Built site for AMR@2.1.1.9136: 22afd91

articles/MDR.html

@@ -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">
@@ -172,11 +172,11 @@ will help reading it if your console supports colours.</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">custom</span></span>
 <span><span class="co">#&gt; A set of custom MDRO rules:</span></span>
-<span><span class="co">#&gt;   1. If CIP is "R" and age is higher than 60 then: Elderly Type A</span></span>
-<span><span class="co">#&gt;   2. If ERY is "R" and age is higher than 60 then: Elderly Type B</span></span>
-<span><span class="co">#&gt;   3. Otherwise: Negative</span></span>
+<span><span class="co">#&gt;   1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">CIP</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #080808;"> is higher than </span><span style="color: #0000BB;">60</span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Elderly Type A</span></span></span>
+<span><span class="co">#&gt;   2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">ERY</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #080808;"> is higher than </span><span style="color: #0000BB;">60</span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Elderly Type B</span></span></span>
+<span><span class="co">#&gt;   3. <span style="font-weight: bold;">Otherwise: </span><span style="color: #BB0000;">Negative</span></span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; Unmatched rows will return NA.</span></span>
+<span><span class="co">#&gt; Unmatched rows will return <span style="color: #BB0000;">NA</span>.</span></span>
 <span><span class="co">#&gt; Results will be of class 'factor', with ordered levels: Negative &lt; Elderly Type A &lt; Elderly Type B</span></span></code></pre></div>
 <p>The outcome of the function can be used for the
 <code>guideline</code> argument in the <code><a href="../reference/mdro.html">mdro()</a></code> function:</p>
@@ -212,8 +212,8 @@ on this data set, we get:</p>
 <code class="sourceCode R"><span><span class="va">example_isolates</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="../reference/mdro.html">mdro</a></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="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span></span>
-<span><span class="co">#&gt; Warning: in mdro(): NA introduced for isolates where the available percentage of</span></span>
-<span><span class="co">#&gt; antimicrobial classes was below 50% (set with pct_required_classes)</span></span></code></pre></div>
+<span><span class="co">#&gt; Warning: in <span style="background-color: #EEEEEE;">mdro()</span>: NA introduced for isolates where the available percentage of</span></span>
+<span><span class="co">#&gt; antimicrobial classes was below 50% (set with <span style="background-color: #EEEEEE;">pct_required_classes</span>)</span></span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: factor &gt; ordered (numeric)<br>
 Length: 2,000<br>
@@ -307,8 +307,8 @@ use:</p>
 <p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
 <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
-<span><span class="co">#&gt; ℹ No column found as input for col_mo, assuming all rows contain</span></span>
-<span><span class="co">#&gt;   Mycobacterium tuberculosis.</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ No column found as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">col_mo</span><span style="color: #0000BB;">, </span><span style="color: #0000BB; font-weight: bold;">assuming all rows contain</span></span></span>
+<span><span class="co"><span style="color: #0000BB; font-weight: bold;">#&gt;   </span><span style="color: #0000BB; font-weight: bold; font-style: italic;">Mycobacterium tuberculosis</span><span style="color: #0000BB; font-weight: bold;">.</span></span></span></code></pre></div>
 <p>Create a frequency table of the results:</p>
 <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></span></code></pre></div>