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@@ -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="">3.0.1.9034</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9035</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">
@@ -179,9 +179,9 @@ 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; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`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">#&gt; <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;">#&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: #444444;">`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">#&gt; <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;">#&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>
@@ -227,9 +227,9 @@ 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">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`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">#&gt; <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;">#&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: #444444;">`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">#&gt; <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;">#&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>
@@ -737,10 +737,10 @@ 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">%&gt;%</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">&amp;</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">&amp;</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">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #444444;">`col_mo`</span><span style="color: #0000BB;">.</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ </span><span style="color: #0000BB; background-color: #444444;">`resistance()`</span><span style="color: #0000BB;"> assumes the EUCAST guideline and thus considers the 'I'</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; category susceptible. Set the </span><span style="color: #0000BB; background-color: #444444;">`guideline`</span><span style="color: #0000BB;"> argument or the </span><span style="color: #0000BB; background-color: #444444;">`AMR_guideline`</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; option to either "CLSI" or "EUCAST", see </span><span style="color: #0000BB; background-color: #444444;">`?AMR-options`</span><span style="color: #0000BB;">.</span></span></span>
<span><span class="co">#&gt; <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">#&gt; <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;">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span>
<span></span>
<span><span class="va">data_time</span></span>