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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="">2.0.0.9011</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9012</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 18 April 2023.</p>
generated on 20 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">2023-04-18</td>
<td align="center">2023-04-20</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">2023-04-18</td>
<td align="center">2023-04-20</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">2023-04-18</td>
<td align="center">2023-04-20</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> (400-400)</td>
<td align="right">68</td>
<td align="right">57</td>
<em>E. coli</em> (394-394)</td>
<td align="right">61</td>
<td align="right">65</td>
<td align="right">60</td>
<td align="right">54</td>
<td align="right">60</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>E. coli</em> (442-442)</td>
<td align="right">62</td>
<em>E. coli</em> (448-448)</td>
<td align="right">68</td>
<td align="right">58</td>
<td align="right">60</td>
<td align="right">56</td>
<td align="right">62</td>
<td align="right">64</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>E. coli</em> (408-408)</td>
<td align="right">62</td>
<td align="right">58</td>
<td align="right">57</td>
<td align="right">62</td>
<td align="right">56</td>
<td align="right">59</td>
<td align="right">65</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>K. pneumoniae</em> (114-114)</td>
<em>K. pneumoniae</em> (93-93)</td>
<td align="right">60</td>
<td align="right">49</td>
<td align="right">60</td>
<td align="right">61</td>
<td align="right">53</td>
<td align="right">55</td>
<td align="right">54</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (99-99)</td>
<td align="right">64</td>
<td align="right">56</td>
<em>K. pneumoniae</em> (116-116)</td>
<td align="right">67</td>
<td align="right">53</td>
<td align="right">63</td>
<td align="right">66</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (107-107)</td>
<td align="right">61</td>
<td align="right">51</td>
<td align="right">58</td>
<td align="right">60</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (215-215)</td>
<td align="right">67</td>
<td align="right">57</td>
<td align="right">57</td>
<td align="right">67</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (222-222)</td>
<td align="right">62</td>
<td align="right">59</td>
<td align="right">59</td>
<td align="right">58</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (103-103)</td>
<td align="right">66</td>
<td align="right">53</td>
<td align="right">58</td>
<td align="right">61</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (246-246)</td>
<td align="right">61</td>
<td align="right">57</td>
<td align="right">57</td>
<td align="right">60</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (213-213)</td>
<td align="right">66</td>
<td align="right">55</td>
<td align="right">57</td>
<td align="right">68</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. aureus</em> (202-202)</td>
<td align="right">68</td>
<td align="right">57</td>
<td align="right">58</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (129-129)</td>
<td align="right">60</td>
<em>S. aureus</em> (224-224)</td>
<td align="right">65</td>
<td align="right">54</td>
<td align="right">61</td>
<td align="right">67</td>
<td align="right">57</td>
<td align="right">65</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (130-130)</td>
<td align="right">62</td>
<td align="right">58</td>
<td align="right">58</td>
<td align="right">65</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>S. pneumoniae</em> (139-139)</td>
<td align="right">64</td>
<td align="right">63</td>
<td align="right">58</td>
<em>S. pneumoniae</em> (125-125)</td>
<td align="right">65</td>
<td align="right">54</td>
<td align="right">59</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. pneumoniae</em> (131-131)</td>
<em>S. pneumoniae</em> (144-144)</td>
<td align="right">65</td>
<td align="right">56</td>
<td align="right">61</td>
<td align="right">68</td>
<td align="right">50</td>
<td align="right">60</td>
<td align="right">67</td>
</tr>
</tbody>
</table>
@ -1090,45 +1090,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (514-514)</td>
<td align="right">66</td>
<td align="right">55</td>
<td align="right">64</td>
<td align="left">Gram-negative (487-487)</td>
<td align="right">61</td>
<td align="right">59</td>
<td align="right">59</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (541-541)</td>
<td align="right">62</td>
<td align="right">59</td>
<td align="right">61</td>
<td align="left">Gram-negative (564-564)</td>
<td align="right">68</td>
<td align="right">57</td>
<td align="right">64</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (511-511)</td>
<td align="right">63</td>
<td align="right">57</td>
<td align="right">61</td>
<td align="left">Gram-negative (515-515)</td>
<td align="right">62</td>
<td align="right">55</td>
<td align="right">64</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (375-375)</td>
<td align="right">60</td>
<td align="right">56</td>
<td align="right">62</td>
<td align="left">Gram-positive (345-345)</td>
<td align="right">65</td>
<td align="right">57</td>
<td align="right">66</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (352-352)</td>
<td align="right">65</td>
<td align="right">58</td>
<td align="right">66</td>
<td align="left">Gram-positive (347-347)</td>
<td align="right">63</td>
<td align="right">57</td>
<td align="right">60</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (333-333)</td>
<td align="right">68</td>
<td align="left">Gram-positive (368-368)</td>
<td align="right">65</td>
<td align="right">55</td>
<td align="right">64</td>
<td align="right">66</td>
</tr>
</tbody>
</table>
@ -1152,44 +1152,44 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (514-514)</td>
<td align="right">66</td>
<td align="right">78</td>
<td align="right">78</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (541-541)</td>
<td align="right">62</td>
<td align="right">75</td>
<td align="left">Gram-negative (487-487)</td>
<td align="right">61</td>
<td align="right">72</td>
<td align="right">72</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (511-511)</td>
<td align="right">63</td>
<td align="right">76</td>
<td align="right">74</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (375-375)</td>
<td align="right">60</td>
<td align="right">75</td>
<td align="right">73</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (352-352)</td>
<td align="right">65</td>
<td align="left">Gram-negative (564-564)</td>
<td align="right">68</td>
<td align="right">80</td>
<td align="right">77</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (515-515)</td>
<td align="right">62</td>
<td align="right">75</td>
<td align="right">75</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (345-345)</td>
<td align="right">65</td>
<td align="right">77</td>
<td align="right">78</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (347-347)</td>
<td align="right">63</td>
<td align="right">77</td>
<td align="right">72</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (333-333)</td>
<td align="right">68</td>
<td align="right">77</td>
<td align="left">Gram-positive (368-368)</td>
<td align="right">65</td>
<td align="right">78</td>
<td align="right">77</td>
</tr>
</tbody>

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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="">2.0.0.9011</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9012</small>
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54
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="">2.0.0.9011</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9012</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">
@ -385,18 +385,18 @@ 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 I S R S I</span></span>
<span><span class="co">#&gt; 2 S S I S I I</span></span>
<span><span class="co">#&gt; 3 R I I R I S</span></span>
<span><span class="co">#&gt; 4 I S S R R I</span></span>
<span><span class="co">#&gt; 5 S R R R R I</span></span>
<span><span class="co">#&gt; 6 R S R I R R</span></span>
<span><span class="co">#&gt; 1 I I R R S I</span></span>
<span><span class="co">#&gt; 2 S S R S S R</span></span>
<span><span class="co">#&gt; 3 R R I S R R</span></span>
<span><span class="co">#&gt; 4 S S R R I I</span></span>
<span><span class="co">#&gt; 5 S S R R R R</span></span>
<span><span class="co">#&gt; 6 I I R R I I</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 R</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 I</span></span>
<span><span class="co">#&gt; 5 S</span></span>
<span><span class="co">#&gt; 4 S</span></span>
<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>
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3221</td>
<td align="right">64.42%</td>
<td align="right">3221</td>
<td align="right">64.42%</td>
<td align="right">3190</td>
<td align="right">63.80%</td>
<td align="right">3190</td>
<td align="right">63.80%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1005</td>
<td align="right">20.10%</td>
<td align="right">4226</td>
<td align="right">84.52%</td>
<td align="right">1015</td>
<td align="right">20.30%</td>
<td align="right">4205</td>
<td align="right">84.10%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">439</td>
<td align="right">8.78%</td>
<td align="right">4665</td>
<td align="right">93.30%</td>
<td align="right">453</td>
<td align="right">9.06%</td>
<td align="right">4658</td>
<td align="right">93.16%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">241</td>
<td align="right">4.82%</td>
<td align="right">4906</td>
<td align="right">98.12%</td>
<td align="right">229</td>
<td align="right">4.58%</td>
<td align="right">4887</td>
<td align="right">97.74%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">94</td>
<td align="right">1.88%</td>
<td align="right">113</td>
<td align="right">2.26%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

4
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="">2.0.0.9011</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9012</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 1.232e-16</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; 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="">2.0.0.9011</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9012</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">18 April 2023</h4>
<h4 data-toc-skip class="date">20 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>

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="">2.0.0.9011</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9012</small>
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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="">2.0.0.9011</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9012</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">18 April 2023</h4>
<h4 data-toc-skip class="date">20 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>
@ -206,7 +206,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<em>gbif_renamed_to</em>, <em>prevalence</em>, and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 15 April 2023 07:32:13 UTC. Find more info
<p>It was last updated on 20 April 2023 13:20:41 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -883,7 +883,7 @@ column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>
<em>breakpoint_S</em>, <em>breakpoint_R</em>, and <em>uti</em>.</p>
<p>This data set is in R available as <code>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 18 April 2023 22:31:31 UTC. Find more info
<p>It was last updated on 20 April 2023 13:20:41 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -900,7 +900,7 @@ Excel workbook</a> (0.8 MB)<br>
Feather file</a> (0.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.parquet" class="external-link">Apache
Parquet file</a> (87 kB)<br>
Parquet file</a> (88 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sas" class="external-link">SAS
data file</a> (3.6 MB)<br>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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