P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 18:27:58 +02:00
Code Releases Activity

Built site for AMR: 2.0.0@dee675e

Browse Source
This commit is contained in:
github-actions
2023-03-12 13:14:27 +00:00
parent 2f947f2a87
commit cb279602b6
91 changed files with 347 additions and 348 deletions
Download Patch File Download Diff File Expand all files Collapse all files

198
articles/AMR.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</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">
@ -962,110 +962,110 @@ antibiograms:</p>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>E. coli</em> (416-416)</td>
<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>
<td align="right">59</td>
<td align="right">57</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>E. coli</em> (406-406)</td>
<td align="right">65</td>
<td align="right">60</td>
<td align="right">55</td>
<td align="right">65</td>
<em>E. coli</em> (432-432)</td>
<td align="right">64</td>
<td align="right">59</td>
<td align="right">58</td>
<td align="right">62</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>E. coli</em> (428-428)</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="right">60</td>
<em>E. coli</em> (403-403)</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>K. pneumoniae</em> (106-106)</td>
<td align="right">57</td>
<td align="right">52</td>
<td align="right">58</td>
<td align="right">59</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (101-101)</td>
<td align="right">60</td>
<td align="right">52</td>
<td align="right">57</td>
<td align="right">53</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (109-109)</td>
<td align="right">72</td>
<td align="right">53</td>
<td align="right">61</td>
<td align="right">67</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (221-221)</td>
<em>K. pneumoniae</em> (98-98)</td>
<td align="right">66</td>
<td align="right">54</td>
<td align="right">57</td>
<td align="right">44</td>
<td align="right">64</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>
<td align="right">65</td>
<td align="right">61</td>
<td align="right">59</td>
<td align="right">59</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">52</td>
<td align="right">54</td>
<td align="right">59</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (212-212)</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> (217-217)</td>
<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">60</td>
<td align="right">58</td>
<td align="right">65</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. aureus</em> (223-223)</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="right">57</td>
<em>S. aureus</em> (213-213)</td>
<td align="right">63</td>
<td align="right">55</td>
<td align="right">56</td>
<td align="right">64</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (134-134)</td>
<em>S. pneumoniae</em> (131-131)</td>
<td align="right">69</td>
<td align="right">56</td>
<td align="right">58</td>
<td align="right">68</td>
<td align="right">66</td>
<td align="right">71</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>S. pneumoniae</em> (138-138)</td>
<td align="right">64</td>
<em>S. pneumoniae</em> (146-146)</td>
<td align="right">62</td>
<td align="right">55</td>
<td align="right">57</td>
<td align="right">61</td>
<td align="right">67</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. pneumoniae</em> (127-127)</td>
<td align="right">59</td>
<td align="right">54</td>
<td align="right">60</td>
<td align="right">62</td>
<em>S. pneumoniae</em> (122-122)</td>
<td align="right">61</td>
<td align="right">57</td>
<td align="right">57</td>
<td align="right">58</td>
</tr>
</tbody>
</table>
@ -1090,45 +1090,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (522-522)</td>
<td align="right">61</td>
<td align="right">57</td>
<td align="right">61</td>
<td align="left">Gram-negative (513-513)</td>
<td align="right">65</td>
<td align="right">55</td>
<td align="right">63</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (507-507)</td>
<td align="left">Gram-negative (542-542)</td>
<td align="right">64</td>
<td align="right">58</td>
<td align="right">60</td>
<td align="right">62</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (537-537)</td>
<td align="right">66</td>
<td align="right">56</td>
<td align="right">64</td>
<td align="left">Gram-negative (511-511)</td>
<td align="right">62</td>
<td align="right">57</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (355-355)</td>
<td align="right">67</td>
<td align="right">55</td>
<td align="left">Gram-positive (343-343)</td>
<td align="right">64</td>
<td align="right">54</td>
<td align="right">64</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (355-355)</td>
<td align="right">64</td>
<td align="left">Gram-positive (382-382)</td>
<td align="right">66</td>
<td align="right">59</td>
<td align="right">65</td>
<td align="right">66</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (350-350)</td>
<td align="right">62</td>
<td align="right">55</td>
<td align="left">Gram-positive (335-335)</td>
<td align="right">63</td>
<td align="right">56</td>
<td align="right">62</td>
</tr>
</tbody>
</table>
@ -1152,45 +1152,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (522-522)</td>
<td align="right">61</td>
<td align="left">Gram-negative (513-513)</td>
<td align="right">65</td>
<td align="right">76</td>
<td align="right">74</td>
<td align="right">75</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (507-507)</td>
<td align="left">Gram-negative (542-542)</td>
<td align="right">64</td>
<td align="right">75</td>
<td align="right">74</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 (537-537)</td>
<td align="right">66</td>
<td align="right">77</td>
<td align="left">Gram-negative (511-511)</td>
<td align="right">62</td>
<td align="right">76</td>
<td align="right">74</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (355-355)</td>
<td align="right">67</td>
<td align="right">80</td>
<td align="right">79</td>
<td align="left">Gram-positive (343-343)</td>
<td align="right">64</td>
<td align="right">75</td>
<td align="right">75</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (355-355)</td>
<td align="right">64</td>
<td align="right">76</td>
<td align="right">75</td>
<td align="left">Gram-positive (382-382)</td>
<td align="right">66</td>
<td align="right">80</td>
<td align="right">79</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (350-350)</td>
<td align="right">62</td>
<td align="left">Gram-positive (335-335)</td>
<td align="right">63</td>
<td align="right">76</td>
<td align="right">72</td>
<td align="right">73</td>
</tr>
</tbody>
</table>

BIN
articles/AMR_files/figure-html/unnamed-chunk-13-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 42 KiB

After

Width:  |  Height:  |  Size: 42 KiB

2
articles/EUCAST.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</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">

54
articles/MDR.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -385,17 +385,17 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 S R I I S I</span></span>
<span><span class="co">#&gt; 2 I I R I R I</span></span>
<span><span class="co">#&gt; 3 S I R I R R</span></span>
<span><span class="co">#&gt; 4 I S R I I S</span></span>
<span><span class="co">#&gt; 5 S S I S I I</span></span>
<span><span class="co">#&gt; 6 I R I R R I</span></span>
<span><span class="co">#&gt; 1 R R I R R I</span></span>
<span><span class="co">#&gt; 2 S R S S I I</span></span>
<span><span class="co">#&gt; 3 S S I R S S</span></span>
<span><span class="co">#&gt; 4 S I S S R I</span></span>
<span><span class="co">#&gt; 5 R I I S S I</span></span>
<span><span class="co">#&gt; 6 I R R I I I</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 S</span></span>
<span><span class="co">#&gt; 2 I</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 4 S</span></span>
<span><span class="co">#&gt; 3 I</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 S</span></span>
<span><span class="co">#&gt; 6 I</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3216</td>
<td align="right">64.32%</td>
<td align="right">3216</td>
<td align="right">64.32%</td>
<td align="right">3189</td>
<td align="right">63.78%</td>
<td align="right">3189</td>
<td align="right">63.78%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">959</td>
<td align="right">19.18%</td>
<td align="right">4175</td>
<td align="right">83.50%</td>
<td align="right">1007</td>
<td align="right">20.14%</td>
<td align="right">4196</td>
<td align="right">83.92%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">462</td>
<td align="right">9.24%</td>
<td align="right">4637</td>
<td align="right">92.74%</td>
<td align="right">464</td>
<td align="right">9.28%</td>
<td align="right">4660</td>
<td align="right">93.20%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">247</td>
<td align="right">4.94%</td>
<td align="right">4884</td>
<td align="right">97.68%</td>
<td align="right">242</td>
<td align="right">4.84%</td>
<td align="right">4902</td>
<td align="right">98.04%</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">98</td>
<td align="right">1.96%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
articles/PCA.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</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
articles/SPSS.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</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
articles/WHONET.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</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
articles/datasets.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</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
articles/index.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="">1.8.2.9152</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</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
articles/resistance_predict.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</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
articles/welcome_to_AMR.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9152</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</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">
@ -267,7 +267,7 @@ every code change.</p>
academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration
with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe
Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>, and
is being <a href="https://msberends.github.io/AMR/news">actively and
is being <a href="https://msberends.github.io/AMR/news/">actively and
durably maintained</a> by two public healthcare organisations in the
Netherlands.</p>
<hr>