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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9135</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9136</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">
@ -162,14 +162,14 @@ 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">%&gt;%</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">#&gt; ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
<span><span class="co">#&gt; (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For betalactams() using columns 'PEN' (benzylpenicillin), 'OXA'</span></span>
<span><span class="co">#&gt; (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'</span></span>
<span><span class="co">#&gt; (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM'</span></span>
<span><span class="co">#&gt; (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),</span></span>
<span><span class="co">#&gt; 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)</span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> 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;">#&gt; (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">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">betalactams()</span><span style="color: #0000BB;"> 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;">#&gt; (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;">#&gt; (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;">#&gt; (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;">#&gt; (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;">#&gt; '</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>
<p><strong>Explanation:</strong></p>
<ul>
<li>
@ -270,14 +270,14 @@ performance.</p>
<span><span class="co"># Fit the workflow to the training data</span></span>
<span><span class="va">fitted_workflow</span> <span class="op">&lt;-</span> <span class="va">resistance_workflow</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">fit</span><span class="op">(</span><span class="va">training_data</span><span class="op">)</span> <span class="co"># Train the model</span></span>
<span><span class="co">#&gt; ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
<span><span class="co">#&gt; (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For betalactams() using columns 'PEN' (benzylpenicillin), 'OXA'</span></span>
<span><span class="co">#&gt; (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span></span>
<span><span class="co">#&gt; (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'</span></span>
<span><span class="co">#&gt; (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM'</span></span>
<span><span class="co">#&gt; (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),</span></span>
<span><span class="co">#&gt; 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)</span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> 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;">#&gt; (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">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">betalactams()</span><span style="color: #0000BB;"> 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;">#&gt; (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;">#&gt; (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;">#&gt; (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;">#&gt; (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;">#&gt; '</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>
<p><strong>Explanation:</strong></p>
<ul>
<li>