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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="">2.0.0.9006</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9007</small>
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@ -962,110 +962,110 @@ antibiograms:</p>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<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">62</td>
<em>E. coli</em> (435-435)</td>
<td align="right">63</td>
<td align="right">58</td>
<td align="right">55</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>E. coli</em> (411-411)</td>
<em>E. coli</em> (398-398)</td>
<td align="right">64</td>
<td align="right">58</td>
<td align="right">60</td>
<td align="right">59</td>
<td align="right">63</td>
<td align="right">64</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>E. coli</em> (389-389)</td>
<td align="right">63</td>
<td align="right">61</td>
<em>E. coli</em> (417-417)</td>
<td align="right">64</td>
<td align="right">57</td>
<td align="right">59</td>
<td align="right">64</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>K. pneumoniae</em> (96-96)</td>
<em>K. pneumoniae</em> (97-97)</td>
<td align="right">70</td>
<td align="right">49</td>
<td align="right">67</td>
<td align="right">48</td>
<td align="right">60</td>
<td align="right">64</td>
<td align="right">71</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (109-109)</td>
<em>K. pneumoniae</em> (108-108)</td>
<td align="right">61</td>
<td align="right">56</td>
<td align="right">60</td>
<td align="right">63</td>
<td align="right">54</td>
<td align="right">53</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (111-111)</td>
<td align="right">62</td>
<td align="right">53</td>
<td align="right">59</td>
<td align="right">48</td>
<td align="right">57</td>
<td align="right">54</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (219-219)</td>
<td align="right">63</td>
<td align="right">53</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> (235-235)</td>
<td align="right">61</td>
<td align="right">58</td>
<td align="right">52</td>
<td align="right">63</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (213-213)</td>
<td align="right">64</td>
<td align="right">58</td>
<td align="right">64</td>
<td align="right">64</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (225-225)</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="right">55</td>
<td align="right">64</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<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>
<em>S. aureus</em> (223-223)</td>
<td align="right">66</td>
<td align="right">56</td>
<td align="right">53</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (141-141)</td>
<td align="right">67</td>
<td align="right">60</td>
<td align="right">60</td>
<td align="right">72</td>
<em>S. pneumoniae</em> (126-126)</td>
<td align="right">65</td>
<td align="right">51</td>
<td align="right">63</td>
<td align="right">55</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>S. pneumoniae</em> (124-124)</td>
<td align="right">62</td>
<td align="right">52</td>
<td align="right">60</td>
<em>S. pneumoniae</em> (131-131)</td>
<td align="right">68</td>
<td align="right">60</td>
<td align="right">59</td>
<td align="right">71</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. pneumoniae</em> (134-134)</td>
<td align="right">63</td>
<td align="right">56</td>
<em>S. pneumoniae</em> (142-142)</td>
<td align="right">59</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="right">58</td>
<td align="right">70</td>
</tr>
</tbody>
</table>
@ -1090,46 +1090,46 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (546-546)</td>
<td align="left">Gram-negative (532-532)</td>
<td align="right">65</td>
<td align="right">56</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (506-506)</td>
<td align="right">64</td>
<td align="right">60</td>
<td align="right">61</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (528-528)</td>
<td align="right">63</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 (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 (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 (360-360)</td>
<td align="left">Gram-positive (339-339)</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="right">62</td>
<td align="right">55</td>
<td align="right">60</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (359-359)</td>
<td align="right">62</td>
<td align="right">56</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (341-341)</td>
<td align="right">67</td>
<td align="left">Gram-positive (356-356)</td>
<td align="right">65</td>
<td align="right">58</td>
<td align="right">67</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (365-365)</td>
<td align="right">63</td>
<td align="right">56</td>
<td align="right">64</td>
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
@ -1152,45 +1152,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (546-546)</td>
<td align="left">Gram-negative (532-532)</td>
<td align="right">65</td>
<td align="right">77</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 (520-520)</td>
<td align="right">63</td>
<td align="left">Gram-negative (506-506)</td>
<td align="right">64</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 (500-500)</td>
<td align="left">Gram-negative (528-528)</td>
<td align="right">63</td>
<td align="right">76</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 (360-360)</td>
<td align="left">Gram-positive (339-339)</td>
<td align="right">64</td>
<td align="right">80</td>
<td align="right">79</td>
<td align="right">75</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (359-359)</td>
<td align="right">62</td>
<td align="right">74</td>
<td align="right">72</td>
<td align="left">Gram-positive (356-356)</td>
<td align="right">65</td>
<td align="right">79</td>
<td align="right">78</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (341-341)</td>
<td align="right">67</td>
<td align="right">78</td>
<td align="right">79</td>
<td align="left">Gram-positive (365-365)</td>
<td align="right">63</td>
<td align="right">75</td>
<td align="right">74</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="">2.0.0.9006</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9007</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">

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="">2.0.0.9006</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9007</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 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; 1 R I R R R I</span></span>
<span><span class="co">#&gt; 2 R S R S S S</span></span>
<span><span class="co">#&gt; 3 I S I I S I</span></span>
<span><span class="co">#&gt; 4 R S S R R I</span></span>
<span><span class="co">#&gt; 5 S R R S S I</span></span>
<span><span class="co">#&gt; 6 R I R R I S</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 I</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; 3 S</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 R</span></span></code></pre></div>
<span><span class="co">#&gt; 4 R</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">3183</td>
<td align="right">63.66%</td>
<td align="right">3183</td>
<td align="right">63.66%</td>
<td align="right">3205</td>
<td align="right">64.10%</td>
<td align="right">3205</td>
<td align="right">64.10%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1002</td>
<td align="right">20.04%</td>
<td align="right">4185</td>
<td align="right">83.70%</td>
<td align="right">987</td>
<td align="right">19.74%</td>
<td align="right">4192</td>
<td align="right">83.84%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">442</td>
<td align="right">8.84%</td>
<td align="right">4627</td>
<td align="right">92.54%</td>
<td align="right">475</td>
<td align="right">9.50%</td>
<td align="right">4667</td>
<td align="right">93.34%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">272</td>
<td align="right">5.44%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
<td align="right">217</td>
<td align="right">4.34%</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">101</td>
<td align="right">2.02%</td>
<td align="right">116</td>
<td align="right">2.32%</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="">2.0.0.9006</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9007</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="">2.0.0.9006</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9007</small>
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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="">2.0.0.9006</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9007</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="">2.0.0.9006</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9007</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">
@ -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 21:14:34 UTC. Find more info
<p>It was last updated on 15 April 2023 07:32:13 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>

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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="">2.0.0.9006</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>
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articles/welcome_to_AMR.html
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@ -38,7 +38,7 @@
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