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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</small>
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@ -962,108 +962,108 @@ antibiograms:</p>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>E. coli</em> (435-435)</td>
<em>E. coli</em> (418-418)</td>
<td align="right">63</td>
<td align="right">61</td>
<td align="right">58</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>E. coli</em> (414-414)</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> (398-398)</td>
<td align="right">64</td>
<td align="right">60</td>
<td align="right">59</td>
<td align="right">64</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<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> (97-97)</td>
<td align="right">70</td>
<td align="right">49</td>
<td align="right">67</td>
<td align="right">71</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (108-108)</td>
<td align="right">61</td>
<td align="right">60</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">59</td>
<td align="right">48</td>
<td align="right">57</td>
<td align="right">58</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>
<td align="right">63</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. aureus</em> (223-223)</td>
<em>E. coli</em> (418-418)</td>
<td align="right">66</td>
<td align="right">56</td>
<td align="right">53</td>
<td align="right">61</td>
<td align="right">58</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (126-126)</td>
<td align="right">65</td>
<em>K. pneumoniae</em> (98-98)</td>
<td align="right">56</td>
<td align="right">51</td>
<td align="right">56</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> (131-131)</td>
<td align="right">68</td>
<em>K. pneumoniae</em> (113-113)</td>
<td align="right">69</td>
<td align="right">50</td>
<td align="right">57</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> (142-142)</td>
<td align="right">59</td>
<em>K. pneumoniae</em> (105-105)</td>
<td align="right">63</td>
<td align="right">56</td>
<td align="right">64</td>
<td align="right">57</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (227-227)</td>
<td align="right">63</td>
<td align="right">55</td>
<td align="right">56</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (204-204)</td>
<td align="right">65</td>
<td align="right">61</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> (230-230)</td>
<td align="right">65</td>
<td align="right">54</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> (139-139)</td>
<td align="right">58</td>
<td align="right">51</td>
<td align="right">60</td>
<td align="right">66</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>S. pneumoniae</em> (128-128)</td>
<td align="right">62</td>
<td align="right">57</td>
<td align="right">61</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. pneumoniae</em> (132-132)</td>
<td align="right">73</td>
<td align="right">60</td>
<td align="right">58</td>
<td align="right">70</td>
</tr>
@ -1090,45 +1090,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (532-532)</td>
<td align="right">65</td>
<td align="right">56</td>
<td align="left">Gram-negative (516-516)</td>
<td align="right">62</td>
<td align="right">59</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="left">Gram-negative (527-527)</td>
<td align="right">64</td>
<td align="right">60</td>
<td align="right">61</td>
<td align="right">56</td>
<td align="right">62</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>
<td align="left">Gram-negative (523-523)</td>
<td align="right">65</td>
<td align="right">56</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (339-339)</td>
<td align="left">Gram-positive (366-366)</td>
<td align="right">61</td>
<td align="right">54</td>
<td align="right">64</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 (356-356)</td>
<td align="right">65</td>
<td align="right">58</td>
<td align="right">67</td>
<td align="left">Gram-positive (332-332)</td>
<td align="right">64</td>
<td align="right">60</td>
<td align="right">60</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="left">Gram-positive (362-362)</td>
<td align="right">68</td>
<td align="right">56</td>
<td align="right">64</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 (532-532)</td>
<td align="left">Gram-negative (516-516)</td>
<td align="right">62</td>
<td align="right">75</td>
<td align="right">74</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (527-527)</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 (523-523)</td>
<td align="right">65</td>
<td align="right">77</td>
<td align="right">76</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">76</td>
<td align="right">75</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">76</td>
<td align="right">73</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (339-339)</td>
<td align="right">64</td>
<td align="right">79</td>
<td align="right">75</td>
<td align="left">Gram-positive (366-366)</td>
<td align="right">61</td>
<td align="right">78</td>
<td align="right">74</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (356-356)</td>
<td align="right">65</td>
<td align="right">79</td>
<td align="right">78</td>
<td align="left">Gram-positive (332-332)</td>
<td align="right">64</td>
<td align="right">77</td>
<td align="right">74</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">75</td>
<td align="right">74</td>
<td align="left">Gram-positive (362-362)</td>
<td align="right">68</td>
<td align="right">77</td>
<td align="right">78</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="">2.0.0.9007</small>
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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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</small>
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@ -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 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; 1 I R I S S I</span></span>
<span><span class="co">#&gt; 2 I S I I S R</span></span>
<span><span class="co">#&gt; 3 I R S I R I</span></span>
<span><span class="co">#&gt; 4 I S R S R I</span></span>
<span><span class="co">#&gt; 5 R R I S I I</span></span>
<span><span class="co">#&gt; 6 S S R 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 R</span></span>
<span><span class="co">#&gt; 1 I</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 R</span></span>
<span><span class="co">#&gt; 5 S</span></span>
<span><span class="co">#&gt; 6 I</span></span></code></pre></div>
<span><span class="co">#&gt; 4 I</span></span>
<span><span class="co">#&gt; 5 I</span></span>
<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">3205</td>
<td align="right">64.10%</td>
<td align="right">3205</td>
<td align="right">64.10%</td>
<td align="right">3243</td>
<td align="right">64.86%</td>
<td align="right">3243</td>
<td align="right">64.86%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">987</td>
<td align="right">19.74%</td>
<td align="right">4192</td>
<td align="right">83.84%</td>
<td align="right">937</td>
<td align="right">18.74%</td>
<td align="right">4180</td>
<td align="right">83.60%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">475</td>
<td align="right">9.50%</td>
<td align="right">4667</td>
<td align="right">93.34%</td>
<td align="right">463</td>
<td align="right">9.26%</td>
<td align="right">4643</td>
<td align="right">92.86%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">217</td>
<td align="right">4.34%</td>
<td align="right">4884</td>
<td align="right">97.68%</td>
<td align="right">257</td>
<td align="right">5.14%</td>
<td align="right">4900</td>
<td align="right">98.00%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">116</td>
<td align="right">2.32%</td>
<td align="right">100</td>
<td align="right">2.00%</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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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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@ -38,7 +38,7 @@
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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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
authors.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
index.html
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@ -42,7 +42,7 @@
<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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

6
news/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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">
@ -142,9 +142,9 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.0.0.9007" id="amr-2009007">AMR 2.0.0.9007<a class="anchor" aria-label="anchor" href="#amr-2009007"></a></h2>
<h2 class="pkg-version" data-toc-text="2.0.0.9008" id="amr-2009008">AMR 2.0.0.9008<a class="anchor" aria-label="anchor" href="#amr-2009008"></a></h2>
<div class="section level3">
<h3 id="changed-2-0-0-9007">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9007"></a></h3>
<h3 id="changed-2-0-0-9008">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9008"></a></h3>
<ul><li>formatting fix for <code><a href="../reference/as.sir.html">sir_interpretation_history()</a></code>
</li>
<li>Fixed some WHONET codes for microorganisms and consequently a couple of entries in <code>clinical_breakpoints</code>

2
pkgdown.yml
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@ -11,7 +11,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2023-04-15T07:37Z
last_built: 2023-04-15T08:38Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

2
reference/AMR-deprecated.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/AMR-options.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/AMR.html
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@ -24,7 +24,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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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2
reference/WHOCC.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/WHONET.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/ab_from_text.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/ab_property.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/add_custom_antimicrobials.html
View File

@ -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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/add_custom_microorganisms.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

22
reference/age.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">
@ -205,16 +205,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1937-05-14 85 85.92055 62</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-03-15 70 70.08493 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1953-09-11 69 69.59178 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1950-12-19 72 72.32055 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1974-01-01 49 49.28493 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1960-09-22 62 62.56164 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-03-25 83 83.05753 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1957-07-27 65 65.71781 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1986-12-19 36 36.32055 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1998-05-29 24 24.87945 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1948-03-22 75 75.06575 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1971-11-19 51 51.40274 28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1988-03-07 35 35.10685 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1999-11-11 23 23.42466 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1946-07-04 76 76.78082 53</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1974-10-29 48 48.46027 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1969-12-08 53 53.35068 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1969-04-23 53 53.97808 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1954-03-03 69 69.11781 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1966-11-10 56 56.42740 33</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

2
reference/age_groups.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/antibiogram.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

8
reference/antibiotic_class_selectors.html
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@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">
@ -610,10 +610,10 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<span class="r-out co"><span class="r-pr">#&gt;</span> kefzol</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> I </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> I </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> I </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># get AMR for all aminoglycosides e.g., per ward:</span></span></span>

2
reference/antibiotics.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/as.ab.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/as.av.html
View File

@ -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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/as.disk.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/as.mic.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/as.mo.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

22
reference/as.sir.html
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@ -12,7 +12,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">
@ -534,16 +534,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_guideline mo_input mo_guideline </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-04-15 <span style="color: #949494;">07:38:42</span> 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-04-15 <span style="color: #949494;">07:38:42</span> 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-04-15 <span style="color: #949494;">07:38:41</span> 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-04-15 <span style="color: #949494;">07:38:41</span> 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-04-15 <span style="color: #949494;">07:38:35</span> 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-04-15 <span style="color: #949494;">07:38:35</span> 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-04-15 <span style="color: #949494;">07:38:35</span> 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-04-15 <span style="color: #949494;">07:38:35</span> 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-04-15 <span style="color: #949494;">07:38:35</span> 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-04-15 <span style="color: #949494;">07:38:35</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-04-15 <span style="color: #949494;">08:39:30</span> 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-04-15 <span style="color: #949494;">08:39:30</span> 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-04-15 <span style="color: #949494;">08:39:30</span> 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-04-15 <span style="color: #949494;">08:39:29</span> 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-04-15 <span style="color: #949494;">08:39:24</span> 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-04-15 <span style="color: #949494;">08:39:24</span> 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-04-15 <span style="color: #949494;">08:39:24</span> 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-04-15 <span style="color: #949494;">08:39:24</span> 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-04-15 <span style="color: #949494;">08:39:24</span> 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-04-15 <span style="color: #949494;">08:39:24</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 40 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6 more variables: guideline &lt;chr&gt;, ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;sir&gt;, breakpoint_S_R &lt;chr&gt;</span></span>

2
reference/atc_online.html
View File

@ -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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/av_from_text.html
View File

@ -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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/av_property.html
View File

@ -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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/availability.html
View File

@ -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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/bug_drug_combinations.html
View File

@ -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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/clinical_breakpoints.html
View File

@ -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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/count.html
View File

@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/custom_eucast_rules.html
View File

@ -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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/dosage.html
View File

@ -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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/eucast_rules.html
View File

@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/example_isolates.html
View File

@ -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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/example_isolates_unclean.html
View File

@ -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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/first_isolate.html
View File

@ -12,7 +12,7 @@
<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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/g.test.html
View File

@ -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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

109
reference/get_episode.html
View File

@ -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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">
@ -246,28 +246,29 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 5 16 39 37 19 33 24 20 14 18 23 43 40 32 25 31 11 23 13 13 22 3 24 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 13 1 8 2 15 38 40 37 46 7 30 17 3 2 7 5 19 35 18 28 5 46 17 28 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 41 13 41 39 34 9 45 45 41 21 18 11 14 10 30 46 22 45 12 4 26 41 4 1 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 1 20 33 44 19 45 21 7 38 46 4 41 19 43 41 35 47 44 8 39 36 6 9 43 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 49 45 51 50 37 4 15 52 11 2 35 26 12 9 18 8 27 48 16 17 31 23 6 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 18 24 51 5 45 52 52 14 44 20 18 27 25 47 16 3 29 13 42 3 33 35 21 20 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 25 1 6 28 36 9 7 7 19 12 4 41 8 33 46 43 3 33 52 42 4 38 39 9 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 32 34 51 11 22 8 22 10 37 48 19 49 40 36 43 53 13 22 42 30 5 10 24 26 22</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE TRUE TRUE TRUE TRUE TRUE FALSE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-08-28 390178 57 M Clinical B_STRPT_SLVR S NA NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-08-19 A49852 70 M Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-08-14 785317 51 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-08-19 A49852 70 M Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-10-11 974319 78 M Outpatie… B_MCRCCC S NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span>
@ -304,16 +305,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [97]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 066601 2013-10-30 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 067927 2002-01-16 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 069276 2015-06-18 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 077552 2002-05-14 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 09B453 2010-03-21 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 0E2483 2007-08-10 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 0E2483 2007-08-10 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 118928 2004-02-01 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 1435C8 2004-03-03 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 151041 2006-02-09 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 005088 2007-08-22 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 005088 2017-09-28 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 010257 2004-04-03 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 05C73F 2006-01-12 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 066895 2002-02-27 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 078381 2014-07-17 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 080086 2010-08-08 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 0DBF93 2015-10-12 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 0E2483 2007-04-06 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 122506 2007-08-11 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -327,19 +328,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [93]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [94]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2013-10-30 066601 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2002-01-16 067927 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2015-06-18 069276 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2002-05-14 077552 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2010-03-21 09B453 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2007-08-10 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2007-08-10 0E2483 1 FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2004-02-01 118928 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2004-03-03 1435C8 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2006-02-09 151041 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2007-08-22 005088 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2017-09-28 005088 2 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2004-04-03 010257 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2006-01-12 05C73F 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2002-02-27 066895 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2014-07-17 078381 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2010-08-08 080086 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2015-10-12 0DBF93 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2007-04-06 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2007-08-10 122506 1 FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -355,9 +356,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 60 13 40 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 27 9 19 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 6 5 6 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 62 13 40 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 25 9 21 22</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 7 5 6 7</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@ -386,19 +387,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [96]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [97]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 92F410 B_PROTS_MRBL Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 501429 B_HMPHL_PRNF ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 978801 B_STPHY_CONS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> A76045 B_STPHY_HMNS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 188588 B_CTRBC_KOSR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 43F266 B_STPHY_AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 729574 B_STRPT_GRPB ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 973274 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> F3BD65 B_STRPT_ANGN Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 578848 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 710157 B_STPHY_CONS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 716939 B_STPHY_HMNS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> A84726 B_STPHY_CPTS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D80438 B_CRYNB_STRT Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 658640 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 686445 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E44854 B_STRPT_PNMN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 6B8C75 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 005088 B_STRPT_AGLC Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 696587 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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="">2.0.0.9007</small>
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6
reference/kurtosis.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</small>
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@ -182,9 +182,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.960476</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.017473</span>
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.01258413</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.005038699</span>
</code></pre></div>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -201,31 +201,31 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R S S S R R I R I</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R R R R S R R I I I</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.7745967 1.1618950 -0.7745967 -0.7745967 -0.7745967 1.1618950</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.1618950 -0.7745967 1.1618950 -0.7745967</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.7745967 0.7745967 0.7745967 0.7745967 -1.1618950 0.7745967</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.7745967 -1.1618950 -1.1618950 -1.1618950</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.001 0.025 32 0.01 0.0625 0.125 0.5 0.01 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.005 0.125 0.025 0.01 0.25 0.5 &gt;=128 2 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 2 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.5257422 -0.5427941 1.6420106 -0.8226018 -0.2629864 -0.0513201</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.3720126 -0.8226018 1.2186779 0.7953453</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.34952811 -0.26581181 -0.80766996 -1.11616251 -0.03244621 0.20091939</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 2.06784421 0.66765060 -0.03244621 0.66765060</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.5257422 -0.5427941 1.6420106 -0.8226018 -0.2629864 -0.0513201</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.3720126 -0.8226018 1.2186779 0.7953453</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.34952811 -0.26581181 -0.80766996 -1.11616251 -0.03244621 0.20091939</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 2.06784421 0.66765060 -0.03244621 0.66765060</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 44 41 26 44 46 48 50 48 40</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 18 34 13 40 31 21 44 32 40 41</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -2.23059935 0.33963858 0.06425595 -1.31265723 0.33963858 0.52322701</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.70681543 0.89040385 0.70681543 -0.02753826</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.25112890 0.24275635 -1.71796804 0.80296332 -0.03734713 -0.97102541</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.17643463 0.05602070 0.80296332 0.89633115</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@ -235,22 +235,22 @@
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A I 21 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 28 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 23 &gt;=4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D I 20 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E I 27 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 20 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 25 &gt;=4 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 25 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 20 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 22 &gt;=4 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 18 &lt;=0.5 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 23 2 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 19 2 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D I 24 4 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E R 23 8 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F R 27 8 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 21 1 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 18 16 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I S 21 &lt;=0.5 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J I 20 1 4</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.37458457 0.92678423 0.01430793 -0.80688677 -0.22319302 -0.25784351</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.08244556 0.15908059 -0.28933760 0.18494914</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.56956384 0.09857482 -0.33782767 -0.23465405 0.85843659 1.20624076</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.25625432 -0.33010519 -0.36084739 -0.58650835</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -266,17 +266,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C S 23 &gt;=4 1 0.01430793 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 G I 25 &gt;=4 &lt;=0.5 -0.08244556 0.0967535</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 H S 25 2 2 0.15908059 0.1447727</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 J R 22 &gt;=4 &lt;=0.5 0.18494914 0.1706412</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E I 27 1 1 -0.22319302 0.2375010</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 20 2 2 -0.25784351 0.2721514</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 I R 20 1 1 -0.28933760 0.3036455</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 A I 21 &gt;=4 4 0.37458457 0.3602766</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 D I 20 1 1 -0.80688677 0.8211947</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 B R 28 2 2 0.92678423 0.9124763</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C R 19 2 &lt;=1 -0.33782767 0.000000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 H S 18 16 2 -0.33010519 0.007722481</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 I S 21 &lt;=0.5 16 -0.36084739 0.023019715</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D I 24 4 &lt;=1 -0.23465405 0.103173626</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 A R 18 &lt;=0.5 2 -0.56956384 0.231736171</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 J I 20 1 4 -0.58650835 0.248680682</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 B I 23 2 16 0.09857482 0.436402492</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 G R 21 1 16 0.25625432 0.594081995</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 E R 23 8 16 0.85843659 1.196264261</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 F R 27 8 16 1.20624076 1.544068433</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>

2
reference/microorganisms.codes.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/microorganisms.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/mo_matching_score.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/mo_property.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/mo_source.html
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@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/pca.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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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2
reference/plot.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

2
reference/proportion.html
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

34
reference/random.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">
@ -193,42 +193,42 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 64 16 2 64 0.005 2 0.0625 32 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 128 &lt;=0.001 0.025 0.5 2 1 2 0.5 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 4 0.0625 1 0.25 &gt;=256 8 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01 0.025 0.005 1 0.5 0.25 0.25 &lt;=0.001 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.001 0.025 0.005 8 32 &gt;=128 16 4 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 4 0.5 2 2 16 &lt;=0.001 8 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 38 33 42 7 18 50 44 28 17 8 35 37 48 17 43 41 46 41 36 22 43 50 8 40 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 45 30 36 15 21 12 49 24 19 17 31 44 41 45 36 11 27 9 48 42 42 24 41 23 13</span>
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I I I I R R S S R I R S R I I R S I I S S I S R I</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R S S S I S S S R I S S I S S R R I R S I I S R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=128 0.002 0.01 0.025 &gt;=128 0.025 4 0.01 4 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.5 2 0.001 0.025 0.025 0.0625 0.25 4 1 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.025 0.125 0.5 1 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 0.01 0.01 0.002 8 0.125 0.001 0.025 1 0.001 1 0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 2 32 0.5 0.005 1 2 0.125 2 4 0.25 0.005 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.01 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 64 8 4 8 16 8 &lt;=1 &lt;=1 &lt;=1 64 16 4 2 64 2 64 16 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [20] 16 2 64 8 8 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 2 0.5 1 0.5 16 1 32 8 0.5 16 0.5 1 32 64 32 8 1 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [20] 64 8 32 16 32 2 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.025 0.025 2 0.025 2 0.025 &gt;=8 1 0.0625 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 4 4 0.0625 &gt;=8 4 0.025 2 1 &gt;=8 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 1 4 0.25 0.5 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25 0.5 4 2 4 4 &gt;=16 4 2 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] &gt;=16 0.5 4 &gt;=16 0.0625 0.125 0.25 8 0.25 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 2 0.25 2 2 0.5 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 40 32 29 24 30 25 28 46 35 17 16 45 35 30 48 17 45 20 39 41 18 24 48 22 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 24 18 17 31 47 37 24 43 10 22 43 32 37 33 26 11 19 38 43 43 41 47 34 48 11</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 12 11 11 11 12 12 11 16 12 17 15 13 11 13 16 15 16 15 13 12 16 11 13 15 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 14 16 15 15 16 12 11 16 12 17 12 16 17 11 16 11 11 15 16 16 14 16 16 12 14</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 26 20 25 26 22 18 24 23 23 23 26 21 25 16 17 24 26 22 22 20 18 27 23 25 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 18 23 23 17 15 15 22 19 18 20 16 27 27 20 25 15 26 17 23 24 19 16 16 22 23</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

2
reference/resistance_predict.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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">

4
reference/skewness.html
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@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">
@ -181,7 +181,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.006476613</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.1146568</span>
</code></pre></div>
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<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="">2.0.0.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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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