Built site for AMR@2.1.1.9158: 122bca0

articles/AMR.html

@@ -31,7 +31,7 @@
 
     <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="">2.1.1.9156</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9158</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">
@@ -90,7 +90,7 @@
 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 23 February 2025.</p>
+generated on 26 February 2025.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -146,21 +146,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2025-02-23</td>
+<td align="center">2025-02-26</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">2025-02-23</td>
+<td align="center">2025-02-26</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">2025-02-23</td>
+<td align="center">2025-02-26</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -697,9 +697,9 @@ previously mentioned antibiotic class selectors:</p>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span></code></pre></div>
-<table style="width:100%;" class="table">
+<table class="table">
 <colgroup>
-<col width="16%">
+<col width="14%">
 <col width="14%">
 <col width="14%">
 <col width="14%">
@@ -727,7 +727,7 @@ previously mentioned antibiotic class selectors:</p>
 <td align="left">22% (12-35%)</td>
 </tr>
 <tr class="even">
-<td align="left"><em>E. coli</em></td>
+<td align="left">E. coli</td>
 <td align="left">100% (98-100%)</td>
 <td align="left">98% (96-99%)</td>
 <td align="left">100% (99-100%)</td>
@@ -736,7 +736,7 @@ previously mentioned antibiotic class selectors:</p>
 <td align="left">97% (96-99%)</td>
 </tr>
 <tr class="odd">
-<td align="left"><em>E. faecalis</em></td>
+<td align="left">E. faecalis</td>
 <td align="left">0% (0-9%)</td>
 <td align="left">0% (0-9%)</td>
 <td align="left">100% (91-100%)</td>
@@ -745,7 +745,7 @@ previously mentioned antibiotic class selectors:</p>
 <td align="left">0% (0-9%)</td>
 </tr>
 <tr class="even">
-<td align="left"><em>K. pneumoniae</em></td>
+<td align="left">K. pneumoniae</td>
 <td align="left"></td>
 <td align="left">90% (79-96%)</td>
 <td align="left">100% (93-100%)</td>
@@ -754,7 +754,7 @@ previously mentioned antibiotic class selectors:</p>
 <td align="left">90% (79-96%)</td>
 </tr>
 <tr class="odd">
-<td align="left"><em>P. aeruginosa</em></td>
+<td align="left">P. aeruginosa</td>
 <td align="left"></td>
 <td align="left">100% (88-100%)</td>
 <td align="left"></td>
@@ -763,7 +763,7 @@ previously mentioned antibiotic class selectors:</p>
 <td align="left">100% (88-100%)</td>
 </tr>
 <tr class="even">
-<td align="left"><em>P. mirabilis</em></td>
+<td align="left">P. mirabilis</td>
 <td align="left"></td>
 <td align="left">94% (80-99%)</td>
 <td align="left">94% (79-99%)</td>
@@ -772,7 +772,7 @@ previously mentioned antibiotic class selectors:</p>
 <td align="left">94% (80-99%)</td>
 </tr>
 <tr class="odd">
-<td align="left"><em>S. aureus</em></td>
+<td align="left">S. aureus</td>
 <td align="left"></td>
 <td align="left">99% (97-100%)</td>
 <td align="left"></td>
@@ -781,7 +781,7 @@ previously mentioned antibiotic class selectors:</p>
 <td align="left">98% (92-100%)</td>
 </tr>
 <tr class="even">
-<td align="left"><em>S. epidermidis</em></td>
+<td align="left">S. epidermidis</td>
 <td align="left">0% (0-8%)</td>
 <td align="left">79% (71-85%)</td>
 <td align="left"></td>
@@ -790,7 +790,7 @@ previously mentioned antibiotic class selectors:</p>
 <td align="left">51% (40-61%)</td>
 </tr>
 <tr class="odd">
-<td align="left"><em>S. hominis</em></td>
+<td align="left">S. hominis</td>
 <td align="left"></td>
 <td align="left">92% (84-97%)</td>
 <td align="left"></td>
@@ -799,7 +799,7 @@ previously mentioned antibiotic class selectors:</p>
 <td align="left">85% (74-93%)</td>
 </tr>
 <tr class="even">
-<td align="left"><em>S. pneumoniae</em></td>
+<td align="left">S. pneumoniae</td>
 <td align="left">0% (0-3%)</td>
 <td align="left">0% (0-3%)</td>
 <td align="left"></td>
@@ -877,49 +877,49 @@ a plus <code>+</code> character like this:</p>
 <td align="left"></td>
 </tr>
 <tr class="even">
-<td align="left"><em>E. coli</em></td>
+<td align="left">E. coli</td>
 <td align="left">94% (92-96%)</td>
 <td align="left">100% (98-100%)</td>
 <td align="left">99% (97-100%)</td>
 </tr>
 <tr class="odd">
-<td align="left"><em>K. pneumoniae</em></td>
+<td align="left">K. pneumoniae</td>
 <td align="left">89% (77-96%)</td>
 <td align="left">93% (83-98%)</td>
 <td align="left">93% (83-98%)</td>
 </tr>
 <tr class="even">
-<td align="left"><em>P. aeruginosa</em></td>
+<td align="left">P. aeruginosa</td>
 <td align="left"></td>
 <td align="left">100% (88-100%)</td>
 <td align="left">100% (88-100%)</td>
 </tr>
 <tr class="odd">
-<td align="left"><em>P. mirabilis</em></td>
+<td align="left">P. mirabilis</td>
 <td align="left"></td>
 <td align="left">100% (90-100%)</td>
 <td align="left">100% (90-100%)</td>
 </tr>
 <tr class="even">
-<td align="left"><em>S. aureus</em></td>
+<td align="left">S. aureus</td>
 <td align="left"></td>
 <td align="left">100% (98-100%)</td>
 <td align="left">100% (96-100%)</td>
 </tr>
 <tr class="odd">
-<td align="left"><em>S. epidermidis</em></td>
+<td align="left">S. epidermidis</td>
 <td align="left"></td>
 <td align="left">100% (97-100%)</td>
 <td align="left">100% (92-100%)</td>
 </tr>
 <tr class="even">
-<td align="left"><em>S. hominis</em></td>
+<td align="left">S. hominis</td>
 <td align="left"></td>
 <td align="left">100% (95-100%)</td>
 <td align="left">100% (93-100%)</td>
 </tr>
 <tr class="odd">
-<td align="left"><em>S. pneumoniae</em></td>
+<td align="left">S. pneumoniae</td>
 <td align="left">100% (97-100%)</td>
 <td align="left">100% (97-100%)</td>
 <td align="left">100% (97-100%)</td>
@@ -940,10 +940,10 @@ argument must be used. This can be any column in the data, or e.g. an
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span></code></pre></div>
-<table class="table">
+<table style="width:100%;" class="table">
 <colgroup>
 <col width="13%">
-<col width="14%">
+<col width="12%">
 <col width="12%">
 <col width="12%">
 <col width="12%">
@@ -994,7 +994,7 @@ argument must be used. This can be any column in the data, or e.g. an
 </tr>
 <tr class="even">
 <td align="left">Clinical</td>
-<td align="left"><em>E. coli</em></td>
+<td align="left">E. coli</td>
 <td align="left">100% (97-100%)</td>
 <td align="left">98% (96-99%)</td>
 <td align="left">100% (99-100%)</td>
@@ -1004,7 +1004,7 @@ argument must be used. This can be any column in the data, or e.g. an
 </tr>
 <tr class="odd">
 <td align="left">ICU</td>
-<td align="left"><em>E. coli</em></td>
+<td align="left">E. coli</td>
 <td align="left">100% (93-100%)</td>
 <td align="left">99% (95-100%)</td>
 <td align="left">100% (97-100%)</td>
@@ -1014,7 +1014,7 @@ argument must be used. This can be any column in the data, or e.g. an
 </tr>
 <tr class="even">
 <td align="left">Clinical</td>
-<td align="left"><em>K. pneumoniae</em></td>
+<td align="left">K. pneumoniae</td>
 <td align="left"></td>
 <td align="left">92% (81-98%)</td>
 <td align="left">100% (92-100%)</td>
@@ -1024,7 +1024,7 @@ argument must be used. This can be any column in the data, or e.g. an
 </tr>
 <tr class="odd">
 <td align="left">Clinical</td>
-<td align="left"><em>P. mirabilis</em></td>
+<td align="left">P. mirabilis</td>
 <td align="left"></td>
 <td align="left">100% (88-100%)</td>
 <td align="left"></td>
@@ -1034,7 +1034,7 @@ argument must be used. This can be any column in the data, or e.g. an
 </tr>
 <tr class="even">
 <td align="left">Clinical</td>
-<td align="left"><em>S. aureus</em></td>
+<td align="left">S. aureus</td>
 <td align="left"></td>
 <td align="left">99% (95-100%)</td>
 <td align="left"></td>
@@ -1044,7 +1044,7 @@ argument must be used. This can be any column in the data, or e.g. an
 </tr>
 <tr class="odd">
 <td align="left">ICU</td>
-<td align="left"><em>S. aureus</em></td>
+<td align="left">S. aureus</td>
 <td align="left"></td>
 <td align="left">100% (95-100%)</td>
 <td align="left"></td>
@@ -1054,7 +1054,7 @@ argument must be used. This can be any column in the data, or e.g. an
 </tr>
 <tr class="even">
 <td align="left">Clinical</td>
-<td align="left"><em>S. epidermidis</em></td>
+<td align="left">S. epidermidis</td>
 <td align="left"></td>
 <td align="left">82% (72-90%)</td>
 <td align="left"></td>
@@ -1064,7 +1064,7 @@ argument must be used. This can be any column in the data, or e.g. an
 </tr>
 <tr class="odd">
 <td align="left">ICU</td>
-<td align="left"><em>S. epidermidis</em></td>
+<td align="left">S. epidermidis</td>
 <td align="left"></td>
 <td align="left">72% (60-82%)</td>
 <td align="left"></td>
@@ -1074,7 +1074,7 @@ argument must be used. This can be any column in the data, or e.g. an
 </tr>
 <tr class="even">
 <td align="left">Clinical</td>
-<td align="left"><em>S. hominis</em></td>
+<td align="left">S. hominis</td>
 <td align="left"></td>
 <td align="left">96% (85-99%)</td>
 <td align="left"></td>
@@ -1084,7 +1084,7 @@ argument must be used. This can be any column in the data, or e.g. an
 </tr>
 <tr class="odd">
 <td align="left">Clinical</td>
-<td align="left"><em>S. pneumoniae</em></td>
+<td align="left">S. pneumoniae</td>
 <td align="left">0% (0-5%)</td>
 <td align="left">0% (0-5%)</td>
 <td align="left"></td>
@@ -1094,7 +1094,7 @@ argument must be used. This can be any column in the data, or e.g. an
 </tr>
 <tr class="even">
 <td align="left">ICU</td>
-<td align="left"><em>S. pneumoniae</em></td>
+<td align="left">S. pneumoniae</td>
 <td align="left">0% (0-12%)</td>
 <td align="left">0% (0-12%)</td>
 <td align="left"></td>

articles/AMR_for_Python.html

@@ -31,7 +31,7 @@
 
     <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="">2.1.1.9156</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9158</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">

articles/AMR_with_tidymodels.html

@@ -31,7 +31,7 @@
 
     <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="">2.1.1.9156</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9158</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">
@@ -144,9 +144,6 @@ package.</p>
 <span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">recipes</span>::<span style="color: #00BB00;">step()</span>  masks <span style="color: #0000BB;">stats</span>::step()</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>          <span class="co"># For AMR data analysis</span></span>
 <span></span>
-<span><span class="co"># Load the example_isolates dataset</span></span>
-<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"example_isolates"</span><span class="op">)</span>  <span class="co"># Preloaded dataset with AMR results</span></span>
-<span></span>
 <span><span class="co"># Select relevant columns for prediction</span></span>
 <span><span class="va">data</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="co"># select AB results dynamically</span></span>
@@ -338,7 +335,7 @@ set.</li>
 <code>metrics()</code> computes evaluation metrics like accuracy and
 kappa.</li>
 </ul>
-<p>It appears we can predict the Gram based on AMR results with a 0.995
+<p>It appears we can predict the Gram based on AMR results with a 99.5%
 accuracy based on AMR results of aminoglycosides and beta-lactam
 antibiotics. The ROC curve looks like this:</p>
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">

articles/EUCAST.html

@@ -31,7 +31,7 @@
 
     <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="">2.1.1.9156</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9158</small>
 
 
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articles/MDR.html

@@ -31,7 +31,7 @@
 
     <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="">2.1.1.9156</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9158</small>
 
 
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articles/PCA.html

@@ -31,7 +31,7 @@
 
     <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="">2.1.1.9156</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9158</small>
 
 
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articles/WHONET.html

@@ -31,7 +31,7 @@
 
     <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="">2.1.1.9156</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9158</small>
 
 
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articles/datasets.html

@@ -31,7 +31,7 @@
 
     <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="">2.1.1.9156</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9158</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">
@@ -79,7 +79,7 @@
   <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">23 February 2025</h4>
+            <h4 data-toc-skip class="date">26 February 2025</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="d-none name"><code>datasets.Rmd</code></div>

articles/index.html

@@ -7,7 +7,7 @@
 
     <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="">2.1.1.9156</small>
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articles/resistance_predict.html

@@ -31,7 +31,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
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articles/welcome_to_AMR.html

@@ -31,7 +31,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
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