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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="">2.0.0.9022</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -118,28 +118,28 @@
</li>
<li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span>
<span class="fa fa-layer-group"></span>
With other pkgs
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span>
<span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span>
<span class="fa fa-layer-group"></span>
AMR &amp; data.table
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span>
<span class="fa fa-layer-group"></span>
AMR &amp; tidymodels
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span>
<span class="fa fa-layer-group"></span>
AMR &amp; base R
</a>
@ -402,17 +402,17 @@ 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 R R R S S S</span></span>
<span><span class="co">#&gt; 2 S R S S R S</span></span>
<span><span class="co">#&gt; 3 S R I R I I</span></span>
<span><span class="co">#&gt; 4 R I S I S R</span></span>
<span><span class="co">#&gt; 5 S I R I I S</span></span>
<span><span class="co">#&gt; 6 R R I S S I</span></span>
<span><span class="co">#&gt; 1 R S S R R S</span></span>
<span><span class="co">#&gt; 2 R R I I S S</span></span>
<span><span class="co">#&gt; 3 S R S S I S</span></span>
<span><span class="co">#&gt; 4 R R S R R R</span></span>
<span><span class="co">#&gt; 5 I I I S R R</span></span>
<span><span class="co">#&gt; 6 S I R R S R</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 I</span></span>
<span><span class="co">#&gt; 2 I</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 I</span></span>
<span><span class="co">#&gt; 4 S</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 S</span></span>
<span><span class="co">#&gt; 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
@ -455,40 +455,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3180</td>
<td align="right">63.60%</td>
<td align="right">3180</td>
<td align="right">63.60%</td>
<td align="right">3225</td>
<td align="right">64.50%</td>
<td align="right">3225</td>
<td align="right">64.50%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1032</td>
<td align="right">20.64%</td>
<td align="right">4212</td>
<td align="right">84.24%</td>
<td align="right">963</td>
<td align="right">19.26%</td>
<td align="right">4188</td>
<td align="right">83.76%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">462</td>
<td align="right">9.24%</td>
<td align="right">4674</td>
<td align="right">93.48%</td>
<td align="right">478</td>
<td align="right">9.56%</td>
<td align="right">4666</td>
<td align="right">93.32%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">226</td>
<td align="right">4.52%</td>
<td align="right">4900</td>
<td align="right">98.00%</td>
<td align="right">228</td>
<td align="right">4.56%</td>
<td align="right">4894</td>
<td align="right">97.88%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">100</td>
<td align="right">2.00%</td>
<td align="right">106</td>
<td align="right">2.12%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>