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articles/AMR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9003</small>
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@ -38,7 +38,7 @@
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articles/MDR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9003</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9004</small>
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@ -401,19 +401,19 @@ 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 I</span></span>
<span><span class="co">#&gt; 2 S I I I I S</span></span>
<span><span class="co">#&gt; 3 I S R I S R</span></span>
<span><span class="co">#&gt; 4 S S I R S S</span></span>
<span><span class="co">#&gt; 5 I S R R S I</span></span>
<span><span class="co">#&gt; 6 R S I R S R</span></span>
<span><span class="co">#&gt; 1 R I R S R R</span></span>
<span><span class="co">#&gt; 2 R S R R I R</span></span>
<span><span class="co">#&gt; 3 S S R I I I</span></span>
<span><span class="co">#&gt; 4 S R S I R S</span></span>
<span><span class="co">#&gt; 5 I S I S I R</span></span>
<span><span class="co">#&gt; 6 I I I I I R</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 I</span></span>
<span><span class="co">#&gt; 3 I</span></span>
<span><span class="co">#&gt; 1 I</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 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">
@ -454,40 +454,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3207</td>
<td align="right">64.14%</td>
<td align="right">3207</td>
<td align="right">64.14%</td>
<td align="right">3166</td>
<td align="right">63.32%</td>
<td align="right">3166</td>
<td align="right">63.32%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">959</td>
<td align="right">19.18%</td>
<td align="right">4166</td>
<td align="right">83.32%</td>
<td align="right">1004</td>
<td align="right">20.08%</td>
<td align="right">4170</td>
<td align="right">83.40%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">471</td>
<td align="right">9.42%</td>
<td align="right">4637</td>
<td align="right">92.74%</td>
<td align="right">445</td>
<td align="right">8.90%</td>
<td align="right">4615</td>
<td align="right">92.30%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">255</td>
<td align="right">5.10%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
<td align="right">270</td>
<td align="right">5.40%</td>
<td align="right">4885</td>
<td align="right">97.70%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">115</td>
<td align="right">2.30%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

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articles/PCA.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9003</small>
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@ -38,7 +38,7 @@
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articles/datasets.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9003</small>
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@ -274,7 +274,7 @@ International Journal of Systematic and Evolutionary Microbiology, 70,
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on December 11th, 2022.</li>
<li>Public Health Information Network Vocabulary Access and Distribution
System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value
Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link uri">https://phinvads.cdc.gov</a>
Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link uri">https://phinvads.cdc.gov</a>
</li>
</ul>
</div>

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articles/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9003</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9004</small>
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articles/other_pkg.html
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@ -38,7 +38,7 @@
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articles/resistance_predict.html
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@ -38,7 +38,7 @@
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articles/welcome_to_AMR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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