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dr. M.S. (Matthijs) Berends
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@ -41,7 +41,7 @@
</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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 November 2019</h4>
<h4 class="date">10 November 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -237,7 +237,7 @@ The German national guideline - Mueller et al. (2015) Antimicrobial Resistance a
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Auto-guessing columns suitable for analysis...OK.</span></a>
<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Reliability will be improved if these antimicrobial results would be available too: SAM (ampicillin/sulbactam), ATM (aztreonam), CTT (cefotetan), CPT (ceftaroline), DAP (daptomycin), DOR (doripenem), ETP (ertapenem), FUS (fusidic acid), GEH (gentamicin-high), LVX (levofloxacin), MNO (minocycline), NET (netilmicin), PLB (polymyxin B), QDA (quinupristin/dalfopristin), STH (streptomycin-high), TLV (telavancin), TCC (ticarcillin/clavulanic acid)</span></a>
<a class="sourceLine" id="cb2-7" data-line-number="7"><span class="co"># Table 1 - S. aureus ... OK</span></a>
<a class="sourceLine" id="cb2-7" data-line-number="7"><span class="co"># Table 1 - Staphylococcus aureus ... OK</span></a>
<a class="sourceLine" id="cb2-8" data-line-number="8"><span class="co"># Table 2 - Enterococcus spp. ... OK</span></a>
<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="co"># Table 3 - Enterobacteriaceae ... OK</span></a>
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co"># Table 4 - Pseudomonas aeruginosa ... OK</span></a>
@ -306,19 +306,19 @@ Unique: 2</p>
<p>The data set now looks like this:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co"># 1 S S R R S R</span></a>
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co"># 2 S R S S R S</span></a>
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="co"># 3 R S R S R R</span></a>
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># 4 S S R S S I</span></a>
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># 5 R R S R S S</span></a>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># 6 S S R R R S</span></a>
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co"># 1 S R S R I R</span></a>
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co"># 2 I S R I R R</span></a>
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="co"># 3 S R S S S R</span></a>
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># 4 R S S S R S</span></a>
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># 5 S S S S I R</span></a>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># 6 I S R I S S</span></a>
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># 1 S</span></a>
<a class="sourceLine" id="cb5-11" data-line-number="11"><span class="co"># 2 S</span></a>
<a class="sourceLine" id="cb5-11" data-line-number="11"><span class="co"># 2 R</span></a>
<a class="sourceLine" id="cb5-12" data-line-number="12"><span class="co"># 3 R</span></a>
<a class="sourceLine" id="cb5-13" data-line-number="13"><span class="co"># 4 R</span></a>
<a class="sourceLine" id="cb5-13" data-line-number="13"><span class="co"># 4 S</span></a>
<a class="sourceLine" id="cb5-14" data-line-number="14"><span class="co"># 5 S</span></a>
<a class="sourceLine" id="cb5-15" data-line-number="15"><span class="co"># 6 R</span></a></code></pre></div>
<a class="sourceLine" id="cb5-15" data-line-number="15"><span class="co"># 6 S</span></a></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="../reference/mdro.html">mdro</a></span>(my_TB_data, <span class="dt">guideline =</span> <span class="st">"TB"</span>)</a></code></pre></div>
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
@ -335,7 +335,7 @@ Unique: 2</p>
<a class="sourceLine" id="cb7-11" data-line-number="11"><span class="co"># Author: WHO (World Health Organization)</span></a>
<a class="sourceLine" id="cb7-12" data-line-number="12"><span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
<a class="sourceLine" id="cb7-13" data-line-number="13"><span class="co"># </span></a>
<a class="sourceLine" id="cb7-14" data-line-number="14"><span class="co"># =&gt; Found 4371 MDROs out of 5000 tested isolates (87.4%)</span></a></code></pre></div>
<a class="sourceLine" id="cb7-14" data-line-number="14"><span class="co"># =&gt; Found 4320 MDROs out of 5000 tested isolates (86.4%)</span></a></code></pre></div>
<p>Create a frequency table of the results:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
@ -356,40 +356,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3301</td>
<td align="right">66.02%</td>
<td align="right">3301</td>
<td align="right">66.02%</td>
<td align="right">3243</td>
<td align="right">64.86%</td>
<td align="right">3243</td>
<td align="right">64.86%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">629</td>
<td align="right">12.58%</td>
<td align="right">3930</td>
<td align="right">78.60%</td>
<td align="right">680</td>
<td align="right">13.60%</td>
<td align="right">3923</td>
<td align="right">78.46%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">596</td>
<td align="right">11.92%</td>
<td align="right">4526</td>
<td align="right">90.52%</td>
<td align="right">587</td>
<td align="right">11.74%</td>
<td align="right">4510</td>
<td align="right">90.20%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">282</td>
<td align="right">5.64%</td>
<td align="right">4808</td>
<td align="right">96.16%</td>
<td align="right">302</td>
<td align="right">6.04%</td>
<td align="right">4812</td>
<td align="right">96.24%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">192</td>
<td align="right">3.84%</td>
<td align="right">188</td>
<td align="right">3.76%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>