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(v1.5.0.9018) fix unit tests

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dr. M.S. (Matthijs) Berends
2021-02-09 12:28:15 +01:00
parent cb404492b2
commit 2dd0656355
24 changed files with 414 additions and 409 deletions
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docs/articles/MDR.html
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@ -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">1.5.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
</span>
</div>
@ -285,7 +285,7 @@
<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: 1,747 (87.35%, NA: 253 = 12.65%)<br>
Available: 1,745 (87.25%, NA: 255 = 12.75%)<br>
Unique: 2</p>
<table class="table">
<thead><tr class="header">
@ -301,16 +301,16 @@ Unique: 2</p>
<td align="left">1</td>
<td align="left">Negative</td>
<td align="right">1617</td>
<td align="right">92.56%</td>
<td align="right">92.66%</td>
<td align="right">1617</td>
<td align="right">92.56%</td>
<td align="right">92.66%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Multi-drug-resistant (MDR)</td>
<td align="right">130</td>
<td align="right">7.44%</td>
<td align="right">1747</td>
<td align="right">128</td>
<td align="right">7.34%</td>
<td align="right">1745</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -339,18 +339,18 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 I R R I I S</span>
<span class="co"># 2 I S R I R R</span>
<span class="co"># 3 S I S I S S</span>
<span class="co"># 4 S R I S S S</span>
<span class="co"># 5 I S I R S S</span>
<span class="co"># 6 S R I R S S</span>
<span class="co"># 1 S R S S S I</span>
<span class="co"># 2 S I R R R R</span>
<span class="co"># 3 R S S I S I</span>
<span class="co"># 4 I S S S I S</span>
<span class="co"># 5 I I I S I R</span>
<span class="co"># 6 S I S R S S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 S</span>
<span class="co"># 2 S</span>
<span class="co"># 1 R</span>
<span class="co"># 2 I</span>
<span class="co"># 3 R</span>
<span class="co"># 4 I</span>
<span class="co"># 5 R</span>
<span class="co"># 4 S</span>
<span class="co"># 5 S</span>
<span class="co"># 6 R</span></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="cb9"><pre class="downlit sourceCode r">
@ -382,40 +382,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3211</td>
<td align="right">64.22%</td>
<td align="right">3211</td>
<td align="right">64.22%</td>
<td align="right">3246</td>
<td align="right">64.92%</td>
<td align="right">3246</td>
<td align="right">64.92%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">990</td>
<td align="right">19.80%</td>
<td align="right">4201</td>
<td align="right">84.02%</td>
<td align="right">976</td>
<td align="right">19.52%</td>
<td align="right">4222</td>
<td align="right">84.44%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">435</td>
<td align="right">8.70%</td>
<td align="right">4636</td>
<td align="right">92.72%</td>
<td align="right">467</td>
<td align="right">9.34%</td>
<td align="right">4689</td>
<td align="right">93.78%</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">4894</td>
<td align="right">97.88%</td>
<td align="right">230</td>
<td align="right">4.60%</td>
<td align="right">4919</td>
<td align="right">98.38%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">106</td>
<td align="right">2.12%</td>
<td align="right">81</td>
<td align="right">1.62%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>