P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 06:51:48 +02:00
Code Releases Activity

(v1.4.0.9042) auto dark theme website

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-12-21 22:46:29 +01:00
parent 81af41da3a
commit ee70883246
105 changed files with 4069 additions and 1785 deletions
Download Patch File Download Diff File Expand all files Collapse all files

91
docs/articles/EUCAST.html
View File

@ -5,15 +5,32 @@
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>How to apply EUCAST rules • AMR (for R)</title>
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. --><meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script><title>How to apply EUCAST rules • AMR (for R)</title>
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- Flatly Theme - Light --><link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<!-- Darkly Theme - Dark --><link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
<!-- preferably CSS --><link rel="stylesheet" href="../preferably.css">
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
<!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
@ -39,7 +56,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
</span>
</div>
@ -47,14 +64,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@ -63,77 +80,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@ -142,21 +159,21 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
<span class="fas fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
<span class="far fa-newspaper"></span>
Changelog
</a>
@ -165,14 +182,14 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
<span class="fas fa-clipboard-list"></span>
Survey
</a>
@ -187,7 +204,7 @@
</header><script src="EUCAST_files/header-attrs-2.4/header-attrs.js"></script><script src="EUCAST_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
</header><script src="EUCAST_files/header-attrs-2.6/header-attrs.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>How to apply EUCAST rules</h1>
@ -215,8 +232,8 @@
<a href="#examples" class="anchor"></a>Examples</h2>
<p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
<p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
<div class="sourceCode" id="cb1"><pre class="downlit">
<span class="va">oops</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>,
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">oops</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>,
<span class="st">"Escherichia"</span><span class="op">)</span>,
ampicillin <span class="op">=</span> <span class="st">"S"</span><span class="op">)</span>
<span class="va">oops</span>
@ -227,19 +244,19 @@
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">oops</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class="co"># mo ampicillin</span>
<span class="co"># 1 Klebsiella R</span>
<span class="co"># 2 Escherichia S</span></pre></div>
<span class="co"># 2 Escherichia S</span></code></pre></div>
<p>A more convenient function is <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline, but allows to check for one or more specific microorganisms or antibiotics:</p>
<div class="sourceCode" id="cb2"><pre class="downlit">
<span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,
<span class="st">"ampicillin"</span><span class="op">)</span>
<span class="co"># [1] TRUE FALSE</span>
<span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>,
<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span><span class="op">)</span>
<span class="co"># [1] TRUE FALSE</span></pre></div>
<span class="co"># [1] TRUE FALSE</span></code></pre></div>
<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em>, is basically a form of imputation, and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
<div class="sourceCode" id="cb3"><pre class="downlit">
<span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span>,
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span>,
<span class="st">"Enterococcus faecalis"</span>,
<span class="st">"Escherichia coli"</span>,
<span class="st">"Klebsiella pneumoniae"</span>,
@ -251,9 +268,9 @@
CXM <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span>
PEN <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Benzylenicillin</span>
FOX <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span>
stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></pre></div>
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="va">data</span></pre></div>
stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data</span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">mo</th>
@ -318,8 +335,8 @@
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></pre></div>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">mo</th>
@ -402,7 +419,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
</div>
</footer>