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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="">1.8.2.9150</small>
<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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@ -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">65</td>
<em>E. coli</em> (415-415)</td>
<td align="right">63</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>
</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>
</tr>
<tr class="even">
<td align="left">Cardial</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">60</td>
<td align="right">64</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>E. coli</em> (414-414)</td>
<td align="right">62</td>
<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>
</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">60</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>E. coli</em> (436-436)</td>
<td align="right">65</td>
<td align="right">60</td>
<td align="right">60</td>
<td align="right">58</td>
<td align="right">65</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>K. pneumoniae</em> (110-110)</td>
<td align="right">61</td>
<td align="right">47</td>
<td align="right">62</td>
<td align="right">61</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (102-102)</td>
<td align="right">63</td>
<td align="right">54</td>
<td align="right">54</td>
<td align="right">56</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (104-104)</td>
<em>S. pneumoniae</em> (122-122)</td>
<td align="right">65</td>
<td align="right">57</td>
<td align="right">61</td>
<td align="right">63</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (226-226)</td>
<td align="right">65</td>
<td align="right">61</td>
<td align="right">55</td>
<td align="right">64</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (215-215)</td>
<td align="right">63</td>
<td align="right">53</td>
<td align="right">58</td>
<td align="right">60</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. aureus</em> (220-220)</td>
<td align="right">55</td>
<td align="right">65</td>
<td align="right">57</td>
<td align="right">60</td>
<td align="right">65</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (127-127)</td>
<td align="right">61</td>
<td align="right">57</td>
<td align="right">61</td>
<td align="right">67</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>S. pneumoniae</em> (137-137)</td>
<td align="right">69</td>
<td align="right">57</td>
<td align="right">58</td>
<td align="right">63</td>
<td align="right">51</td>
<td align="right">65</td>
<td align="right">66</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. pneumoniae</em> (135-135)</td>
<em>S. pneumoniae</em> (140-140)</td>
<td align="right">64</td>
<td align="right">61</td>
<td align="right">54</td>
<td align="right">60</td>
<td align="right">65</td>
<td align="right">59</td>
<td align="right">66</td>
</tr>
</tbody>
</table>
@ -1090,45 +1090,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (510-510)</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="left">Gram-negative (516-516)</td>
<td align="right">63</td>
<td align="right">55</td>
<td align="right">60</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (516-516)</td>
<td align="right">62</td>
<td align="right">56</td>
<td align="left">Gram-negative (474-474)</td>
<td align="right">61</td>
<td align="right">59</td>
<td align="right">60</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (540-540)</td>
<td align="right">65</td>
<td align="right">59</td>
<td align="right">65</td>
<td align="left">Gram-negative (576-576)</td>
<td align="right">66</td>
<td align="right">57</td>
<td align="right">66</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (353-353)</td>
<td align="right">64</td>
<td align="right">59</td>
<td align="left">Gram-positive (347-347)</td>
<td align="right">65</td>
<td align="right">57</td>
<td align="right">65</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (352-352)</td>
<td align="right">66</td>
<td align="right">54</td>
<td align="right">62</td>
<td align="left">Gram-positive (340-340)</td>
<td align="right">61</td>
<td align="right">56</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (355-355)</td>
<td align="right">63</td>
<td align="left">Gram-positive (373-373)</td>
<td align="right">66</td>
<td align="right">56</td>
<td align="right">65</td>
<td align="right">66</td>
</tr>
</tbody>
</table>
@ -1152,45 +1152,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (510-510)</td>
<td align="right">64</td>
<td align="right">78</td>
<td align="left">Gram-negative (516-516)</td>
<td align="right">63</td>
<td align="right">75</td>
<td align="right">72</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (516-516)</td>
<td align="right">62</td>
<td align="right">74</td>
<td align="right">72</td>
<td align="left">Gram-negative (474-474)</td>
<td align="right">61</td>
<td align="right">75</td>
<td align="right">73</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (540-540)</td>
<td align="right">65</td>
<td align="right">77</td>
<td align="right">77</td>
<td align="left">Gram-negative (576-576)</td>
<td align="right">66</td>
<td align="right">78</td>
<td align="right">78</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (353-353)</td>
<td align="right">64</td>
<td align="right">76</td>
<td align="right">76</td>
<td align="left">Gram-positive (347-347)</td>
<td align="right">65</td>
<td align="right">77</td>
<td align="right">75</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (352-352)</td>
<td align="right">66</td>
<td align="right">79</td>
<td align="right">75</td>
<td align="left">Gram-positive (340-340)</td>
<td align="right">61</td>
<td align="right">77</td>
<td align="right">73</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (355-355)</td>
<td align="right">63</td>
<td align="right">77</td>
<td align="right">75</td>
<td align="left">Gram-positive (373-373)</td>
<td align="right">66</td>
<td align="right">78</td>
<td align="right">78</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="">1.8.2.9150</small>
<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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58
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="">1.8.2.9150</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9151</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 R I S S I</span></span>
<span><span class="co">#&gt; 2 S S S I I I</span></span>
<span><span class="co">#&gt; 3 I R S I I I</span></span>
<span><span class="co">#&gt; 4 I I R I S R</span></span>
<span><span class="co">#&gt; 5 R I I S R R</span></span>
<span><span class="co">#&gt; 6 R I S R I R</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; kanamycin</span></span>
<span><span class="co">#&gt; 1 I</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 R</span></span>
<span><span class="co">#&gt; 4 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 S</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">3198</td>
<td align="right">63.96%</td>
<td align="right">3198</td>
<td align="right">63.96%</td>
<td align="right">3262</td>
<td align="right">65.24%</td>
<td align="right">3262</td>
<td align="right">65.24%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">966</td>
<td align="right">19.32%</td>
<td align="right">4164</td>
<td align="right">83.28%</td>
<td align="right">950</td>
<td align="right">19.00%</td>
<td align="right">4212</td>
<td align="right">84.24%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">456</td>
<td align="right">9.12%</td>
<td align="right">4620</td>
<td align="right">92.40%</td>
<td align="right">459</td>
<td align="right">9.18%</td>
<td align="right">4671</td>
<td align="right">93.42%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">278</td>
<td align="right">5.56%</td>
<td align="right">4898</td>
<td align="right">97.96%</td>
<td align="right">222</td>
<td align="right">4.44%</td>
<td align="right">4893</td>
<td align="right">97.86%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">102</td>
<td align="right">2.04%</td>
<td align="right">107</td>
<td align="right">2.14%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

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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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@ -38,7 +38,7 @@
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@ -38,7 +38,7 @@
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@ -38,7 +38,7 @@
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@ -10,7 +10,7 @@
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@ -38,7 +38,7 @@
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