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articles/AMR.html
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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> (415-415)</td>
<td align="right">64</td>
<td align="right">58</td>
<td align="right">56</td>
<td align="right">63</td>
<em>E. coli</em> (431-431)</td>
<td align="right">65</td>
<td align="right">57</td>
<td align="right">55</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>E. coli</em> (432-432)</td>
<td align="right">64</td>
<td align="right">59</td>
<td align="right">58</td>
<em>E. coli</em> (411-411)</td>
<td align="right">62</td>
<td align="right">56</td>
<td align="right">58</td>
<td align="right">61</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>E. coli</em> (403-403)</td>
<td align="right">63</td>
<td align="right">58</td>
<td align="right">59</td>
<td align="right">63</td>
<em>E. coli</em> (408-408)</td>
<td align="right">65</td>
<td align="right">62</td>
<td align="right">61</td>
<td align="right">66</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>K. pneumoniae</em> (98-98)</td>
<td align="right">66</td>
<td align="right">44</td>
<td align="right">64</td>
<em>K. pneumoniae</em> (100-100)</td>
<td align="right">63</td>
<td align="right">50</td>
<td align="right">59</td>
<td align="right">62</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (110-110)</td>
<em>K. pneumoniae</em> (108-108)</td>
<td align="right">65</td>
<td align="right">61</td>
<td align="right">59</td>
<td align="right">59</td>
<td align="right">56</td>
<td align="right">64</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (108-108)</td>
<td align="right">57</td>
<td align="right">61</td>
<td align="right">52</td>
<td align="right">54</td>
<td align="right">59</td>
<td align="right">56</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (212-212)</td>
<em>S. aureus</em> (211-211)</td>
<td align="right">64</td>
<td align="right">52</td>
<td align="right">61</td>
<td align="right">61</td>
<td align="right">53</td>
<td align="right">51</td>
<td align="right">59</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (236-236)</td>
<td align="right">68</td>
<td align="right">62</td>
<td align="right">64</td>
<td align="right">65</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. aureus</em> (213-213)</td>
<em>S. aureus</em> (226-226)</td>
<td align="right">63</td>
<td align="right">55</td>
<td align="right">56</td>
<td align="right">64</td>
<td align="right">58</td>
<td align="right">54</td>
<td align="right">60</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. aureus</em> (224-224)</td>
<td align="right">67</td>
<td align="right">60</td>
<td align="right">57</td>
<td align="right">68</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (131-131)</td>
<td align="right">69</td>
<em>S. pneumoniae</em> (121-121)</td>
<td align="right">67</td>
<td align="right">56</td>
<td align="right">66</td>
<td align="right">71</td>
<td align="right">53</td>
<td align="right">60</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>S. pneumoniae</em> (146-146)</td>
<em>S. pneumoniae</em> (128-128)</td>
<td align="right">59</td>
<td align="right">54</td>
<td align="right">59</td>
<td align="right">62</td>
<td align="right">55</td>
<td align="right">57</td>
<td align="right">67</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. pneumoniae</em> (122-122)</td>
<td align="right">61</td>
<em>S. pneumoniae</em> (150-150)</td>
<td align="right">66</td>
<td align="right">57</td>
<td align="right">57</td>
<td align="right">58</td>
<td align="right">65</td>
<td align="right">73</td>
</tr>
</tbody>
</table>
@ -1090,45 +1090,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (513-513)</td>
<td align="right">65</td>
<td align="right">55</td>
<td align="right">63</td>
<td align="left">Gram-negative (531-531)</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (542-542)</td>
<td align="right">64</td>
<td align="right">60</td>
<td align="right">62</td>
<td align="left">Gram-negative (519-519)</td>
<td align="right">63</td>
<td align="right">56</td>
<td align="right">61</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (511-511)</td>
<td align="right">62</td>
<td align="right">57</td>
<td align="right">62</td>
<td align="left">Gram-negative (516-516)</td>
<td align="right">64</td>
<td align="right">59</td>
<td align="right">64</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (343-343)</td>
<td align="right">64</td>
<td align="left">Gram-positive (332-332)</td>
<td align="right">65</td>
<td align="right">54</td>
<td align="right">64</td>
<td align="right">61</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (382-382)</td>
<td align="right">66</td>
<td align="right">59</td>
<td align="right">66</td>
<td align="left">Gram-positive (354-354)</td>
<td align="right">61</td>
<td align="right">56</td>
<td align="right">60</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (335-335)</td>
<td align="right">63</td>
<td align="right">56</td>
<td align="right">62</td>
<td align="left">Gram-positive (374-374)</td>
<td align="right">66</td>
<td align="right">59</td>
<td align="right">70</td>
</tr>
</tbody>
</table>
@ -1152,45 +1152,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (513-513)</td>
<td align="right">65</td>
<td align="right">76</td>
<td align="right">75</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (542-542)</td>
<td align="left">Gram-negative (531-531)</td>
<td align="right">64</td>
<td align="right">76</td>
<td align="right">76</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (511-511)</td>
<td align="right">62</td>
<td align="right">76</td>
<td align="right">75</td>
<td align="right">74</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (343-343)</td>
<td align="left">Respiratory</td>
<td align="left">Gram-negative (519-519)</td>
<td align="right">63</td>
<td align="right">75</td>
<td align="right">74</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (516-516)</td>
<td align="right">64</td>
<td align="right">75</td>
<td align="right">75</td>
<td align="right">78</td>
<td align="right">77</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (332-332)</td>
<td align="right">65</td>
<td align="right">79</td>
<td align="right">74</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (382-382)</td>
<td align="right">66</td>
<td align="right">80</td>
<td align="right">79</td>
<td align="left">Gram-positive (354-354)</td>
<td align="right">61</td>
<td align="right">75</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">63</td>
<td align="right">76</td>
<td align="right">73</td>
<td align="left">Gram-positive (374-374)</td>
<td align="right">66</td>
<td align="right">79</td>
<td align="right">80</td>
</tr>
</tbody>
</table>

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articles/MDR.html
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@ -385,17 +385,17 @@ 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 R I R R I</span></span>
<span><span class="co">#&gt; 2 S R S S I I</span></span>
<span><span class="co">#&gt; 3 S S I R S S</span></span>
<span><span class="co">#&gt; 4 S I S S R I</span></span>
<span><span class="co">#&gt; 5 R I I S S I</span></span>
<span><span class="co">#&gt; 6 I R R I I I</span></span>
<span><span class="co">#&gt; 1 I R S I S R</span></span>
<span><span class="co">#&gt; 2 R S R S S I</span></span>
<span><span class="co">#&gt; 3 R I I I S S</span></span>
<span><span class="co">#&gt; 4 S I S I R S</span></span>
<span><span class="co">#&gt; 5 R S S I S R</span></span>
<span><span class="co">#&gt; 6 S S S I 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 I</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; 3 R</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
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3189</td>
<td align="right">63.78%</td>
<td align="right">3189</td>
<td align="right">63.78%</td>
<td align="right">3232</td>
<td align="right">64.64%</td>
<td align="right">3232</td>
<td align="right">64.64%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1007</td>
<td align="right">20.14%</td>
<td align="right">4196</td>
<td align="right">83.92%</td>
<td align="right">952</td>
<td align="right">19.04%</td>
<td align="right">4184</td>
<td align="right">83.68%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">464</td>
<td align="right">9.28%</td>
<td align="right">4660</td>
<td align="right">93.20%</td>
<td align="right">465</td>
<td align="right">9.30%</td>
<td align="right">4649</td>
<td align="right">92.98%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">242</td>
<td align="right">4.84%</td>
<td align="right">4902</td>
<td align="right">98.04%</td>
<td align="right">248</td>
<td align="right">4.96%</td>
<td align="right">4897</td>
<td align="right">97.94%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">98</td>
<td align="right">1.96%</td>
<td align="right">103</td>
<td align="right">2.06%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>