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dr. M.S. (Matthijs) Berends
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@ -20,7 +20,7 @@
<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="How to determine multi-drug resistance (MDR)">
<meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
</span>
</div>
@ -247,9 +247,6 @@
<span class="kw">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/mdro.html">mdro</a></span>() <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>() <span class="co"># show frequency table of the result</span>
<span class="co"># NOTE: Using column `mo` as input for `col_mo`.</span>
<span class="co"># NOTE: Auto-guessing columns suitable for analysis...OK.</span>
<span class="co"># NOTE: Reliability would be improved if these antimicrobial results would be available too: ceftaroline (CPT), fusidic acid (FUS), telavancin (TLV), daptomycin (DAP), quinupristin/dalfopristin (QDA), minocycline (MNO), gentamicin-high (GEH), streptomycin-high (STH), doripenem (DOR), levofloxacin (LVX), netilmicin (NET), ticarcillin/clavulanic acid (TCC), ertapenem (ETP), cefotetan (CTT), aztreonam (ATM), ampicillin/sulbactam (SAM), polymyxin B (PLB)</span>
<span class="co"># Warning in mdro(.): NA introduced for isolates where the available percentage of</span>
<span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span>
</pre></div>
@ -257,7 +254,7 @@
<p>Class: factor &gt; ordered (numeric)<br>
Length: 2,000<br>
Levels: 4: Negative &lt; Multi-drug-resistant (MDR) &lt; Extensively drug-resistant …<br>
Available: 1,711 (85.55%, NA: 289 = 14.45%)<br>
Available: 1,747 (87.35%, NA: 253 = 12.65%)<br>
Unique: 2</p>
<table class="table">
<thead><tr class="header">
@ -272,17 +269,17 @@ Unique: 2</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Negative</td>
<td align="right">1595</td>
<td align="right">93.22%</td>
<td align="right">1595</td>
<td align="right">93.22%</td>
<td align="right">1616</td>
<td align="right">92.50%</td>
<td align="right">1616</td>
<td align="right">92.50%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Multi-drug-resistant (MDR)</td>
<td align="right">116</td>
<td align="right">6.78%</td>
<td align="right">1711</td>
<td align="right">131</td>
<td align="right">7.50%</td>
<td align="right">1747</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -320,18 +317,18 @@ Unique: 2</p>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="kw">my_TB_data</span>)
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 S R S S R S</span>
<span class="co"># 2 S R R S R S</span>
<span class="co"># 3 S R R S S R</span>
<span class="co"># 4 R R S S S R</span>
<span class="co"># 5 I S I S S S</span>
<span class="co"># 6 S S R R S S</span>
<span class="co"># 1 I R S R R S</span>
<span class="co"># 2 R R S S S R</span>
<span class="co"># 3 S S R S S S</span>
<span class="co"># 4 R R R S R R</span>
<span class="co"># 5 S R S R R S</span>
<span class="co"># 6 S S R R R S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 R</span>
<span class="co"># 2 I</span>
<span class="co"># 3 S</span>
<span class="co"># 1 I</span>
<span class="co"># 2 R</span>
<span class="co"># 3 R</span>
<span class="co"># 4 R</span>
<span class="co"># 5 S</span>
<span class="co"># 5 R</span>
<span class="co"># 6 S</span>
</pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
@ -342,8 +339,6 @@ Unique: 2</p>
<div class="sourceCode" id="cb7"><pre class="downlit">
<span class="kw">my_TB_data</span><span class="op">$</span><span class="kw">mdr</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span>(<span class="kw">my_TB_data</span>)
<span class="co"># NOTE: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span>
<span class="co"># NOTE: Auto-guessing columns suitable for analysis...OK.</span>
<span class="co"># NOTE: Reliability would be improved if these antimicrobial results would be available too: capreomycin (CAP), rifabutin (RIB), rifapentine (RFP)</span>
</pre></div>
<p>Create a frequency table of the results:</p>
<div class="sourceCode" id="cb8"><pre class="downlit">
@ -368,40 +363,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3297</td>
<td align="right">65.94%</td>
<td align="right">3297</td>
<td align="right">65.94%</td>
<td align="right">3235</td>
<td align="right">64.70%</td>
<td align="right">3235</td>
<td align="right">64.70%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">614</td>
<td align="right">12.28%</td>
<td align="right">3911</td>
<td align="right">78.22%</td>
<td align="left">Negative</td>
<td align="right">657</td>
<td align="right">13.14%</td>
<td align="right">3892</td>
<td align="right">77.84%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Negative</td>
<td align="right">603</td>
<td align="right">12.06%</td>
<td align="right">4514</td>
<td align="right">90.28%</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">595</td>
<td align="right">11.90%</td>
<td align="right">4487</td>
<td align="right">89.74%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">278</td>
<td align="right">5.56%</td>
<td align="right">4792</td>
<td align="right">95.84%</td>
<td align="right">306</td>
<td align="right">6.12%</td>
<td align="right">4793</td>
<td align="right">95.86%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">208</td>
<td align="right">4.16%</td>
<td align="right">207</td>
<td align="right">4.14%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>