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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="">2.0.0.9003</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9004</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 16 March 2023.</p>
generated on 20 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">2023-03-16</td>
<td align="center">2023-03-20</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">2023-03-16</td>
<td align="center">2023-03-20</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">2023-03-16</td>
<td align="center">2023-03-20</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -962,111 +962,111 @@ antibiograms:</p>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>E. coli</em> (386-386)</td>
<td align="right">61</td>
<em>E. coli</em> (410-410)</td>
<td align="right">64</td>
<td align="right">58</td>
<td align="right">57</td>
<td align="right">59</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>E. coli</em> (400-400)</td>
<td align="right">65</td>
<td align="right">61</td>
<td align="right">56</td>
<td align="right">62</td>
<em>E. coli</em> (430-430)</td>
<td align="right">64</td>
<td align="right">57</td>
<td align="right">59</td>
<td align="right">63</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>E. coli</em> (464-464)</td>
<td align="right">65</td>
<em>E. coli</em> (410-410)</td>
<td align="right">63</td>
<td align="right">60</td>
<td align="right">56</td>
<td align="right">59</td>
<td align="right">65</td>
<td align="right">64</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>K. pneumoniae</em> (104-104)</td>
<em>K. pneumoniae</em> (96-96)</td>
<td align="right">65</td>
<td align="right">45</td>
<td align="right">57</td>
<td align="right">62</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (108-108)</td>
<td align="right">68</td>
<td align="right">62</td>
<td align="right">64</td>
<td align="right">60</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (112-112)</td>
<td align="right">57</td>
<td align="right">50</td>
<td align="right">55</td>
<td align="right">58</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (220-220)</td>
<td align="right">64</td>
<td align="right">61</td>
<td align="right">57</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (198-198)</td>
<td align="right">64</td>
<td align="right">52</td>
<td align="right">58</td>
<td align="right">62</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (94-94)</td>
<td align="right">66</td>
<td align="right">45</td>
<td align="right">60</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (118-118)</td>
<td align="right">59</td>
<td align="right">59</td>
<td align="right">59</td>
<td align="right">58</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (230-230)</td>
<td align="right">63</td>
<td align="right">57</td>
<td align="right">56</td>
<td align="right">66</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (222-222)</td>
<td align="right">66</td>
<td align="right">58</td>
<td align="right">57</td>
<td align="right">60</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. aureus</em> (209-209)</td>
<td align="right">65</td>
<td align="right">56</td>
<td align="right">60</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (110-110)</td>
<td align="right">68</td>
<td align="right">57</td>
<td align="right">60</td>
<td align="right">64</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>S. pneumoniae</em> (142-142)</td>
<td align="right">67</td>
<td align="right">62</td>
<td align="right">65</td>
<td align="right">72</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. pneumoniae</em> (147-147)</td>
<em>S. aureus</em> (243-243)</td>
<td align="right">65</td>
<td align="right">57</td>
<td align="right">58</td>
<td align="right">49</td>
<td align="right">54</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (124-124)</td>
<td align="right">62</td>
<td align="right">56</td>
<td align="right">60</td>
<td align="right">63</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>S. pneumoniae</em> (141-141)</td>
<td align="right">62</td>
<td align="right">52</td>
<td align="right">58</td>
<td align="right">65</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. pneumoniae</em> (134-134)</td>
<td align="right">67</td>
<td align="right">60</td>
<td align="right">61</td>
<td align="right">69</td>
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
@ -1090,45 +1090,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (490-490)</td>
<td align="right">62</td>
<td align="right">56</td>
<td align="left">Gram-negative (506-506)</td>
<td align="right">64</td>
<td align="right">55</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (494-494)</td>
<td align="left">Gram-negative (538-538)</td>
<td align="right">65</td>
<td align="right">58</td>
<td align="right">63</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (522-522)</td>
<td align="right">62</td>
<td align="right">58</td>
<td align="right">62</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (582-582)</td>
<td align="right">64</td>
<td align="right">57</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (340-340)</td>
<td align="right">64</td>
<td align="right">57</td>
<td align="right">65</td>
<td align="left">Gram-positive (344-344)</td>
<td align="right">63</td>
<td align="right">59</td>
<td align="right">63</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (364-364)</td>
<td align="right">66</td>
<td align="right">59</td>
<td align="left">Gram-positive (339-339)</td>
<td align="right">63</td>
<td align="right">52</td>
<td align="right">65</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (356-356)</td>
<td align="right">62</td>
<td align="right">53</td>
<td align="right">62</td>
<td align="left">Gram-positive (377-377)</td>
<td align="right">66</td>
<td align="right">58</td>
<td align="right">64</td>
</tr>
</tbody>
</table>
@ -1152,45 +1152,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (490-490)</td>
<td align="right">62</td>
<td align="left">Gram-negative (506-506)</td>
<td align="right">64</td>
<td align="right">76</td>
<td align="right">75</td>
<td align="right">74</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (494-494)</td>
<td align="left">Gram-negative (538-538)</td>
<td align="right">65</td>
<td align="right">78</td>
<td align="right">77</td>
<td align="right">75</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (582-582)</td>
<td align="right">64</td>
<td align="right">75</td>
<td align="right">75</td>
<td align="left">Gram-negative (522-522)</td>
<td align="right">62</td>
<td align="right">74</td>
<td align="right">73</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (340-340)</td>
<td align="right">64</td>
<td align="left">Gram-positive (344-344)</td>
<td align="right">63</td>
<td align="right">75</td>
<td align="right">75</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (364-364)</td>
<td align="right">66</td>
<td align="right">80</td>
<td align="left">Gram-positive (339-339)</td>
<td align="right">63</td>
<td align="right">77</td>
<td align="right">74</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (356-356)</td>
<td align="right">62</td>
<td align="left">Gram-positive (377-377)</td>
<td align="right">66</td>
<td align="right">79</td>
<td align="right">77</td>
<td align="right">74</td>
</tr>
</tbody>
</table>

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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="">2.0.0.9003</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9004</small>
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50
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="">2.0.0.9003</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9004</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 R R R I R I</span></span>
<span><span class="co">#&gt; 2 I R S I I R</span></span>
<span><span class="co">#&gt; 3 I R I I I R</span></span>
<span><span class="co">#&gt; 4 R I I S S I</span></span>
<span><span class="co">#&gt; 5 I R R R I S</span></span>
<span><span class="co">#&gt; 6 S S S R I R</span></span>
<span><span class="co">#&gt; 1 I R I I S R</span></span>
<span><span class="co">#&gt; 2 I R R S S I</span></span>
<span><span class="co">#&gt; 3 I R S R R R</span></span>
<span><span class="co">#&gt; 4 R R I R I R</span></span>
<span><span class="co">#&gt; 5 R R R R R S</span></span>
<span><span class="co">#&gt; 6 S R S S R S</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 R</span></span>
<span><span class="co">#&gt; 3 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 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 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">
@ -438,32 +438,32 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3239</td>
<td align="right">64.78%</td>
<td align="right">3239</td>
<td align="right">64.78%</td>
<td align="right">3251</td>
<td align="right">65.02%</td>
<td align="right">3251</td>
<td align="right">65.02%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1004</td>
<td align="right">20.08%</td>
<td align="right">4243</td>
<td align="right">84.86%</td>
<td align="right">971</td>
<td align="right">19.42%</td>
<td align="right">4222</td>
<td align="right">84.44%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">423</td>
<td align="right">8.46%</td>
<td align="right">4666</td>
<td align="right">93.32%</td>
<td align="right">468</td>
<td align="right">9.36%</td>
<td align="right">4690</td>
<td align="right">93.80%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">250</td>
<td align="right">5.00%</td>
<td align="right">226</td>
<td align="right">4.52%</td>
<td align="right">4916</td>
<td align="right">98.32%</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="">2.0.0.9003</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9004</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">

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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="">2.0.0.9003</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9004</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">16 March 2023</h4>
<h4 data-toc-skip class="date">20 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>
@ -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">484 006
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">484 734
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="">2.0.0.9003</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9004</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/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="">2.0.0.9003</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9004</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">16 March 2023</h4>
<h4 data-toc-skip class="date">20 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="">2.0.0.9003</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9004</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="">2.0.0.9003</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9004</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">

2
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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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">