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2024-05-20 17:04:05 +00:00
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commit 704eb041fa
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@@ -39,7 +39,7 @@
<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="">2.1.1.9029</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9031</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">
@@ -248,8 +248,9 @@ be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</
<span><span class="va">oops</span></span>
<span><span class="co">#&gt; mo ampicillin</span></span>
<span><span class="co">#&gt; 1 Klebsiella S</span></span>
<span><span class="co">#&gt; 2 Escherichia S</span></span>
<span></span>
<span><span class="co">#&gt; 2 Escherichia S</span></span></code></pre></div>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><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>
<span><span class="co">#&gt; mo ampicillin</span></span>
<span><span class="co">#&gt; 1 Klebsiella R</span></span>
@@ -258,13 +259,14 @@ be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</
<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 sourceCode r">
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,</span>
<span> <span class="st">"ampicillin"</span></span>
<span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] TRUE FALSE</span></span>
<span></span>
<span><span class="co">#&gt; [1] TRUE FALSE</span></span></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span></span>
<span> <span class="st">"Klebsiella"</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span></span>
@@ -275,7 +277,7 @@ 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 sourceCode r">
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data</span> <span class="op">&lt;-</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> mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span>
<span> <span class="st">"Staphylococcus aureus"</span>,</span>
@@ -293,7 +295,7 @@ reading</em>, is basically a form of imputation, and is part of the
<span> FOX <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span></span>
<span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span></span>
<span><span class="op">)</span></span></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
@@ -359,7 +361,7 @@ reading</em>, is basically a form of imputation, and is part of the
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><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></span></code></pre></div>
<table class="table">
<thead><tr class="header">