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(v0.6.1.9044) first_isolate fix for species

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dr. M.S. (Matthijs) Berends
2019-05-31 14:25:11 +02:00
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docs/articles/MDR.html
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@ -40,7 +40,7 @@
</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="Released version">0.6.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
</span>
</div>
@ -199,7 +199,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">28 May 2019</h4>
<h4 class="date">31 May 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -242,19 +242,19 @@
<p>The data set looks like this now:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 S S R R S R</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 R S S S S R</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 S S S S I I</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 S I R I I S</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 S R S R R R</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 R R R R S S</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 R R S R R S</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 I S R R I I</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 S I R R R R</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 S R S R R S</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 S S I S S S</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 R R S S R S</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1 S</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 R</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 R</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1 I</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 S</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 S</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 S</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 R</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6 I</span></a></code></pre></div>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 S</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6 R</span></a></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">my_TB_data<span class="op">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
@ -285,40 +285,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3,214</td>
<td align="right">64.3%</td>
<td align="right">3,214</td>
<td align="right">64.3%</td>
<td align="right">3,232</td>
<td align="right">64.6%</td>
<td align="right">3,232</td>
<td align="right">64.6%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">685</td>
<td align="right">13.7%</td>
<td align="right">3,899</td>
<td align="right">78.0%</td>
<td align="right">693</td>
<td align="right">13.9%</td>
<td align="right">3,925</td>
<td align="right">78.5%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">576</td>
<td align="right">11.5%</td>
<td align="right">4,475</td>
<td align="right">89.5%</td>
<td align="right">603</td>
<td align="right">12.1%</td>
<td align="right">4,528</td>
<td align="right">90.6%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">294</td>
<td align="right">5.9%</td>
<td align="right">4,769</td>
<td align="right">95.4%</td>
<td align="right">276</td>
<td align="right">5.5%</td>
<td align="right">4,804</td>
<td align="right">96.1%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensive drug resistance</td>
<td align="right">231</td>
<td align="right">4.6%</td>
<td align="right">196</td>
<td align="right">3.9%</td>
<td align="right">5,000</td>
<td align="right">100.0%</td>
</tr>