX</span>' (cefoxitin), '<span style="font-weight: bold;">CTX</span>' (cefotaxime), '<span style="font-weight: bold;">CAZ</span>' (ceftazidime),</span></span>
|
||||
<span><span class="co">#> '<span style="font-weight: bold;">CRO</span>' (ceftriaxone), '<span style="font-weight: bold;">IPM</span>' (imipenem), and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span></span></code></pre></div>
|
||||
<p><strong>Explanation:</strong></p>
|
||||
<ul>
|
||||
<li>
|
||||
@@ -227,26 +227,37 @@ we have with <code>step_corr()</code>, the necessary parameters can be
|
||||
estimated from a training set using <code>prep()</code>:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu">prep</span><span class="op">(</span><span class="va">resistance_recipe</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ For `betalactams()` using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (piperacillin/tazobactam), '</span><span style="color: #0000BB; font-weight: bold;">CZO</span><span style="color: #0000BB;">' (cefazolin), '</span><span style="color: #0000BB; font-weight: bold;">FEP</span><span style="color: #0000BB;">' (cefepime), '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> (cefuroxime), '</span><span style="color: #0000BB; font-weight: bold;">FOX</span><span style="color: #0000BB;">' (cefoxitin), '</span><span style="color: #0000BB; font-weight: bold;">CTX</span><span style="color: #0000BB;">' (cefotaxime), '</span><span style="color: #0000BB; font-weight: bold;">CAZ</span><span style="color: #0000BB;">' (ceftazidime),</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> '</span><span style="color: #0000BB; font-weight: bold;">CRO</span><span style="color: #0000BB;">' (ceftriaxone), '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem), and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
|
||||
<span><span class="co">#> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">PEN</span>' (benzylpenicillin), '<span style="font-weight: bold;">OXA</span>'</span></span>
|
||||
<span><span class="co">#> (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span></span>
|
||||
<span><span class="co">#> (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">TZP</span>'</span></span>
|
||||
<span><span class="co">#> (piperacillin/tazobactam), '<span style="font-weight: bold;">CZO</span>' (cefazolin), '<span style="font-weight: bold;">FEP</span>' (cefepime), '<span style="font-weight: bold;">CXM</span>'</span></span>
|
||||
<span><span class="co">#> (cefuroxime), '<span style="font-weight: bold;">FOX</span>' (cefoxitin), '<span style="font-weight: bold;">CTX</span>' (cefotaxime), '<span style="font-weight: bold;">CAZ</span>' (ceftazidime),</span></span>
|
||||
<span><span class="co">#> '<span style="font-weight: bold;">CRO</span>' (ceftriaxone), '<span style="font-weight: bold;">IPM</span>' (imipenem), and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Recipe</span> <span style="color: #00BBBB;">──────────────────────────────────────────────────────────────────────</span></span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> ── Inputs</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> ── Inputs </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> Number of variables by role</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> outcome: 1</span></span>
|
||||
<span><span class="co">#> predictor: 20</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> ── Training information</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> ── Training information </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> Training data contained 1968 data points and no incomplete rows.</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> ── Operations</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> ── Operations </span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">•</span> Correlation filter on: <span style="color: #0000BB;">AMX</span> <span style="color: #0000BB;">CTX</span> | <span style="font-style: italic;">Trained</span></span></span></code></pre></div>
|
||||
<p><strong>Explanation:</strong></p>
|
||||
<ul>
|
||||
@@ -737,11 +748,12 @@ into a structured time-series format.</p>
|
||||
<span> .names <span class="op">=</span> <span class="st">"res_{.col}"</span><span class="op">)</span>, </span>
|
||||
<span> .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
|
||||
<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="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMX</span><span class="op">)</span> <span class="op">&</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMC</span><span class="op">)</span> <span class="op">&</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_CIP</span><span class="op">)</span><span class="op">)</span> <span class="co"># Drop missing values</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for `col_mo`.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `col_mo`.</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span></span>
|
||||
<span><span class="co">#> considers the 'I' category susceptible. Set the `guideline` argument or the</span></span>
|
||||
<span><span class="co">#> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
|
||||
<span><span class="co">#> (`?AMR::AMR-options`).</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
|
||||
<span></span>
|
||||
<span><span class="va">data_time</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 32 × 5</span></span></span>
|
||||
|
||||
@@ -94,8 +94,8 @@ data <- example_isolates %>%
|
||||
mo = as.factor(mo_gramstain(mo))) %>%
|
||||
# drop NAs - the ones without a Gramstain (fungi, etc.)
|
||||
drop_na()
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `betalactams()` using columns 'PEN' (benzylpenicillin), 'OXA'
|
||||
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
|
||||
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'
|
||||
@@ -144,8 +144,8 @@ a training set using `prep()`:
|
||||
|
||||
``` r
|
||||
prep(resistance_recipe)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
|
||||
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For `betalactams()` using columns 'PEN' (benzylpenicillin), 'OXA'
|
||||
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
|
||||
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'
|
||||
@@ -153,17 +153,28 @@ prep(resistance_recipe)
|
||||
#> (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),
|
||||
#> 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)
|
||||
#>
|
||||
#>
|
||||
#> ── Recipe ──────────────────────────────────────────────────────────────────────
|
||||
#>
|
||||
#> ── Inputs
|
||||
#>
|
||||
#>
|
||||
#> ── Inputs
|
||||
#>
|
||||
#> Number of variables by role
|
||||
#>
|
||||
#> outcome: 1
|
||||
#> predictor: 20
|
||||
#>
|
||||
#> ── Training information
|
||||
#>
|
||||
#>
|
||||
#> ── Training information
|
||||
#>
|
||||
#> Training data contained 1968 data points and no incomplete rows.
|
||||
#>
|
||||
#> ── Operations
|
||||
#>
|
||||
#>
|
||||
#> ── Operations
|
||||
#>
|
||||
#> • Correlation filter on: AMX CTX | Trained
|
||||
```
|
||||
|
||||
@@ -636,9 +647,10 @@ data_time <- example_isolates %>%
|
||||
.groups = "drop") %>%
|
||||
filter(!is.na(res_AMX) & !is.na(res_AMC) & !is.na(res_CIP)) # Drop missing values
|
||||
#> ℹ Using column 'mo' as input for `col_mo`.
|
||||
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
|
||||
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
|
||||
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
|
||||
#> ℹ `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus
|
||||
#> considers the 'I' category susceptible. Set the `guideline` argument or the
|
||||
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
|
||||
#> (`?AMR::AMR-options`).
|
||||
#> ℹ This message will be shown once per session.
|
||||
|
||||
data_time
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<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="">3.0.1.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<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="">3.0.1.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
|
||||
@@ -163,10 +163,11 @@ per taxonomic order and genus:</p>
|
||||
<span> <span class="va">order</span>, <span class="va">genus</span>, <span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>,</span>
|
||||
<span> <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span></span>
|
||||
<span> <span class="op">)</span> <span class="co"># and select only relevant columns</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span></span>
|
||||
<span><span class="co">#> considers the 'I' category susceptible. Set the `guideline` argument or the</span></span>
|
||||
<span><span class="co">#> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
|
||||
<span><span class="co">#> (`?AMR::AMR-options`).</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
|
||||
<span></span>
|
||||
<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">resistance_data</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 6 × 10</span></span></span>
|
||||
@@ -188,8 +189,8 @@ that contain numeric values in all selected variables, so we now only
|
||||
need to do:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">pca_result</span> <span class="op"><-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ Columns selected for PCA: "</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CAZ</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CTX</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">SXT</span><span style="color: #0000BB;">",</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> "</span><span style="color: #0000BB; font-weight: bold;">TMP</span><span style="color: #0000BB;">", and "</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">". Total observations available: 7.</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Columns selected for PCA: "<span style="font-weight: bold;">AMC</span>", "<span style="font-weight: bold;">CAZ</span>", "<span style="font-weight: bold;">CTX</span>", "<span style="font-weight: bold;">CXM</span>", "<span style="font-weight: bold;">GEN</span>", "<span style="font-weight: bold;">SXT</span>", "<span style="font-weight: bold;">TMP</span>",</span></span>
|
||||
<span><span class="co">#> and "<span style="font-weight: bold;">TOB</span>". Total observations available: 7.</span></span></code></pre></div>
|
||||
<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code>
|
||||
function:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
|
||||
@@ -78,9 +78,10 @@ resistance_data <- example_isolates %>%
|
||||
order, genus, AMC, CXM, CTX,
|
||||
CAZ, GEN, TOB, TMP, SXT
|
||||
) # and select only relevant columns
|
||||
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
|
||||
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
|
||||
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
|
||||
#> ℹ `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus
|
||||
#> considers the 'I' category susceptible. Set the `guideline` argument or the
|
||||
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
|
||||
#> (`?AMR::AMR-options`).
|
||||
#> ℹ This message will be shown once per session.
|
||||
|
||||
head(resistance_data)
|
||||
@@ -104,8 +105,8 @@ variables, so we now only need to do:
|
||||
|
||||
``` r
|
||||
pca_result <- pca(resistance_data)
|
||||
#> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT",
|
||||
#> "TMP", and "TOB". Total observations available: 7.
|
||||
#> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP",
|
||||
#> and "TOB". Total observations available: 7.
|
||||
```
|
||||
|
||||
The result can be reviewed with the good old
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<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="">3.0.1.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
|
||||
@@ -255,10 +255,11 @@ Longest: 40</p>
|
||||
<code class="sourceCode R"><span><span class="co"># our transformed antibiotic columns</span></span>
|
||||
<span><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></span>
|
||||
<span><span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">AMC_ND2</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> 'I' category susceptible. Set the `guideline` argument or the</span></span></span>
|
||||
<span><span class="co"><span style="color: #0000BB;">#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> `susceptibility()` (`?AMR::susceptibility()`) assumes the EUCAST guideline</span></span>
|
||||
<span><span class="co">#> and thus considers the 'I' category susceptible. Set the `guideline` argument</span></span>
|
||||
<span><span class="co">#> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
|
||||
<span><span class="co">#> (`?AMR::AMR-options`).</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: factor > ordered > sir (numeric)<br>
|
||||
Length: 500<br>
|
||||
|
||||
@@ -101,9 +101,10 @@ Longest: 40
|
||||
# our transformed antibiotic columns
|
||||
# amoxicillin/clavulanic acid (J01CR02) as an example
|
||||
data %>% freq(AMC_ND2)
|
||||
#> ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the
|
||||
#> 'I' category susceptible. Set the `guideline` argument or the
|
||||
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.
|
||||
#> ℹ `susceptibility()` (`?AMR::susceptibility()`) assumes the EUCAST guideline
|
||||
#> and thus considers the 'I' category susceptible. Set the `guideline` argument
|
||||
#> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
|
||||
#> (`?AMR::AMR-options`).
|
||||
#> ℹ This message will be shown once per session.
|
||||
```
|
||||
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<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="">3.0.1.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
|
||||
|
||||
@@ -30,7 +30,7 @@
|
||||
|
||||
<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="">3.0.1.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
|
||||
@@ -80,7 +80,7 @@
|
||||
<main id="main" class="col-md-9"><div class="page-header">
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">18 March 2026</h4>
|
||||
<h4 data-toc-skip class="date">20 March 2026</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>datasets.Rmd</code></div>
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<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="">3.0.1.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
|
||||
|
||||
Reference in New Issue
Block a user