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@ -15,7 +15,7 @@
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@ -38,7 +38,7 @@
<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="">1.8.2.9052</small>
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@ -299,8 +299,8 @@ 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"># Warning: in `mdro()`: NA introduced for isolates where the available percentage of</span></span>
<span><span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></span></code></pre></div>
<span><span class="co"># Warning: in mdro(): NA introduced for isolates where the available percentage of</span></span>
<span><span class="co"># antimicrobial classes was below 50% (set with pct_required_classes)</span></span></code></pre></div>
<p>(16 isolates had no test results)</p>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
@ -375,17 +375,17 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S R S I S R</span></span>
<span><span class="co"># 2 R I R S R I</span></span>
<span><span class="co"># 3 S I S R S I</span></span>
<span><span class="co"># 4 I I I I R R</span></span>
<span><span class="co"># 5 S I R S I I</span></span>
<span><span class="co"># 6 R R S S R I</span></span>
<span><span class="co"># 1 S I S I R R</span></span>
<span><span class="co"># 2 S R I S R S</span></span>
<span><span class="co"># 3 I S R I R R</span></span>
<span><span class="co"># 4 S S S S I R</span></span>
<span><span class="co"># 5 R S I R R S</span></span>
<span><span class="co"># 6 R R R I R S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
@ -395,7 +395,7 @@ 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"># ℹ No column found as input for `col_mo`, assuming all rows contain</span></span>
<span><span class="co"># ℹ No column found as input for col_mo, assuming all rows contain</span></span>
<span><span class="co"># Mycobacterium tuberculosis.</span></span></code></pre></div>
<p>Create a frequency table of the results:</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3220</td>
<td align="right">64.40%</td>
<td align="right">3220</td>
<td align="right">64.40%</td>
<td align="right">3125</td>
<td align="right">62.50%</td>
<td align="right">3125</td>
<td align="right">62.50%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1018</td>
<td align="right">20.36%</td>
<td align="right">4238</td>
<td align="right">84.76%</td>
<td align="right">1008</td>
<td align="right">20.16%</td>
<td align="right">4133</td>
<td align="right">82.66%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">403</td>
<td align="right">8.06%</td>
<td align="right">4641</td>
<td align="right">92.82%</td>
<td align="right">506</td>
<td align="right">10.12%</td>
<td align="right">4639</td>
<td align="right">92.78%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">258</td>
<td align="right">5.16%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
<td align="right">259</td>
<td align="right">5.18%</td>
<td align="right">4898</td>
<td align="right">97.96%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">101</td>
<td align="right">2.02%</td>
<td align="right">102</td>
<td align="right">2.04%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>