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@@ -962,110 +962,110 @@ antibiograms:</p>
|
||||
<tr class="odd">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">
|
||||
<em>E. coli</em> (415-415)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">58</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">63</td>
|
||||
<em>E. coli</em> (431-431)</td>
|
||||
<td align="right">65</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">55</td>
|
||||
<td align="right">62</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">
|
||||
<em>E. coli</em> (432-432)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">58</td>
|
||||
<em>E. coli</em> (411-411)</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">58</td>
|
||||
<td align="right">61</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">
|
||||
<em>E. coli</em> (403-403)</td>
|
||||
<td align="right">63</td>
|
||||
<td align="right">58</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">63</td>
|
||||
<em>E. coli</em> (408-408)</td>
|
||||
<td align="right">65</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">61</td>
|
||||
<td align="right">66</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">
|
||||
<em>K. pneumoniae</em> (98-98)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">44</td>
|
||||
<td align="right">64</td>
|
||||
<em>K. pneumoniae</em> (100-100)</td>
|
||||
<td align="right">63</td>
|
||||
<td align="right">50</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">62</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">
|
||||
<em>K. pneumoniae</em> (110-110)</td>
|
||||
<em>K. pneumoniae</em> (108-108)</td>
|
||||
<td align="right">65</td>
|
||||
<td align="right">61</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">62</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">
|
||||
<em>K. pneumoniae</em> (108-108)</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">61</td>
|
||||
<td align="right">52</td>
|
||||
<td align="right">54</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">56</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">
|
||||
<em>S. aureus</em> (212-212)</td>
|
||||
<em>S. aureus</em> (211-211)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">52</td>
|
||||
<td align="right">61</td>
|
||||
<td align="right">61</td>
|
||||
<td align="right">53</td>
|
||||
<td align="right">51</td>
|
||||
<td align="right">59</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">
|
||||
<em>S. aureus</em> (236-236)</td>
|
||||
<td align="right">68</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">65</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">
|
||||
<em>S. aureus</em> (213-213)</td>
|
||||
<em>S. aureus</em> (226-226)</td>
|
||||
<td align="right">63</td>
|
||||
<td align="right">55</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">58</td>
|
||||
<td align="right">54</td>
|
||||
<td align="right">60</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">
|
||||
<em>S. aureus</em> (224-224)</td>
|
||||
<td align="right">67</td>
|
||||
<td align="right">60</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">68</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">
|
||||
<em>S. pneumoniae</em> (131-131)</td>
|
||||
<td align="right">69</td>
|
||||
<em>S. pneumoniae</em> (121-121)</td>
|
||||
<td align="right">67</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">71</td>
|
||||
<td align="right">53</td>
|
||||
<td align="right">60</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">
|
||||
<em>S. pneumoniae</em> (146-146)</td>
|
||||
<em>S. pneumoniae</em> (128-128)</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">54</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">55</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">67</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">
|
||||
<em>S. pneumoniae</em> (122-122)</td>
|
||||
<td align="right">61</td>
|
||||
<em>S. pneumoniae</em> (150-150)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">58</td>
|
||||
<td align="right">65</td>
|
||||
<td align="right">73</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1090,45 +1090,45 @@ antibiograms:</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">Gram-negative (513-513)</td>
|
||||
<td align="right">65</td>
|
||||
<td align="right">55</td>
|
||||
<td align="right">63</td>
|
||||
<td align="left">Gram-negative (531-531)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">62</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">Gram-negative (542-542)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">60</td>
|
||||
<td align="right">62</td>
|
||||
<td align="left">Gram-negative (519-519)</td>
|
||||
<td align="right">63</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">61</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">Gram-negative (511-511)</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">62</td>
|
||||
<td align="left">Gram-negative (516-516)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">64</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">Gram-positive (343-343)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="left">Gram-positive (332-332)</td>
|
||||
<td align="right">65</td>
|
||||
<td align="right">54</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">61</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">Gram-positive (382-382)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">66</td>
|
||||
<td align="left">Gram-positive (354-354)</td>
|
||||
<td align="right">61</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">60</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">Gram-positive (335-335)</td>
|
||||
<td align="right">63</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">62</td>
|
||||
<td align="left">Gram-positive (374-374)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">70</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1152,45 +1152,45 @@ antibiograms:</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">Gram-negative (513-513)</td>
|
||||
<td align="right">65</td>
|
||||
<td align="right">76</td>
|
||||
<td align="right">75</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">Gram-negative (542-542)</td>
|
||||
<td align="left">Gram-negative (531-531)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">76</td>
|
||||
<td align="right">76</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">Gram-negative (511-511)</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">76</td>
|
||||
<td align="right">75</td>
|
||||
<td align="right">74</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">Gram-positive (343-343)</td>
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">Gram-negative (519-519)</td>
|
||||
<td align="right">63</td>
|
||||
<td align="right">75</td>
|
||||
<td align="right">74</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">Gram-negative (516-516)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">75</td>
|
||||
<td align="right">75</td>
|
||||
<td align="right">78</td>
|
||||
<td align="right">77</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">Gram-positive (332-332)</td>
|
||||
<td align="right">65</td>
|
||||
<td align="right">79</td>
|
||||
<td align="right">74</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">Gram-positive (382-382)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">80</td>
|
||||
<td align="right">79</td>
|
||||
<td align="left">Gram-positive (354-354)</td>
|
||||
<td align="right">61</td>
|
||||
<td align="right">75</td>
|
||||
<td align="right">72</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">Gram-positive (335-335)</td>
|
||||
<td align="right">63</td>
|
||||
<td align="right">76</td>
|
||||
<td align="right">73</td>
|
||||
<td align="left">Gram-positive (374-374)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">79</td>
|
||||
<td align="right">80</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 42 KiB After Width: | Height: | Size: 42 KiB |
+26
-26
@@ -385,17 +385,17 @@ names or codes, this would have worked exactly the same way:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
|
||||
<span><span class="co">#> 1 R R I R R I</span></span>
|
||||
<span><span class="co">#> 2 S R S S I I</span></span>
|
||||
<span><span class="co">#> 3 S S I R S S</span></span>
|
||||
<span><span class="co">#> 4 S I S S R I</span></span>
|
||||
<span><span class="co">#> 5 R I I S S I</span></span>
|
||||
<span><span class="co">#> 6 I R R I I I</span></span>
|
||||
<span><span class="co">#> 1 I R S I S R</span></span>
|
||||
<span><span class="co">#> 2 R S R S S I</span></span>
|
||||
<span><span class="co">#> 3 R I I I S S</span></span>
|
||||
<span><span class="co">#> 4 S I S I R S</span></span>
|
||||
<span><span class="co">#> 5 R S S I S R</span></span>
|
||||
<span><span class="co">#> 6 S S S I I S</span></span>
|
||||
<span><span class="co">#> kanamycin</span></span>
|
||||
<span><span class="co">#> 1 S</span></span>
|
||||
<span><span class="co">#> 2 I</span></span>
|
||||
<span><span class="co">#> 3 I</span></span>
|
||||
<span><span class="co">#> 4 R</span></span>
|
||||
<span><span class="co">#> 3 R</span></span>
|
||||
<span><span class="co">#> 4 S</span></span>
|
||||
<span><span class="co">#> 5 S</span></span>
|
||||
<span><span class="co">#> 6 I</span></span></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can
|
||||
@@ -438,40 +438,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3189</td>
|
||||
<td align="right">63.78%</td>
|
||||
<td align="right">3189</td>
|
||||
<td align="right">63.78%</td>
|
||||
<td align="right">3232</td>
|
||||
<td align="right">64.64%</td>
|
||||
<td align="right">3232</td>
|
||||
<td align="right">64.64%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">1007</td>
|
||||
<td align="right">20.14%</td>
|
||||
<td align="right">4196</td>
|
||||
<td align="right">83.92%</td>
|
||||
<td align="right">952</td>
|
||||
<td align="right">19.04%</td>
|
||||
<td align="right">4184</td>
|
||||
<td align="right">83.68%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">464</td>
|
||||
<td align="right">9.28%</td>
|
||||
<td align="right">4660</td>
|
||||
<td align="right">93.20%</td>
|
||||
<td align="right">465</td>
|
||||
<td align="right">9.30%</td>
|
||||
<td align="right">4649</td>
|
||||
<td align="right">92.98%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">242</td>
|
||||
<td align="right">4.84%</td>
|
||||
<td align="right">4902</td>
|
||||
<td align="right">98.04%</td>
|
||||
<td align="right">248</td>
|
||||
<td align="right">4.96%</td>
|
||||
<td align="right">4897</td>
|
||||
<td align="right">97.94%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">98</td>
|
||||
<td align="right">1.96%</td>
|
||||
<td align="right">103</td>
|
||||
<td align="right">2.06%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
|
||||
@@ -52,7 +52,7 @@ $(document).ready(function() {
|
||||
// add doctoral titles to authors
|
||||
function doct_tit(x) {
|
||||
if (typeof(x) != "undefined") {
|
||||
x = x.replace(/Author, maintainer/g, "Principle maintainer");
|
||||
x = x.replace(/Author, maintainer/g, "Principal maintainer");
|
||||
x = x.replace(/Author, contributor/g, "Contributing maintainer");
|
||||
x = x.replace(/Thesis advisor/g, "(former) Doctoral advisor");
|
||||
// contributors
|
||||
|
||||
+1
-1
@@ -142,7 +142,7 @@
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 class="pkg-version" data-toc-text="2.0.0" id="amr-200">AMR 2.0.0<a class="anchor" aria-label="anchor" href="#amr-200"></a></h2>
|
||||
<h2 class="pkg-version" data-toc-text="2.0.0" id="amr-200">AMR 2.0.0<a class="anchor" aria-label="anchor" href="#amr-200"></a></h2><p class="text-muted">CRAN release: 2023-03-12</p>
|
||||
<p>This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.</p>
|
||||
<p><strong><a href="https://en.wikipedia.org/wiki/TL;DR" class="external-link">TL;DR</a></strong></p>
|
||||
<ul><li>All functions and arguments with ‘rsi’ were replaced with ‘sir’, such as the interpretation of MIC values (now <code><a href="../reference/as.sir.html">as.sir()</a></code> instead of <code><a href="../reference/AMR-deprecated.html">as.rsi()</a></code>) - all old functions still work for now</li>
|
||||
|
||||
+1
-1
@@ -11,7 +11,7 @@ articles:
|
||||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2023-03-12T13:11Z
|
||||
last_built: 2023-03-12T15:02Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR/reference
|
||||
article: https://msberends.github.io/AMR/articles
|
||||
|
||||
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|
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|
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+10
-10
@@ -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">#></span> birth_date age age_exact age_at_y2k</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1967-01-30 56 56.11233 32</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1995-12-14 27 27.24110 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1956-04-27 66 66.87397 43</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1996-08-19 26 26.56164 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1980-07-28 42 42.62192 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1973-05-23 49 49.80274 26</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1988-08-12 34 34.58082 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1959-02-23 64 64.04658 40</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1974-04-16 48 48.90411 25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1956-12-27 66 66.20548 43</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1934-11-22 88 88.30137 65</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1994-03-10 29 29.00548 5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1958-07-03 64 64.69041 41</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1981-12-16 41 41.23562 18</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1962-04-09 60 60.92329 37</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1992-02-23 31 31.04658 7</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1931-10-27 91 91.37260 68</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1938-03-18 84 84.98356 61</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1988-06-05 34 34.76712 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1958-09-19 64 64.47671 41</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -611,9 +611,9 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><sir></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> I </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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>
|
||||
|
||||
+10
-10
@@ -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">#></span> <span style="color: #949494;"># A tibble: 50 × 17</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_input ab_guid…¹ mo_in…² mo_guideline guide…³</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2023-03-12 <span style="color: #949494;">13:11:56</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2023-03-12 <span style="color: #949494;">13:11:55</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2023-03-12 <span style="color: #949494;">13:11:55</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2023-03-12 <span style="color: #949494;">13:11:55</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2023-03-12 <span style="color: #949494;">13:11:50</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2023-03-12 <span style="color: #949494;">13:11:50</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2023-03-12 <span style="color: #949494;">13:11:50</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2023-03-12 <span style="color: #949494;">13:11:50</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2023-03-12 <span style="color: #949494;">13:11:50</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2023-03-12 <span style="color: #949494;">13:11:50</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2023-03-12 <span style="color: #949494;">15:03:10</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2023-03-12 <span style="color: #949494;">15:03:09</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2023-03-12 <span style="color: #949494;">15:03:09</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2023-03-12 <span style="color: #949494;">15:03:09</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2023-03-12 <span style="color: #949494;">15:03:04</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2023-03-12 <span style="color: #949494;">15:03:04</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2023-03-12 <span style="color: #949494;">15:03:04</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2023-03-12 <span style="color: #949494;">15:03:04</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2023-03-12 <span style="color: #949494;">15:03:04</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2023-03-12 <span style="color: #949494;">15:03:04</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 40 more rows, 10 more variables: ref_table <chr>, method <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># input <dbl>, outcome <sir>, breakpoint_S_R <chr>, ab_considered <lgl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># mo_considered <lgl>, breakpoint_S <lgl>, breakpoint_R <lgl>,</span></span>
|
||||
|
||||
+55
-57
@@ -246,30 +246,28 @@
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</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">#></span> [1] 8 47 8 11 43 23 7 20 28 46 43 18 13 4 36 8 24 49 8 41 21 9 2 49 37</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 20 23 9 45 1 8 9 41 2 29 6 24 30 25 12 17 9 26 1 6 27 22 34 19 42</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 38 24 48 43 33 3 14 19 8 24 5 15 3 44 46 39 42 35 23 11 48 7 26 25 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 21 46 43 40 10 1 31 32 3 45 35 7 14 17 16 16 14 19 40 10 24 36 18 7 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 47 25 49 16 43 1 35 21 9 29 11 28 27 26 17 42 29 17 27 10 14 12 9 2 45</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 38 48 47 29 4 25 5 37 4 1 5 33 19 4 50 21 36 46 3 45 20 1 6 16 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 11 13 34 31 10 44 18 23 49 46 37 41 2 42 32 50 39 30 7 15 19 21 6 49 9</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 1 32 20 4 8 4 3 23 36 48 24 30 12 40 48 22 35 32 37 29 44 34 13 18 19</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">#></span> [1] TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] TRUE TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] TRUE TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] TRUE TRUE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE TRUE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> <span style="color: #949494;"># A tibble: 4 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-11-16 762305 87 F Clinical B_BCTRD_FRGL R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-11-16 762305 87 F Clinical B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-11-04 304347 62 M Clinical B_STRPT_PNMN S NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2002-09-23 F35553 51 M ICU B_STPHY_AURS S NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-11-16 762305 87 F Clinical B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-10-14 FCC668 54 F ICU B_STRPT_PNMN S NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>,</span></span>
|
||||
@@ -304,19 +302,19 @@
|
||||
<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">condition</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">#></span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, condition [97]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, condition [100]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient date condition new_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 006827 2009-07-24 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 010257 2004-04-03 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 023456 2002-02-05 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 067927 2002-01-13 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 0E2483 2007-06-21 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 1435C8 2004-03-03 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 15D386 2004-08-01 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 15D386 2004-09-06 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 167474 2008-02-15 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 195736 2008-08-28 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 000090 2003-10-08 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 005088 2007-08-22 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 023456 2009-11-02 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 063988 2006-12-26 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 080086 2010-08-08 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 082622 2014-02-08 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 083080 2010-02-25 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 0D7D34 2011-03-17 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 0E2483 2007-04-06 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 130252 2002-04-08 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 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>
|
||||
@@ -330,19 +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">#></span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [94]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2009-07-24 006827 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2004-04-03 010257 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2002-02-05 023456 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ICU 2002-01-13 067927 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU 2007-06-21 0E2483 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2004-03-03 1435C8 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU 2004-08-01 15D386 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU 2004-09-06 15D386 1 FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2008-02-15 167474 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Outpatient 2008-08-28 195736 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [99]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> ICU 2003-10-08 000090 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2007-08-22 005088 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2009-11-02 023456 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2006-12-26 063988 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2010-08-08 080086 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU 2014-02-08 082622 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2010-02-25 083080 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU 2011-03-17 0D7D34 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2007-04-06 0E2483 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> ICU 2002-04-08 130252 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 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>
|
||||
@@ -358,9 +356,9 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 56 12 36 42</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 31 11 25 29</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 7 4 5 6</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 59 13 39 48</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 33 11 22 27</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 7 6 7 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>
|
||||
@@ -389,19 +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">#></span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [97]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 1435C8 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 7D1606 B_VLLNL_PRVL ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> C58921 B_BCTRD_FRGL Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 628820 B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 3B8892 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> D22254 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 549150 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 43F266 B_STPHY_AURS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 3F562C B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 658640 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [99]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 784436 B_STPHY_HMNS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 023456 B_KLBSL_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 694764 B_STPHY_HMNS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> C58675 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 900485 B_STRPT_MITS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> B30560 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 685398 B_STRPT_ORLS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> A3C336 B_STRPT_PNMN Outpatient TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> D52219 B_STRPT_GRPA ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 0D7D34 F_CANDD ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 90 more rows</span></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
|
||||
@@ -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">#></span> [1] 3.001502</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2.970149</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">#></span> [1] -0.00633944</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.08711231</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -201,30 +201,30 @@
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op"><-</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">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R R S I R S R R S R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] I S S R S S I S R R</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">#></span> [1] 0.7745967 0.7745967 -1.1618950 -1.1618950 0.7745967 -1.1618950</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.7745967 0.7745967 -1.1618950 0.7745967</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.621059 -0.621059 -0.621059 1.449138 -0.621059 -0.621059 -0.621059</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [8] -0.621059 1.449138 1.449138</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">mic</span> <span class="op"><-</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">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.002 0.002 256 0.0625 0.01 0.025 0.002 2 4 0.005 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.002 0.125 0.001 16 16 64 2 16 0.5 0.0625</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">#></span> [1] -0.867240328 -0.867240328 2.066590798 -0.008525384 -0.465717781</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [6] -0.237121583 -0.867240328 0.856106358 1.029032707 -0.638644130</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.45381664 -0.39257207 -1.63170516 0.85264760 0.85264760 1.20842465</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.31898203 0.85264760 -0.03679502 -0.57046060</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">#></span> [1] -0.867240328 -0.867240328 2.066590798 -0.008525384 -0.465717781</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [6] -0.237121583 -0.867240328 0.856106358 1.029032707 -0.638644130</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.45381664 -0.39257207 -1.63170516 0.85264760 0.85264760 1.20842465</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.31898203 0.85264760 -0.03679502 -0.57046060</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">disk</span> <span class="op"><-</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">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 42 21 42 39 44 36 46 41 9 48</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 41 7 31 43 26 15 50 45 50 36</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">#></span> [1] 0.42276578 -1.28455756 0.42276578 0.17886245 0.58536800 -0.06504089</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.74797023 0.34146467 -2.26017090 0.91057245</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.4508859 -1.8718595 -0.2322745 0.5875180 -0.5738547 -1.3253312</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.0657302 0.7241500 1.0657302 0.1093057</span>
|
||||
<span class="r-in"><span></span></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/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>
|
||||
@@ -234,22 +234,22 @@
|
||||
<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">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A S 27 4 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B R 20 1 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C R 31 <=0.5 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D S 23 4 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E R 31 2 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 24 <=0.5 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 28 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H R 22 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 23 8 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 26 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A R 25 >=2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 29 >=2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 30 >=2 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 22 >=2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E R 21 1 0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 >=2 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 20 1 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 19 >=2 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 30 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 27 >=2 0.5</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">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.2706405 -0.6068529 0.2354050 -0.2518529 0.3034383 -0.2313769</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.4976524 0.4511070 -0.3605963 0.2337166</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.65477694 0.24022002 -0.02948384 0.47956157 -0.75261068 0.50188332</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.64696131 -0.67194018 -0.05486954 0.27942371</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
@@ -265,17 +265,17 @@
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C R 31 <=0.5 2 0.2354050 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 J S 26 4 4 0.2337166 0.00168838</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 E R 31 2 <=1 0.3034383 0.06803327</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 H R 22 4 4 0.4511070 0.21570200</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 G R 28 1 4 0.4976524 0.26224741</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 24 <=0.5 2 -0.2313769 0.46678194</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 D S 23 4 2 -0.2518529 0.48725790</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 A S 27 4 <=1 -0.2706405 0.50604549</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 23 8 <=1 -0.3605963 0.59600133</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 B R 20 1 <=1 -0.6068529 0.84225790</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C S 30 >=2 0.5 -0.02948384 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 I S 30 1 4 -0.05486954 0.0253857</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 B I 29 >=2 2 0.24022002 0.2697039</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 J R 27 >=2 0.5 0.27942371 0.3089076</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 D R 22 >=2 4 0.47956157 0.5090454</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 >=2 1 0.50188332 0.5313672</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 20 1 0.5 -0.64696131 0.6174775</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 19 >=2 0.5 -0.67194018 0.6424563</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 A R 25 >=2 4 0.65477694 0.6842608</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 E R 21 1 0.25 -0.75261068 0.7231268</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">%>%</a></span></span></span>
|
||||
|
||||
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+16
-16
@@ -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">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 256 2 0.125 64 0.5 0.025 <=0.001 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 0.025 16 0.0625 0.005 32 <=0.001 0.25 2 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 16 128 64 256 32 256 0.005 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.25 8 64 2 32 2 0.01 4 0.005 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 0.25 0.0625 0.005 8 32 4 4 >=256 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 0.025 0.025 0.025 <=0.002 4 32 >=256 </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">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 12 10 46 48 20 46 12 18 31 21 8 7 24 21 48 48 26 42 40 18 47 7 16 9 9</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 7 23 41 25 42 15 16 30 42 50 7 26 45 23 43 46 32 26 28 50 44 48 37 42 34</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">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S R I S R S I R I S R S I I S I R S S I S I R R I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R S I I I R S S S R I S S R R R I S R R S R 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">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2 32 4 0.25 4 0.5 2 0.5 0.01 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 0.001 1 2 2 0.005 0.5 >=256 0.5 16 0.0625</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 0.002 0.01 0.0625 8 0.125 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 32 8 <=0.001 0.01 2 8 0.5 1 128 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 0.25 0.0625 0.025 4 0.01 0.125 0.25 0.25 0.125 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 32 32 0.01 1 0.01 0.25 32 </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">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2 >=16 4 1 8 4 4 >=16 1 4 8 8 >=16 2 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [16] 1 1 1 2 >=16 >=16 8 1 >=16 1 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 16 64 16 32 64 32 2 2 1 64 8 4 0.5 8 32 8 64 4 32 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [20] 64 4 4 16 2 1 </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">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 4 2 0.0625 0.025 1 0.025 0.125 0.025 0.125 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 0.5 4 0.025 4 8 2 4 0.5 0.0625 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 0.025 0.5 >=16 0.125 0.025 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 2 0.25 0.025 >=16 2 >=16 0.0625 0.125 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 0.125 1 0.0625 0.125 1 1 0.025 0.5 0.25 1 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 0.25 1 0.025 0.0625 0.0625</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">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 47 49 49 45 43 38 34 45 32 20 15 23 21 20 46 21 40 46 46 17 24 33 23 40 49</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 26 30 21 13 11 43 45 9 23 49 44 12 30 34 14 30 17 12 30 42 49 43 23 31 45</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">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 11 15 15 17 17 15 12 14 16 15 16 12 13 12 13 17 17 13 12 14 13 17 16 17 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 12 16 16 12 11 13 14 15 13 17 11 11 14 16 12 11 15 15 11 14 11 14 13 12 12</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">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 27 19 16 24 26 16 22 25 24 24 21 27 17 20 23 18 27 26 15 24 26 22 26 18 24</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 24 25 23 17 21 26 20 19 22 27 23 15 24 19 22 25 26 18 25 21 22 15 23 23 27</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -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">#></span> [1] -0.006901309</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.05333305</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
+1
-1
@@ -1 +1 @@
|
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[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> <chr> <chr> <date> <chr> <chr> <chr> <chr> <chr> #> 1 J3 A 2012-11-21 E. coli R I S S #> 2 R7 A 2018-04-03 K. pneumoniae R I S S #> 3 P3 A 2014-09-19 E. coli R S S S #> 4 P10 A 2015-12-10 E. coli S I S S #> 5 B7 A 2015-03-02 E. coli S S S S #> 6 W3 A 2018-03-31 S. aureus R S R S #> 7 J8 A 2016-06-14 E. coli R S S S #> 8 M3 A 2015-10-25 E. coli R S S S #> 9 J3 A 2019-06-19 E. coli S S S S #> 10 G6 A 2015-04-27 S. aureus S S S S #> # … with 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"How to conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 11 Dec 2022. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") Line truncated
|
||||
[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> <chr> <chr> <date> <chr> <chr> <chr> <chr> <chr> #> 1 J3 A 2012-11-21 E. coli R I S S #> 2 R7 A 2018-04-03 K. pneumoniae R I S S #> 3 P3 A 2014-09-19 E. coli R S S S #> 4 P10 A 2015-12-10 E. coli S I S S #> 5 B7 A 2015-03-02 E. coli S S S S #> 6 W3 A 2018-03-31 S. aureus R S R S #> 7 J8 A 2016-06-14 E. coli R S S S #> 8 M3 A 2015-10-25 E. coli R S S S #> 9 J3 A 2019-06-19 E. coli S S S S #> 10 G6 A 2015-04-27 S. aureus S S S S #> # … with 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"How to conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 11 Dec 2022. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") Line truncated
|
||||
Reference in new issue
Block a user