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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="">2.0.0.9005</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9006</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 14 April 2023.</p>
generated on 15 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">2023-04-14</td>
<td align="center">2023-04-15</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">2023-04-14</td>
<td align="center">2023-04-15</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">2023-04-14</td>
<td align="center">2023-04-15</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> (453-453)</td>
<td align="right">66</td>
<td align="right">60</td>
<em>E. coli</em> (450-450)</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="right">57</td>
<td align="right">66</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>E. coli</em> (387-387)</td>
<em>E. coli</em> (411-411)</td>
<td align="right">64</td>
<td align="right">58</td>
<td align="right">61</td>
<td align="right">61</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> (410-410)</td>
<td align="right">62</td>
<em>E. coli</em> (389-389)</td>
<td align="right">63</td>
<td align="right">61</td>
<td align="right">57</td>
<td align="right">56</td>
<td align="right">60</td>
<td align="right">64</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>K. pneumoniae</em> (113-113)</td>
<td align="right">62</td>
<em>K. pneumoniae</em> (96-96)</td>
<td align="right">67</td>
<td align="right">48</td>
<td align="right">59</td>
<td align="right">58</td>
<td align="right">60</td>
<td align="right">64</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (112-112)</td>
<td align="right">62</td>
<td align="right">56</td>
<em>K. pneumoniae</em> (109-109)</td>
<td align="right">61</td>
<td align="right">56</td>
<td align="right">60</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (91-91)</td>
<td align="right">66</td>
<em>K. pneumoniae</em> (111-111)</td>
<td align="right">62</td>
<td align="right">53</td>
<td align="right">57</td>
<td align="right">54</td>
<td align="right">56</td>
<td align="right">68</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (212-212)</td>
<em>S. aureus</em> (219-219)</td>
<td align="right">63</td>
<td align="right">53</td>
<td align="right">56</td>
<td align="right">61</td>
<td align="right">57</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (234-234)</td>
<td align="right">66</td>
<td align="right">56</td>
<em>S. aureus</em> (235-235)</td>
<td align="right">61</td>
<td align="right">66</td>
<td align="right">58</td>
<td align="right">52</td>
<td align="right">63</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. aureus</em> (215-215)</td>
<td align="right">64</td>
<td align="right">61</td>
<td align="right">55</td>
<td align="right">62</td>
<em>S. aureus</em> (207-207)</td>
<td align="right">70</td>
<td align="right">59</td>
<td align="right">59</td>
<td align="right">70</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (140-140)</td>
<em>S. pneumoniae</em> (141-141)</td>
<td align="right">67</td>
<td align="right">60</td>
<td align="right">54</td>
<td align="right">64</td>
<td align="right">61</td>
<td align="right">60</td>
<td align="right">72</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>S. pneumoniae</em> (139-139)</td>
<td align="right">66</td>
<td align="right">56</td>
<td align="right">57</td>
<td align="right">68</td>
<em>S. pneumoniae</em> (124-124)</td>
<td align="right">62</td>
<td align="right">52</td>
<td align="right">60</td>
<td align="right">60</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. pneumoniae</em> (120-120)</td>
<td align="right">66</td>
<td align="right">57</td>
<td align="right">58</td>
<td align="right">68</td>
<em>S. pneumoniae</em> (134-134)</td>
<td align="right">63</td>
<td align="right">56</td>
<td align="right">59</td>
<td align="right">64</td>
</tr>
</tbody>
</table>
@ -1090,45 +1090,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (566-566)</td>
<td align="right">65</td>
<td align="right">57</td>
<td align="left">Gram-negative (546-546)</td>
<td align="right">65</td>
<td align="right">55</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (499-499)</td>
<td align="right">64</td>
<td align="right">58</td>
<td align="right">60</td>
<td align="left">Gram-negative (520-520)</td>
<td align="right">63</td>
<td align="right">57</td>
<td align="right">63</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (501-501)</td>
<td align="right">62</td>
<td align="right">56</td>
<td align="left">Gram-negative (500-500)</td>
<td align="right">63</td>
<td align="right">59</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (352-352)</td>
<td align="left">Gram-positive (360-360)</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="right">62</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 (373-373)</td>
<td align="right">66</td>
<td align="left">Gram-positive (359-359)</td>
<td align="right">62</td>
<td align="right">56</td>
<td align="right">67</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (335-335)</td>
<td align="right">64</td>
<td align="right">60</td>
<td align="right">64</td>
<td align="left">Gram-positive (341-341)</td>
<td align="right">67</td>
<td align="right">58</td>
<td align="right">67</td>
</tr>
</tbody>
</table>
@ -1152,45 +1152,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (566-566)</td>
<td align="left">Gram-negative (546-546)</td>
<td align="right">65</td>
<td align="right">76</td>
<td align="right">78</td>
<td align="right">74</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (499-499)</td>
<td align="right">64</td>
<td align="right">77</td>
<td align="right">72</td>
<td align="left">Gram-negative (520-520)</td>
<td align="right">63</td>
<td align="right">76</td>
<td align="right">75</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (501-501)</td>
<td align="right">62</td>
<td align="right">74</td>
<td align="right">74</td>
<td align="left">Gram-negative (500-500)</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 (352-352)</td>
<td align="right">62</td>
<td align="left">Gram-positive (360-360)</td>
<td align="right">64</td>
<td align="right">80</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 (373-373)</td>
<td align="right">66</td>
<td align="right">80</td>
<td align="right">77</td>
<td align="left">Gram-positive (359-359)</td>
<td align="right">62</td>
<td align="right">74</td>
<td align="right">72</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (335-335)</td>
<td align="right">64</td>
<td align="right">76</td>
<td align="right">76</td>
<td align="left">Gram-positive (341-341)</td>
<td align="right">67</td>
<td align="right">78</td>
<td align="right">79</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="">2.0.0.9005</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9006</small>
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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="">2.0.0.9005</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9006</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 I I R S S</span></span>
<span><span class="co">#&gt; 2 S R R R R S</span></span>
<span><span class="co">#&gt; 3 I R S I I S</span></span>
<span><span class="co">#&gt; 4 I S S S S R</span></span>
<span><span class="co">#&gt; 5 S I R I R R</span></span>
<span><span class="co">#&gt; 6 S I I I I R</span></span>
<span><span class="co">#&gt; 1 R S I I I I</span></span>
<span><span class="co">#&gt; 2 I R S S I R</span></span>
<span><span class="co">#&gt; 3 S S R I I I</span></span>
<span><span class="co">#&gt; 4 R S S R S S</span></span>
<span><span class="co">#&gt; 5 S R I I R R</span></span>
<span><span class="co">#&gt; 6 S I I R I 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; 2 R</span></span>
<span><span class="co">#&gt; 1 R</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; 4 S</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 6 I</span></span></code></pre></div>
<span><span class="co">#&gt; 6 R</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">3214</td>
<td align="right">64.28%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
<td align="right">3183</td>
<td align="right">63.66%</td>
<td align="right">3183</td>
<td align="right">63.66%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1016</td>
<td align="right">20.32%</td>
<td align="right">4230</td>
<td align="right">84.60%</td>
<td align="right">1002</td>
<td align="right">20.04%</td>
<td align="right">4185</td>
<td align="right">83.70%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">424</td>
<td align="right">8.48%</td>
<td align="right">4654</td>
<td align="right">93.08%</td>
<td align="right">442</td>
<td align="right">8.84%</td>
<td align="right">4627</td>
<td align="right">92.54%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">247</td>
<td align="right">4.94%</td>
<td align="right">4901</td>
<td align="right">98.02%</td>
<td align="right">272</td>
<td align="right">5.44%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">99</td>
<td align="right">1.98%</td>
<td align="right">101</td>
<td align="right">2.02%</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="">2.0.0.9005</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9006</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="">2.0.0.9005</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9006</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">14 April 2023</h4>
<h4 data-toc-skip class="date">15 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>

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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="">2.0.0.9005</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9006</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="">2.0.0.9005</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9006</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">14 April 2023</h4>
<h4 data-toc-skip class="date">15 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>
@ -197,7 +197,7 @@ of the data sets look like.</p>
<h2 id="microorganisms-full-microbial-taxonomy">
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
</h2>
<p>A data set with 52 149 rows and 22 columns, containing the following
<p>A data set with 52 151 rows and 22 columns, containing the following
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
<em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
<em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
@ -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 14 April 2023 09:12:26 UTC. Find more info
<p>It was last updated on 14 April 2023 21:14:34 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>
@ -283,7 +283,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">36 483</td>
<td align="center">36 485</td>
</tr>
<tr class="odd">
<td align="center">Fungi</td>
@ -877,13 +877,13 @@ inhibitors</td>
<code>clinical_breakpoints</code>: Interpretation from MIC values
&amp; disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
</h2>
<p>A data set with 18 308 rows and 11 columns, containing the following
<p>A data set with 17 918 rows and 11 columns, containing the following
column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</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 21 January 2023 22:47:20 UTC. Find more info
<p>It was last updated on 14 April 2023 21:14:34 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>
@ -891,7 +891,7 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
R Data Structure (RDS) file</a> (42 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.txt" class="external-link">tab-separated
text file</a> (1.9 MB)<br>
text file</a> (1.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xlsx" class="external-link">Microsoft
Excel workbook</a> (0.8 MB)<br>
@ -900,16 +900,16 @@ 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> (89 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>
data file</a> (3.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sav" class="external-link">IBM
SPSS Statistics data file</a> (2.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.dta" class="external-link">Stata
DTA file</a> (3.4 MB)</li>
DTA file</a> (3.3 MB)</li>
</ul>
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