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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="">1.8.2.9151</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</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 11 March 2023.</p>
generated on 12 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">2023-03-11</td>
<td align="center">2023-03-12</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">2023-03-11</td>
<td align="center">2023-03-12</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">2023-03-11</td>
<td align="center">2023-03-12</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> (415-415)</td>
<em>E. coli</em> (416-416)</td>
<td align="right">63</td>
<td align="right">59</td>
<td align="right">57</td>
<td align="right">58</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>E. coli</em> (379-379)</td>
<td align="right">63</td>
<td align="right">61</td>
<td align="right">57</td>
<td align="right">61</td>
<em>E. coli</em> (406-406)</td>
<td align="right">65</td>
<td align="right">60</td>
<td align="right">55</td>
<td align="right">65</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>E. coli</em> (456-456)</td>
<td align="right">66</td>
<td align="right">57</td>
<td align="right">58</td>
<td align="right">66</td>
<em>E. coli</em> (428-428)</td>
<td align="right">64</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>K. pneumoniae</em> (106-106)</td>
<td align="right">57</td>
<td align="right">52</td>
<td align="right">58</td>
<td align="right">59</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (101-101)</td>
<td align="right">63</td>
<td align="right">49</td>
<td align="right">54</td>
<td align="right">56</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (95-95)</td>
<td align="right">54</td>
<td align="right">51</td>
<td align="right">65</td>
<td align="right">57</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (120-120)</td>
<td align="right">70</td>
<td align="right">57</td>
<td align="right">57</td>
<td align="right">66</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (225-225)</td>
<td align="right">64</td>
<td align="right">58</td>
<td align="right">58</td>
<td align="right">64</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (203-203)</td>
<td align="right">61</td>
<td align="right">60</td>
<td align="right">56</td>
<td align="right">59</td>
<td align="right">52</td>
<td align="right">57</td>
<td align="right">53</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (109-109)</td>
<td align="right">72</td>
<td align="right">53</td>
<td align="right">61</td>
<td align="right">67</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (221-221)</td>
<td align="right">66</td>
<td align="right">54</td>
<td align="right">57</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (217-217)</td>
<td align="right">64</td>
<td align="right">60</td>
<td align="right">58</td>
<td align="right">65</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. aureus</em> (233-233)</td>
<td align="right">68</td>
<td align="right">53</td>
<td align="right">58</td>
<td align="right">65</td>
<em>S. aureus</em> (223-223)</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="right">57</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (122-122)</td>
<td align="right">65</td>
<td align="right">55</td>
<td align="right">55</td>
<td align="right">65</td>
<em>S. pneumoniae</em> (134-134)</td>
<td align="right">69</td>
<td align="right">56</td>
<td align="right">58</td>
<td align="right">68</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>S. pneumoniae</em> (137-137)</td>
<td align="right">63</td>
<td align="right">51</td>
<td align="right">65</td>
<td align="right">66</td>
<em>S. pneumoniae</em> (138-138)</td>
<td align="right">64</td>
<td align="right">57</td>
<td align="right">61</td>
<td align="right">67</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. pneumoniae</em> (140-140)</td>
<td align="right">64</td>
<td align="right">61</td>
<em>S. pneumoniae</em> (127-127)</td>
<td align="right">59</td>
<td align="right">66</td>
<td align="right">54</td>
<td align="right">60</td>
<td align="right">62</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">63</td>
<td align="right">55</td>
<td align="right">60</td>
<td align="left">Gram-negative (522-522)</td>
<td align="right">61</td>
<td align="right">57</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (474-474)</td>
<td align="right">61</td>
<td align="right">59</td>
<td align="right">60</td>
<td align="left">Gram-negative (507-507)</td>
<td align="right">64</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 (576-576)</td>
<td align="right">66</td>
<td align="right">57</td>
<td align="left">Gram-negative (537-537)</td>
<td align="right">66</td>
<td align="right">56</td>
<td align="right">64</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (347-347)</td>
<td align="right">65</td>
<td align="right">57</td>
<td align="right">65</td>
<td align="left">Gram-positive (355-355)</td>
<td align="right">67</td>
<td align="right">55</td>
<td align="right">64</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (340-340)</td>
<td align="right">61</td>
<td align="right">56</td>
<td align="right">61</td>
<td align="left">Gram-positive (355-355)</td>
<td align="right">64</td>
<td align="right">59</td>
<td align="right">65</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (373-373)</td>
<td align="right">66</td>
<td align="right">56</td>
<td align="right">66</td>
<td align="left">Gram-positive (350-350)</td>
<td align="right">62</td>
<td align="right">55</td>
<td align="right">63</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">63</td>
<td align="right">75</td>
<td align="right">72</td>
<td align="left">Gram-negative (522-522)</td>
<td align="right">61</td>
<td align="right">76</td>
<td align="right">74</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (474-474)</td>
<td align="right">61</td>
<td align="left">Gram-negative (507-507)</td>
<td align="right">64</td>
<td align="right">75</td>
<td align="right">73</td>
<td align="right">74</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (576-576)</td>
<td align="left">Gram-negative (537-537)</td>
<td align="right">66</td>
<td align="right">78</td>
<td align="right">78</td>
<td align="right">77</td>
<td align="right">76</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (347-347)</td>
<td align="right">65</td>
<td align="right">77</td>
<td align="right">75</td>
<td align="left">Gram-positive (355-355)</td>
<td align="right">67</td>
<td align="right">80</td>
<td align="right">79</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (340-340)</td>
<td align="right">61</td>
<td align="right">77</td>
<td align="right">73</td>
<td align="left">Gram-positive (355-355)</td>
<td align="right">64</td>
<td align="right">76</td>
<td align="right">75</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (373-373)</td>
<td align="right">66</td>
<td align="right">78</td>
<td align="right">78</td>
<td align="left">Gram-positive (350-350)</td>
<td align="right">62</td>
<td align="right">76</td>
<td align="right">72</td>
</tr>
</tbody>
</table>

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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="">1.8.2.9151</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</small>
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60
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="">1.8.2.9151</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</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 I S R I R</span></span>
<span><span class="co">#&gt; 2 R R I S R R</span></span>
<span><span class="co">#&gt; 3 R I I R R I</span></span>
<span><span class="co">#&gt; 4 I S S R I R</span></span>
<span><span class="co">#&gt; 5 R I I R R S</span></span>
<span><span class="co">#&gt; 6 R R S I R S</span></span>
<span><span class="co">#&gt; 1 S R I I S I</span></span>
<span><span class="co">#&gt; 2 I I R I R I</span></span>
<span><span class="co">#&gt; 3 S I R I R R</span></span>
<span><span class="co">#&gt; 4 I S R I I S</span></span>
<span><span class="co">#&gt; 5 S S I S I I</span></span>
<span><span class="co">#&gt; 6 I R I R R I</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 S</span></span>
<span><span class="co">#&gt; 3 I</span></span>
<span><span class="co">#&gt; 4 R</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; 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>
<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">3262</td>
<td align="right">65.24%</td>
<td align="right">3262</td>
<td align="right">65.24%</td>
<td align="right">3216</td>
<td align="right">64.32%</td>
<td align="right">3216</td>
<td align="right">64.32%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">950</td>
<td align="right">19.00%</td>
<td align="right">4212</td>
<td align="right">84.24%</td>
<td align="right">959</td>
<td align="right">19.18%</td>
<td align="right">4175</td>
<td align="right">83.50%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">459</td>
<td align="right">9.18%</td>
<td align="right">4671</td>
<td align="right">93.42%</td>
<td align="right">462</td>
<td align="right">9.24%</td>
<td align="right">4637</td>
<td align="right">92.74%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">222</td>
<td align="right">4.44%</td>
<td align="right">4893</td>
<td align="right">97.86%</td>
<td align="right">247</td>
<td align="right">4.94%</td>
<td align="right">4884</td>
<td align="right">97.68%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">107</td>
<td align="right">2.14%</td>
<td align="right">116</td>
<td align="right">2.32%</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="">1.8.2.9151</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</small>
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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="">1.8.2.9151</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</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">11 March 2023</h4>
<h4 data-toc-skip class="date">12 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">483 254
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">484 006
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="">1.8.2.9151</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</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="">1.8.2.9151</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</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">11 March 2023</h4>
<h4 data-toc-skip class="date">12 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
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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="">1.8.2.9151</small>
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@ -196,7 +196,9 @@ antimicrobial data and properties, by using evidence-based methods.
<strong>Our aim is to provide a standard</strong> for clean and
reproducible AMR data analysis, that can therefore empower
epidemiological analyses to continuously enable surveillance and
treatment evaluation in any setting.</p>
treatment evaluation in any setting. <a href="https://msberends.github.io/AMR/authors.html">Many different
researchers</a> from around the globe are continually helping us to make
this a successful and durable project!</p>
<p>This work was published in the Journal of Statistical Software
(Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI
10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
@ -209,11 +211,12 @@ CT), and knows all about valid SIR and MIC values. The integral
breakpoint guidelines from CLSI and EUCAST are included from the last 10
years. It supports and can read any data format, including WHONET
data.</p>
<p>The <code>AMR</code> package is available in English, Chinese,
Danish, Dutch, French, German, Greek, Italian, Japanese, Polish,
Portuguese, Russian, Spanish, Swedish, Turkish and Ukrainian.
Antimicrobial drug (group) names and colloquial microorganism names are
provided in these languages.</p>
<p>With the help of contributors from all corners of the world, the
<code>AMR</code> package is available in English, Czech, Chinese,
Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese,
Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish,
Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial
microorganism names are provided in these languages.</p>
<p>This package is fully independent of any other R package and works on
Windows, macOS and Linux with all versions of R since R-3.0 (April
2013). <strong>It was designed to work in any setting, including those
@ -264,8 +267,9 @@ every code change.</p>
academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration
with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe
Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>, and
is being <a href="./news">actively and durably maintained</a> by two
public healthcare organisations in the Netherlands.</p>
is being <a href="https://msberends.github.io/AMR/news">actively and
durably maintained</a> by two public healthcare organisations in the
Netherlands.</p>
<hr>
<p><small> This AMR package for R is free, open-source software and
licensed under the <a href="https://msberends.github.io/AMR/LICENSE-text.html">GNU General