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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="">2.0.0</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9002</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">
@ -187,7 +187,7 @@
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 12 March 2023.</p>
generated on 14 March 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -243,21 +243,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-03-12</td>
<td align="center">2023-03-14</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">2023-03-12</td>
<td align="center">2023-03-14</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">2023-03-12</td>
<td align="center">2023-03-14</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -962,73 +962,73 @@ antibiograms:</p>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>E. coli</em> (431-431)</td>
<td align="right">65</td>
<em>E. coli</em> (428-428)</td>
<td align="right">64</td>
<td align="right">60</td>
<td align="right">57</td>
<td align="right">55</td>
<td align="right">62</td>
<td align="right">60</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>E. coli</em> (411-411)</td>
<td align="right">62</td>
<em>E. coli</em> (409-409)</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="right">58</td>
<td align="right">61</td>
<td align="right">63</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>E. coli</em> (408-408)</td>
<td align="right">65</td>
<td align="right">62</td>
<td align="right">61</td>
<em>E. coli</em> (413-413)</td>
<td align="right">63</td>
<td align="right">59</td>
<td align="right">58</td>
<td align="right">66</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>K. pneumoniae</em> (100-100)</td>
<td align="right">63</td>
<td align="right">50</td>
<td align="right">59</td>
<td align="right">62</td>
<em>K. pneumoniae</em> (96-96)</td>
<td align="right">71</td>
<td align="right">53</td>
<td align="right">64</td>
<td align="right">64</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (108-108)</td>
<td align="right">65</td>
<td align="right">56</td>
<td align="right">64</td>
<td align="right">62</td>
<em>K. pneumoniae</em> (110-110)</td>
<td align="right">59</td>
<td align="right">53</td>
<td align="right">52</td>
<td align="right">54</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (108-108)</td>
<td align="right">61</td>
<em>K. pneumoniae</em> (110-110)</td>
<td align="right">60</td>
<td align="right">52</td>
<td align="right">54</td>
<td align="right">56</td>
<td align="right">62</td>
<td align="right">64</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (211-211)</td>
<td align="right">64</td>
<td align="right">52</td>
<td align="right">61</td>
<td align="right">61</td>
<em>S. aureus</em> (232-232)</td>
<td align="right">68</td>
<td align="right">51</td>
<td align="right">58</td>
<td align="right">66</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (226-226)</td>
<td align="right">63</td>
<em>S. aureus</em> (205-205)</td>
<td align="right">58</td>
<td align="right">57</td>
<td align="right">58</td>
<td align="right">54</td>
<td align="right">60</td>
</tr>
<tr class="odd">
@ -1036,36 +1036,36 @@ antibiograms:</p>
<td align="left">
<em>S. aureus</em> (224-224)</td>
<td align="right">67</td>
<td align="right">60</td>
<td align="right">62</td>
<td align="right">57</td>
<td align="right">68</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (121-121)</td>
<td align="right">67</td>
<td align="right">56</td>
<td align="right">53</td>
<td align="right">60</td>
<em>S. pneumoniae</em> (154-154)</td>
<td align="right">62</td>
<td align="right">52</td>
<td align="right">57</td>
<td align="right">64</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>S. pneumoniae</em> (128-128)</td>
<td align="right">59</td>
<td align="right">54</td>
<td align="right">59</td>
<td align="right">62</td>
<em>S. pneumoniae</em> (118-118)</td>
<td align="right">68</td>
<td align="right">56</td>
<td align="right">63</td>
<td align="right">65</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. pneumoniae</em> (150-150)</td>
<td align="right">66</td>
<td align="right">57</td>
<td align="right">65</td>
<td align="right">73</td>
<em>S. pneumoniae</em> (127-127)</td>
<td align="right">62</td>
<td align="right">61</td>
<td align="right">60</td>
<td align="right">69</td>
</tr>
</tbody>
</table>
@ -1090,45 +1090,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (531-531)</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="right">62</td>
<td align="left">Gram-negative (524-524)</td>
<td align="right">65</td>
<td align="right">58</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (519-519)</td>
<td align="right">63</td>
<td align="right">56</td>
<td align="right">55</td>
<td align="right">61</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (516-516)</td>
<td align="right">64</td>
<td align="right">59</td>
<td align="right">64</td>
<td align="left">Gram-negative (523-523)</td>
<td align="right">63</td>
<td align="right">57</td>
<td align="right">65</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (332-332)</td>
<td align="left">Gram-positive (386-386)</td>
<td align="right">66</td>
<td align="right">52</td>
<td align="right">65</td>
<td align="right">54</td>
<td align="right">61</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (354-354)</td>
<td align="right">61</td>
<td align="left">Gram-positive (323-323)</td>
<td align="right">62</td>
<td align="right">56</td>
<td align="right">60</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (374-374)</td>
<td align="right">66</td>
<td align="right">59</td>
<td align="right">70</td>
<td align="left">Gram-positive (351-351)</td>
<td align="right">65</td>
<td align="right">62</td>
<td align="right">65</td>
</tr>
</tbody>
</table>
@ -1152,45 +1152,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (531-531)</td>
<td align="right">64</td>
<td align="right">75</td>
<td align="right">74</td>
<td align="left">Gram-negative (524-524)</td>
<td align="right">65</td>
<td align="right">76</td>
<td align="right">76</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (519-519)</td>
<td align="right">63</td>
<td align="right">75</td>
<td align="right">74</td>
<td align="right">76</td>
<td align="right">73</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (516-516)</td>
<td align="right">64</td>
<td align="right">78</td>
<td align="right">77</td>
<td align="left">Gram-negative (523-523)</td>
<td align="right">63</td>
<td align="right">76</td>
<td align="right">75</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (332-332)</td>
<td align="right">65</td>
<td align="right">79</td>
<td align="right">74</td>
<td align="left">Gram-positive (386-386)</td>
<td align="right">66</td>
<td align="right">80</td>
<td align="right">77</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (354-354)</td>
<td align="right">61</td>
<td align="right">75</td>
<td align="right">72</td>
<td align="left">Gram-positive (323-323)</td>
<td align="right">62</td>
<td align="right">76</td>
<td align="right">73</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (374-374)</td>
<td align="right">66</td>
<td align="right">79</td>
<td align="right">80</td>
<td align="left">Gram-positive (351-351)</td>
<td align="right">65</td>
<td align="right">76</td>
<td align="right">76</td>
</tr>
</tbody>
</table>

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articles/EUCAST.html
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<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</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9002</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">

58
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="">2.0.0</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9002</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">
@ -385,19 +385,19 @@ 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 R S I S R</span></span>
<span><span class="co">#&gt; 2 R S R S S I</span></span>
<span><span class="co">#&gt; 3 R I I I S S</span></span>
<span><span class="co">#&gt; 4 S I S I R S</span></span>
<span><span class="co">#&gt; 5 R S S I S R</span></span>
<span><span class="co">#&gt; 6 S S S I I S</span></span>
<span><span class="co">#&gt; 1 S R R R S R</span></span>
<span><span class="co">#&gt; 2 R S I R I I</span></span>
<span><span class="co">#&gt; 3 I I I I I I</span></span>
<span><span class="co">#&gt; 4 R I I I S S</span></span>
<span><span class="co">#&gt; 5 R I R I S I</span></span>
<span><span class="co">#&gt; 6 R I S R R S</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 S</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; 3 R</span></span>
<span><span class="co">#&gt; 3 S</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; 6 I</span></span></code></pre></div>
<span><span class="co">#&gt; 5 I</span></span>
<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">
@ -438,40 +438,40 @@ 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">3267</td>
<td align="right">65.34%</td>
<td align="right">3267</td>
<td align="right">65.34%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">952</td>
<td align="right">19.04%</td>
<td align="right">4184</td>
<td align="right">83.68%</td>
<td align="right">935</td>
<td align="right">18.70%</td>
<td align="right">4202</td>
<td align="right">84.04%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">465</td>
<td align="right">9.30%</td>
<td align="right">4649</td>
<td align="right">92.98%</td>
<td align="right">442</td>
<td align="right">8.84%</td>
<td align="right">4644</td>
<td align="right">92.88%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">248</td>
<td align="right">4.96%</td>
<td align="right">4897</td>
<td align="right">97.94%</td>
<td align="right">242</td>
<td align="right">4.84%</td>
<td align="right">4886</td>
<td align="right">97.72%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">103</td>
<td align="right">2.06%</td>
<td align="right">114</td>
<td align="right">2.28%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
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="">2.0.0</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9002</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">

4
articles/SPSS.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="">2.0.0</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9002</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">
@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">12 March 2023</h4>
<h4 data-toc-skip class="date">14 March 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>

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articles/WHONET.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="">2.0.0</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9002</small>
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4
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="">2.0.0</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9002</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">
@ -176,7 +176,7 @@
<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">12 March 2023</h4>
<h4 data-toc-skip class="date">14 March 2023</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>

2
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="">2.0.0</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9002</small>
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articles/resistance_predict.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="">2.0.0</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9002</small>
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9002</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">