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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="">2.0.0.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9009</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 15 April 2023.</p>
generated on 17 April 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">2023-04-15</td>
<td align="center">2023-04-17</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">2023-04-15</td>
<td align="center">2023-04-17</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">2023-04-15</td>
<td align="center">2023-04-17</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -962,110 +962,110 @@ antibiograms:</p>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>E. coli</em> (418-418)</td>
<td align="right">63</td>
<td align="right">61</td>
<td align="right">58</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>E. coli</em> (414-414)</td>
<td align="right">63</td>
<td align="right">58</td>
<td align="right">57</td>
<td align="right">63</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>E. coli</em> (418-418)</td>
<td align="right">66</td>
<td align="right">56</td>
<td align="right">58</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>K. pneumoniae</em> (98-98)</td>
<td align="right">56</td>
<td align="right">51</td>
<td align="right">56</td>
<td align="right">63</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (113-113)</td>
<td align="right">69</td>
<td align="right">50</td>
<td align="right">57</td>
<td align="right">60</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (105-105)</td>
<td align="right">63</td>
<td align="right">56</td>
<td align="right">64</td>
<td align="right">57</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (227-227)</td>
<td align="right">63</td>
<td align="right">55</td>
<td align="right">56</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (204-204)</td>
<em>E. coli</em> (443-443)</td>
<td align="right">67</td>
<td align="right">59</td>
<td align="right">59</td>
<td align="right">65</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>E. coli</em> (395-395)</td>
<td align="right">65</td>
<td align="right">57</td>
<td align="right">58</td>
<td align="right">60</td>
<td align="right">63</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>E. coli</em> (412-412)</td>
<td align="right">59</td>
<td align="right">58</td>
<td align="right">56</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>K. pneumoniae</em> (108-108)</td>
<td align="right">61</td>
<td align="right">55</td>
<td align="right">48</td>
<td align="right">59</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (109-109)</td>
<td align="right">62</td>
<td align="right">51</td>
<td align="right">64</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (99-99)</td>
<td align="right">66</td>
<td align="right">52</td>
<td align="right">65</td>
<td align="right">59</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (230-230)</td>
<td align="right">65</td>
<td align="right">54</td>
<td align="right">67</td>
<td align="right">56</td>
<td align="right">57</td>
<td align="right">65</td>
<td align="right">58</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (227-227)</td>
<td align="right">60</td>
<td align="right">56</td>
<td align="right">59</td>
<td align="right">67</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. aureus</em> (204-204)</td>
<td align="right">66</td>
<td align="right">59</td>
<td align="right">55</td>
<td align="right">64</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (139-139)</td>
<em>S. pneumoniae</em> (145-145)</td>
<td align="right">63</td>
<td align="right">58</td>
<td align="right">51</td>
<td align="right">60</td>
<td align="right">66</td>
<td align="right">61</td>
<td align="right">68</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>S. pneumoniae</em> (128-128)</td>
<td align="right">62</td>
<td align="right">57</td>
<td align="right">61</td>
<td align="right">61</td>
<em>S. pneumoniae</em> (123-123)</td>
<td align="right">60</td>
<td align="right">59</td>
<td align="right">63</td>
<td align="right">60</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. pneumoniae</em> (132-132)</td>
<td align="right">73</td>
<td align="right">60</td>
<td align="right">58</td>
<td align="right">70</td>
<em>S. pneumoniae</em> (131-131)</td>
<td align="right">69</td>
<td align="right">51</td>
<td align="right">55</td>
<td align="right">68</td>
</tr>
</tbody>
</table>
@ -1090,45 +1090,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (516-516)</td>
<td align="right">62</td>
<td align="right">59</td>
<td align="right">63</td>
<td align="left">Gram-negative (551-551)</td>
<td align="right">66</td>
<td align="right">58</td>
<td align="right">64</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (527-527)</td>
<td align="left">Gram-negative (504-504)</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="right">62</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (523-523)</td>
<td align="right">65</td>
<td align="right">56</td>
<td align="right">62</td>
<td align="left">Gram-negative (511-511)</td>
<td align="right">60</td>
<td align="right">57</td>
<td align="right">60</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (366-366)</td>
<td align="right">61</td>
<td align="right">54</td>
<td align="right">64</td>
<td align="left">Gram-positive (375-375)</td>
<td align="right">66</td>
<td align="right">57</td>
<td align="right">62</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (332-332)</td>
<td align="right">64</td>
<td align="right">60</td>
<td align="left">Gram-positive (350-350)</td>
<td align="right">60</td>
<td align="right">57</td>
<td align="right">65</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (362-362)</td>
<td align="right">68</td>
<td align="right">56</td>
<td align="left">Gram-positive (335-335)</td>
<td align="right">67</td>
<td align="right">56</td>
<td align="right">66</td>
</tr>
</tbody>
</table>
@ -1152,45 +1152,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (516-516)</td>
<td align="right">62</td>
<td align="right">75</td>
<td align="right">74</td>
<td align="left">Gram-negative (551-551)</td>
<td align="right">66</td>
<td align="right">77</td>
<td align="right">77</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (527-527)</td>
<td align="left">Gram-negative (504-504)</td>
<td align="right">64</td>
<td align="right">76</td>
<td align="right">75</td>
<td align="right">77</td>
<td align="right">74</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (523-523)</td>
<td align="right">65</td>
<td align="right">77</td>
<td align="right">76</td>
<td align="left">Gram-negative (511-511)</td>
<td align="right">60</td>
<td align="right">75</td>
<td align="right">73</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (366-366)</td>
<td align="right">61</td>
<td align="right">78</td>
<td align="right">74</td>
<td align="left">Gram-positive (375-375)</td>
<td align="right">66</td>
<td align="right">79</td>
<td align="right">77</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (332-332)</td>
<td align="right">64</td>
<td align="right">77</td>
<td align="right">74</td>
<td align="left">Gram-positive (350-350)</td>
<td align="right">60</td>
<td align="right">75</td>
<td align="right">73</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (362-362)</td>
<td align="right">68</td>
<td align="right">77</td>
<td align="left">Gram-positive (335-335)</td>
<td align="right">67</td>
<td align="right">78</td>
<td align="right">76</td>
</tr>
</tbody>
</table>

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articles/EUCAST.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="">2.0.0.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9009</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">

62
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="">2.0.0.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9009</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 I S S I</span></span>
<span><span class="co">#&gt; 2 I S I I S R</span></span>
<span><span class="co">#&gt; 3 I R S I R I</span></span>
<span><span class="co">#&gt; 4 I S R S R I</span></span>
<span><span class="co">#&gt; 5 R R I S I I</span></span>
<span><span class="co">#&gt; 6 S S R I I S</span></span>
<span><span class="co">#&gt; 1 R I S I S I</span></span>
<span><span class="co">#&gt; 2 S R R R I R</span></span>
<span><span class="co">#&gt; 3 R R I I S R</span></span>
<span><span class="co">#&gt; 4 I R S I R R</span></span>
<span><span class="co">#&gt; 5 R S S S R R</span></span>
<span><span class="co">#&gt; 6 R S R R R 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; 3 S</span></span>
<span><span class="co">#&gt; 4 I</span></span>
<span><span class="co">#&gt; 5 I</span></span>
<span><span class="co">#&gt; 6 R</span></span></code></pre></div>
<span><span class="co">#&gt; 1 R</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 S</span></span>
<span><span class="co">#&gt; 5 R</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">3243</td>
<td align="right">64.86%</td>
<td align="right">3243</td>
<td align="right">64.86%</td>
<td align="right">3238</td>
<td align="right">64.76%</td>
<td align="right">3238</td>
<td align="right">64.76%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">937</td>
<td align="right">18.74%</td>
<td align="right">4180</td>
<td align="right">83.60%</td>
<td align="right">1002</td>
<td align="right">20.04%</td>
<td align="right">4240</td>
<td align="right">84.80%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">463</td>
<td align="right">9.26%</td>
<td align="right">4643</td>
<td align="right">92.86%</td>
<td align="right">408</td>
<td align="right">8.16%</td>
<td align="right">4648</td>
<td align="right">92.96%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">257</td>
<td align="right">5.14%</td>
<td align="right">4900</td>
<td align="right">98.00%</td>
<td align="right">244</td>
<td align="right">4.88%</td>
<td align="right">4892</td>
<td align="right">97.84%</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">108</td>
<td align="right">2.16%</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="">2.0.0.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9009</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">
@ -290,7 +290,7 @@ function:</p>
<span><span class="co">#&gt; [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co">#&gt; Importance of components:</span></span>
<span><span class="co">#&gt; PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
<span><span class="co">#&gt; Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co">#&gt; Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>

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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="">2.0.0.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9009</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">15 April 2023</h4>
<h4 data-toc-skip class="date">17 April 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>
@ -257,7 +257,7 @@ data using a custom made website. The webdesign knowledge needed
<li>
<p><strong>R has a huge community.</strong></p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">486 808
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">487 449
R-related questions</a> have already been asked on this platform (that
covers questions and answers for any programming language). In my own
experience, most questions are answered within a couple of

2
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="">2.0.0.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9009</small>
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@ -38,7 +38,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9009</small>
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@ -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">15 April 2023</h4>
<h4 data-toc-skip class="date">17 April 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>

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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="">2.0.0.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9009</small>
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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="">2.0.0.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9009</small>
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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="">2.0.0.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9009</small>
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