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@ -204,7 +204,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 04 December 2023.</p>
generated on 13 February 2024.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -260,21 +260,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-12-04</td>
<td align="center">2024-02-13</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2023-12-04</td>
<td align="center">2024-02-13</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2023-12-04</td>
<td align="center">2024-02-13</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

2
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@ -401,18 +401,18 @@ 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 S R S I</span></span>
<span><span class="co">#&gt; 2 S S S S R I</span></span>
<span><span class="co">#&gt; 3 S S R S S I</span></span>
<span><span class="co">#&gt; 4 I I R I I I</span></span>
<span><span class="co">#&gt; 5 I I I R I R</span></span>
<span><span class="co">#&gt; 6 R S I R I I</span></span>
<span><span class="co">#&gt; 1 S R S S S S</span></span>
<span><span class="co">#&gt; 2 R S S S I I</span></span>
<span><span class="co">#&gt; 3 I S I R R S</span></span>
<span><span class="co">#&gt; 4 R R S S S S</span></span>
<span><span class="co">#&gt; 5 R R S I R I</span></span>
<span><span class="co">#&gt; 6 I R 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 R</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; 5 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 R</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 6 I</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -454,40 +454,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3252</td>
<td align="right">65.04%</td>
<td align="right">3252</td>
<td align="right">65.04%</td>
<td align="right">3206</td>
<td align="right">64.12%</td>
<td align="right">3206</td>
<td align="right">64.12%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">927</td>
<td align="right">18.54%</td>
<td align="right">4179</td>
<td align="right">83.58%</td>
<td align="right">991</td>
<td align="right">19.82%</td>
<td align="right">4197</td>
<td align="right">83.94%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">475</td>
<td align="right">9.50%</td>
<td align="right">4654</td>
<td align="right">93.08%</td>
<td align="right">434</td>
<td align="right">8.68%</td>
<td align="right">4631</td>
<td align="right">92.62%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">242</td>
<td align="right">4.84%</td>
<td align="right">4896</td>
<td align="right">97.92%</td>
<td align="right">260</td>
<td align="right">5.20%</td>
<td align="right">4891</td>
<td align="right">97.82%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">104</td>
<td align="right">2.08%</td>
<td align="right">109</td>
<td align="right">2.18%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
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@ -193,7 +193,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">04 December 2023</h4>
<h4 data-toc-skip class="date">13 February 2024</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>

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@ -255,7 +255,7 @@ number of observations, the actual observed resistance, the estimated
resistance and the standard error below and above the estimation:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">predict_TZP</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 32 × 7</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 33 × 7</span></span></span>
<span><span class="co">#&gt; year value se_min se_max observations observed estimated</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> <span style="text-decoration: underline;">2</span>002 0.2 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 15 0.2 0.056<span style="text-decoration: underline;">2</span></span></span>
@ -268,7 +268,7 @@ resistance and the standard error below and above the estimation:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> <span style="text-decoration: underline;">2</span>009 0.016<span style="text-decoration: underline;">4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 61 0.016<span style="text-decoration: underline;">4</span> 0.106 </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> <span style="text-decoration: underline;">2</span>010 0.056<span style="text-decoration: underline;">6</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 53 0.056<span style="text-decoration: underline;">6</span> 0.116 </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> <span style="text-decoration: underline;">2</span>011 0.183 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 93 0.183 0.127 </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 22 more rows</span></span></span></code></pre></div>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 23 more rows</span></span></span></code></pre></div>
<p>The function <code>plot</code> is available in base R, and can be
extended by other packages to depend the output based on the type of
input. We extended its function to cope with resistance predictions:</p>

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