P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 17:07:54 +02:00
Code Releases Activity

Built site for AMR: 2.0.0.9011@2758615

Browse Source
This commit is contained in:
github-actions
2023-04-18 22:44:09 +00:00
parent dd75cf872c
commit b7bbc5c384
91 changed files with 432 additions and 395 deletions
Download Patch File Download Diff File Expand all files Collapse all files

230
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="">2.0.0.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9011</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">
@ -187,7 +187,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 17 April 2023.</p>
generated on 18 April 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -243,21 +243,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-04-17</td>
<td align="center">2023-04-18</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2023-04-17</td>
<td align="center">2023-04-18</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2023-04-17</td>
<td align="center">2023-04-18</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -962,110 +962,110 @@ antibiograms:</p>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>E. coli</em> (443-443)</td>
<td align="right">67</td>
<td align="right">59</td>
<td align="right">59</td>
<td align="right">65</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>E. coli</em> (395-395)</td>
<td align="right">65</td>
<em>E. coli</em> (400-400)</td>
<td align="right">68</td>
<td align="right">57</td>
<td align="right">58</td>
<td align="right">63</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>E. coli</em> (412-412)</td>
<td align="right">59</td>
<td align="right">58</td>
<td align="right">56</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>K. pneumoniae</em> (108-108)</td>
<td align="right">61</td>
<td align="right">55</td>
<td align="right">48</td>
<td align="right">59</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (109-109)</td>
<td align="right">62</td>
<td align="right">51</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> (99-99)</td>
<td align="right">66</td>
<td align="right">52</td>
<td align="right">65</td>
<td align="right">59</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (230-230)</td>
<td align="right">67</td>
<td align="right">56</td>
<td align="right">57</td>
<td align="right">58</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (227-227)</td>
<em>E. coli</em> (442-442)</td>
<td align="right">62</td>
<td align="right">60</td>
<td align="right">56</td>
<td align="right">59</td>
<td align="right">67</td>
<td align="right">62</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. aureus</em> (204-204)</td>
<td align="right">66</td>
<td align="right">59</td>
<td align="right">55</td>
<td align="right">64</td>
<em>E. coli</em> (408-408)</td>
<td align="right">62</td>
<td align="right">58</td>
<td align="right">57</td>
<td align="right">62</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (145-145)</td>
<td align="right">63</td>
<em>K. pneumoniae</em> (114-114)</td>
<td align="right">60</td>
<td align="right">49</td>
<td align="right">60</td>
<td align="right">61</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>K. pneumoniae</em> (99-99)</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="right">59</td>
<td align="right">58</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>K. pneumoniae</em> (103-103)</td>
<td align="right">66</td>
<td align="right">53</td>
<td align="right">58</td>
<td align="right">61</td>
</tr>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">
<em>S. aureus</em> (246-246)</td>
<td align="right">61</td>
<td align="right">57</td>
<td align="right">57</td>
<td align="right">60</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">
<em>S. aureus</em> (213-213)</td>
<td align="right">66</td>
<td align="right">55</td>
<td align="right">57</td>
<td align="right">68</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. aureus</em> (202-202)</td>
<td align="right">68</td>
<td align="right">57</td>
<td align="right">58</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">
<em>S. pneumoniae</em> (129-129)</td>
<td align="right">60</td>
<td align="right">54</td>
<td align="right">61</td>
<td align="right">67</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">
<em>S. pneumoniae</em> (123-123)</td>
<td align="right">60</td>
<td align="right">59</td>
<em>S. pneumoniae</em> (139-139)</td>
<td align="right">64</td>
<td align="right">63</td>
<td align="right">58</td>
<td align="right">63</td>
<td align="right">60</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">
<em>S. pneumoniae</em> (131-131)</td>
<td align="right">69</td>
<td align="right">51</td>
<td align="right">55</td>
<td align="right">68</td>
<td align="right">50</td>
<td align="right">60</td>
<td align="right">67</td>
</tr>
</tbody>
</table>
@ -1090,45 +1090,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (551-551)</td>
<td align="left">Gram-negative (514-514)</td>
<td align="right">66</td>
<td align="right">58</td>
<td align="right">55</td>
<td align="right">64</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (504-504)</td>
<td align="right">64</td>
<td align="right">56</td>
<td align="left">Gram-negative (541-541)</td>
<td align="right">62</td>
<td align="right">59</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">60</td>
<td align="right">63</td>
<td align="right">57</td>
<td align="right">60</td>
<td align="right">61</td>
</tr>
<tr class="even">
<td align="left">Cardial</td>
<td align="left">Gram-positive (375-375)</td>
<td align="right">66</td>
<td align="right">57</td>
<td align="right">60</td>
<td align="right">56</td>
<td align="right">62</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (350-350)</td>
<td align="right">60</td>
<td align="right">57</td>
<td align="left">Gram-positive (352-352)</td>
<td align="right">65</td>
<td align="right">58</td>
<td align="right">66</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (335-335)</td>
<td align="right">67</td>
<td align="right">56</td>
<td align="right">66</td>
<td align="left">Gram-positive (333-333)</td>
<td align="right">68</td>
<td align="right">55</td>
<td align="right">64</td>
</tr>
</tbody>
</table>
@ -1152,45 +1152,45 @@ antibiograms:</p>
<tbody>
<tr class="odd">
<td align="left">Cardial</td>
<td align="left">Gram-negative (551-551)</td>
<td align="left">Gram-negative (514-514)</td>
<td align="right">66</td>
<td align="right">77</td>
<td align="right">77</td>
<td align="right">78</td>
<td align="right">78</td>
</tr>
<tr class="even">
<td align="left">Respiratory</td>
<td align="left">Gram-negative (504-504)</td>
<td align="right">64</td>
<td align="right">77</td>
<td align="right">74</td>
<td align="left">Gram-negative (541-541)</td>
<td align="right">62</td>
<td align="right">75</td>
<td align="right">72</td>
</tr>
<tr class="odd">
<td align="left">Rheumatic</td>
<td align="left">Gram-negative (511-511)</td>
<td align="right">60</td>
<td align="right">75</td>
<td align="right">73</td>
<td align="right">63</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 (375-375)</td>
<td align="right">66</td>
<td align="right">79</td>
<td align="right">77</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (350-350)</td>
<td align="right">60</td>
<td align="right">75</td>
<td align="right">73</td>
</tr>
<tr class="odd">
<td align="left">Respiratory</td>
<td align="left">Gram-positive (352-352)</td>
<td align="right">65</td>
<td align="right">80</td>
<td align="right">77</td>
</tr>
<tr class="even">
<td align="left">Rheumatic</td>
<td align="left">Gram-positive (335-335)</td>
<td align="right">67</td>
<td align="right">78</td>
<td align="right">76</td>
<td align="left">Gram-positive (333-333)</td>
<td align="right">68</td>
<td align="right">77</td>
<td align="right">77</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="">2.0.0.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9011</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">

58
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="">2.0.0.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9011</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">
@ -385,18 +385,18 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 R I S I S I</span></span>
<span><span class="co">#&gt; 2 S R R R I R</span></span>
<span><span class="co">#&gt; 3 R R I I S R</span></span>
<span><span class="co">#&gt; 4 I R S I R R</span></span>
<span><span class="co">#&gt; 5 R S S S R R</span></span>
<span><span class="co">#&gt; 6 R S R R R R</span></span>
<span><span class="co">#&gt; 1 R I S R S I</span></span>
<span><span class="co">#&gt; 2 S S I S I I</span></span>
<span><span class="co">#&gt; 3 R I I R I S</span></span>
<span><span class="co">#&gt; 4 I S S R R I</span></span>
<span><span class="co">#&gt; 5 S R R R R I</span></span>
<span><span class="co">#&gt; 6 R S R I R R</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 R</span></span>
<span><span class="co">#&gt; 2 S</span></span>
<span><span class="co">#&gt; 3 R</span></span>
<span><span class="co">#&gt; 4 S</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 2 R</span></span>
<span><span class="co">#&gt; 3 I</span></span>
<span><span class="co">#&gt; 4 I</span></span>
<span><span class="co">#&gt; 5 S</span></span>
<span><span class="co">#&gt; 6 S</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3238</td>
<td align="right">64.76%</td>
<td align="right">3238</td>
<td align="right">64.76%</td>
<td align="right">3221</td>
<td align="right">64.42%</td>
<td align="right">3221</td>
<td align="right">64.42%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1002</td>
<td align="right">20.04%</td>
<td align="right">4240</td>
<td align="right">84.80%</td>
<td align="right">1005</td>
<td align="right">20.10%</td>
<td align="right">4226</td>
<td align="right">84.52%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">408</td>
<td align="right">8.16%</td>
<td align="right">4648</td>
<td align="right">92.96%</td>
<td align="right">439</td>
<td align="right">8.78%</td>
<td align="right">4665</td>
<td align="right">93.30%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">244</td>
<td align="right">4.88%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
<td align="right">241</td>
<td align="right">4.82%</td>
<td align="right">4906</td>
<td align="right">98.12%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">94</td>
<td align="right">1.88%</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="">2.0.0.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9011</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/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="">2.0.0.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9011</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">
@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">17 April 2023</h4>
<h4 data-toc-skip class="date">18 April 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>

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="">2.0.0.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9011</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">

16
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="">2.0.0.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9011</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">
@ -176,7 +176,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">17 April 2023</h4>
<h4 data-toc-skip class="date">18 April 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -877,21 +877,21 @@ inhibitors</td>
<code>clinical_breakpoints</code>: Interpretation from MIC values
&amp; disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
</h2>
<p>A data set with 17 918 rows and 11 columns, containing the following
<p>A data set with 18 271 rows and 11 columns, containing the following
column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
<em>breakpoint_S</em>, <em>breakpoint_R</em>, and <em>uti</em>.</p>
<p>This data set is in R available as <code>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 14 April 2023 21:14:34 UTC. Find more info
<p>It was last updated on 18 April 2023 22:31:31 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.rds" class="external-link">original
R Data Structure (RDS) file</a> (42 kB)<br>
R Data Structure (RDS) file</a> (43 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.txt" class="external-link">tab-separated
text file</a> (1.8 MB)<br>
text file</a> (1.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xlsx" class="external-link">Microsoft
Excel workbook</a> (0.8 MB)<br>
@ -900,10 +900,10 @@ Excel workbook</a> (0.8 MB)<br>
Feather file</a> (0.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.parquet" class="external-link">Apache
Parquet file</a> (89 kB)<br>
Parquet file</a> (87 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sas" class="external-link">SAS
data file</a> (3.5 MB)<br>
data file</a> (3.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sav" class="external-link">IBM
SPSS Statistics data file</a> (2.3 MB)<br>

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="">2.0.0.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9011</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="">2.0.0.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9011</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/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="">2.0.0.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9011</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">