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articles/AMR.html
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@ -39,7 +39,7 @@
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articles/MDR.html
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -402,19 +402,19 @@ 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">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 I S S S S R</span></span>
<span><span class="co">#&gt; 2 I S R R S S</span></span>
<span><span class="co">#&gt; 3 R I R R S I</span></span>
<span><span class="co">#&gt; 4 R R S S R I</span></span>
<span><span class="co">#&gt; 5 R R I S R I</span></span>
<span><span class="co">#&gt; 6 R R R S R S</span></span>
<span><span class="co">#&gt; 1 R S R S R I</span></span>
<span><span class="co">#&gt; 2 R I S I R R</span></span>
<span><span class="co">#&gt; 3 I I R I S I</span></span>
<span><span class="co">#&gt; 4 S I S R I I</span></span>
<span><span class="co">#&gt; 5 I R S R R S</span></span>
<span><span class="co">#&gt; 6 I I R S R I</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 S</span></span>
<span><span class="co">#&gt; 2 S</span></span>
<span><span class="co">#&gt; 3 R</span></span>
<span><span class="co">#&gt; 4 I</span></span>
<span><span class="co">#&gt; 1 R</span></span>
<span><span class="co">#&gt; 2 R</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 I</span></span>
<span><span class="co">#&gt; 6 I</span></span></code></pre></div>
<span><span class="co">#&gt; 6 S</span></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">
@ -455,40 +455,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3232</td>
<td align="right">64.64%</td>
<td align="right">3232</td>
<td align="right">64.64%</td>
<td align="right">3128</td>
<td align="right">62.56%</td>
<td align="right">3128</td>
<td align="right">62.56%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">991</td>
<td align="right">19.82%</td>
<td align="right">4223</td>
<td align="right">84.46%</td>
<td align="right">1033</td>
<td align="right">20.66%</td>
<td align="right">4161</td>
<td align="right">83.22%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">441</td>
<td align="right">8.82%</td>
<td align="right">4664</td>
<td align="right">93.28%</td>
<td align="right">478</td>
<td align="right">9.56%</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">246</td>
<td align="right">4.92%</td>
<td align="right">4910</td>
<td align="right">98.20%</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">90</td>
<td align="right">1.80%</td>
<td align="right">102</td>
<td align="right">2.04%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
articles/PCA.html
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@ -39,7 +39,7 @@
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@ -39,7 +39,7 @@
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@ -39,7 +39,7 @@
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@ -573,10 +573,10 @@ brand names (synonyms) as found on PubChem and Defined Daily Doses
(DDDs) for oral and parenteral administration.</p>
<ul>
<li>
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO
Collaborating Centre for Drug Statistics Methodology</a> (note: this may
not be used for commercial purposes, but is freely available from the
WHO CC website for personal use)</li>
<a href="https://atcddd.fhi.no/atc_ddd_index/" class="external-link">ATC/DDD index from
WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this
may not be used for commercial purposes, but is freely available from
the WHO CC website for personal use)</li>
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
National Library of Medicine</a></li>
<li><a href="https://whonet.org" class="external-link">WHONET software 2019</a></li>
@ -773,10 +773,10 @@ as found on PubChem and Defined Daily Doses (DDDs) for oral and
parenteral administration.</p>
<ul>
<li>
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO
Collaborating Centre for Drug Statistics Methodology</a> (note: this may
not be used for commercial purposes, but is freely available from the
WHO CC website for personal use)</li>
<a href="https://atcddd.fhi.no/atc_ddd_index/" class="external-link">ATC/DDD index from
WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this
may not be used for commercial purposes, but is freely available from
the WHO CC website for personal use)</li>
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
National Library of Medicine</a></li>
<li><a href="https://loinc.org" class="external-link">LOINC (Logical Observation Identifiers

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articles/index.html
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@ -10,7 +10,7 @@
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articles/resistance_predict.html
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