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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="">3.0.1.9038</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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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@@ -147,16 +147,16 @@ package.</p>
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<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span>
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<span><span class="co">#> date patient age gender ward mo PEN OXA FLC AMX </span></span>
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<span><span class="co">#> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <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;"><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></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span></span>
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<span><span class="co">#> <span style="color: #949494;"># ℹ 1,990 more rows</span></span></span>
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<span><span class="co">#> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span></span>
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<span><span class="co">#> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span></span>
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@@ -179,9 +179,9 @@ package.</p>
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<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>
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<span> <span class="co"># drop NAs - the ones without a Gramstain (fungi, etc.)</span></span>
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<span> <span class="fu">drop_na</span><span class="op">(</span><span class="op">)</span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span></span>
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<span><span class="co">#> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `?betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span>
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<span><span class="co">#> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span></span>
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<span><span class="co">#> <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span></span>
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<span><span class="co">#> <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam), <span style="color: #00BB00; font-weight: bold;">CZO</span> (cefazolin), <span style="color: #00BB00; font-weight: bold;">FEP</span></span></span>
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<span><span class="co">#> (cefepime), <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime), <span style="color: #00BB00; font-weight: bold;">FOX</span> (cefoxitin), <span style="color: #00BB00; font-weight: bold;">CTX</span> (cefotaxime), <span style="color: #00BB00; font-weight: bold;">CAZ</span></span></span>
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@@ -226,9 +226,9 @@ we have with <code>step_corr()</code>, the necessary parameters can be
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estimated from a training set using <code>prep()</code>:</p>
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<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
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<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>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `?aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin),</span></span>
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<span><span class="co">#> <span style="color: #00BB00; font-weight: bold;">AMK</span> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `?betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span>
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<span><span class="co">#> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">PEN</span> (benzylpenicillin), <span style="color: #00BB00; font-weight: bold;">OXA</span> (oxacillin),</span></span>
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<span><span class="co">#> <span style="color: #00BB00; font-weight: bold;">FLC</span> (flucloxacillin), <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin), <span style="color: #00BB00; font-weight: bold;">AMC</span> (amoxicillin/clavulanic acid),</span></span>
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<span><span class="co">#> <span style="color: #00BB00; font-weight: bold;">AMP</span> (ampicillin), <span style="color: #00BB00; font-weight: bold;">TZP</span> (piperacillin/tazobactam), <span style="color: #00BB00; font-weight: bold;">CZO</span> (cefazolin), <span style="color: #00BB00; font-weight: bold;">FEP</span></span></span>
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<span><span class="co">#> (cefepime), <span style="color: #00BB00; font-weight: bold;">CXM</span> (cefuroxime), <span style="color: #00BB00; font-weight: bold;">FOX</span> (cefoxitin), <span style="color: #00BB00; font-weight: bold;">CTX</span> (cefotaxime), <span style="color: #00BB00; font-weight: bold;">CAZ</span></span></span>
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@@ -482,16 +482,16 @@ package.</p>
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<span><span class="co">#> <span style="color: #949494;"># A tibble: 500 × 19</span></span></span>
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<span><span class="co">#> esbl genus AMC AMP TZP CXM FOX CTX CAZ GEN TOB TMP SXT</span></span>
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<span><span class="co">#> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><mic></span></span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> FALSE Esch… 32 32 4 64 64 8<span style="color: #555555;">.00</span> 8<span style="color: #555555;">.00</span> 1 1 16<span style="color: #555555;">.0</span> 20</span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> FALSE Esch… 32 32 4 64 64 4<span style="color: #555555;">.00</span> 8<span style="color: #555555;">.00</span> 1 1 16<span style="color: #555555;">.0</span> 320</span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> FALSE Esch… 4 2 64 8 4 8<span style="color: #555555;">.00</span> 0.12 16 16 0.5 20</span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> FALSE Kleb… 32 32 16 64 64 8<span style="color: #555555;">.00</span> 8<span style="color: #555555;">.00</span> 1 1 0.5 20</span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> FALSE Esch… 32 32 4 4 4 0.25 2<span style="color: #555555;">.00</span> 1 1 16<span style="color: #555555;">.0</span> 320</span></span>
|
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<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> FALSE Citr… 32 32 16 64 64 64<span style="color: #555555;">.00</span> 32<span style="color: #555555;">.00</span> 1 1 0.5 20</span></span>
|
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<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> FALSE Morg… 32 32 4 64 64 16<span style="color: #555555;">.00</span> 2<span style="color: #555555;">.00</span> 1 1 0.5 20</span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> FALSE Prot… 16 32 4 1 4 8<span style="color: #555555;">.00</span> 0.12 1 1 16<span style="color: #555555;">.0</span> 320</span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> FALSE Ente… 32 32 8 64 64 32<span style="color: #555555;">.00</span> 4<span style="color: #555555;">.00</span> 1 1 0.5 20</span></span>
|
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<span><span class="co">#> <span style="color: #BCBCBC;">10</span> FALSE Citr… 32 32 32 64 64 8<span style="color: #555555;">.00</span> 64<span style="color: #555555;">.00</span> 1 1 16<span style="color: #555555;">.0</span> 320</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> FALSE Esch… 32 32 4 64 64 8<span style="color: #949494;">.00</span> 8<span style="color: #949494;">.00</span> 1 1 16<span style="color: #949494;">.0</span> 20</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> FALSE Esch… 32 32 4 64 64 4<span style="color: #949494;">.00</span> 8<span style="color: #949494;">.00</span> 1 1 16<span style="color: #949494;">.0</span> 320</span></span>
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<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> FALSE Esch… 4 2 64 8 4 8<span style="color: #949494;">.00</span> 0.12 16 16 0.5 20</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> FALSE Kleb… 32 32 16 64 64 8<span style="color: #949494;">.00</span> 8<span style="color: #949494;">.00</span> 1 1 0.5 20</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> FALSE Esch… 32 32 4 4 4 0.25 2<span style="color: #949494;">.00</span> 1 1 16<span style="color: #949494;">.0</span> 320</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> FALSE Citr… 32 32 16 64 64 64<span style="color: #949494;">.00</span> 32<span style="color: #949494;">.00</span> 1 1 0.5 20</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> FALSE Morg… 32 32 4 64 64 16<span style="color: #949494;">.00</span> 2<span style="color: #949494;">.00</span> 1 1 0.5 20</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> FALSE Prot… 16 32 4 1 4 8<span style="color: #949494;">.00</span> 0.12 1 1 16<span style="color: #949494;">.0</span> 320</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> FALSE Ente… 32 32 8 64 64 32<span style="color: #949494;">.00</span> 4<span style="color: #949494;">.00</span> 1 1 0.5 20</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> FALSE Citr… 32 32 32 64 64 8<span style="color: #949494;">.00</span> 64<span style="color: #949494;">.00</span> 1 1 16<span style="color: #949494;">.0</span> 320</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 490 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 6 more variables: NIT <mic>, FOS <mic>, CIP <mic>, IPM <mic>, MEM <mic>,</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># COL <mic></span></span></span>
|
||||
@@ -746,10 +746,10 @@ 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">%>%</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: #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()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `col_mo`.</span></span>
|
||||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
|
||||
<span><span class="co">#> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
|
||||
<span><span class="co">#> option to either "CLSI" or "EUCAST", see AMR-options.</span></span>
|
||||
<span><span class="co">#> option to either "CLSI" or "EUCAST", see `?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>
|
||||
|
||||
Reference in New Issue
Block a user