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Built site for AMR: 1.8.2.9096@98e62c9

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2023-01-21 22:53:21 +00:00
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commit e289d2568d
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reference/custom_eucast_rules.html
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@@ -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="">1.8.2.9095</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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">
@@ -179,9 +179,9 @@
<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP)</span></span></code></pre><p></p></div>
<p>The rules (the part <em>before</em> the tilde, in above example <code>TZP == "S"</code> and <code>TZP == "R"</code>) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column <code>TZP</code> must exist. We will create a sample data set and test the rules set:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">df</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>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 class="st">"Escherichia coli"</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span>,</span>
<span> TZP <span class="op">=</span> <span class="fu"><a href="../reference/as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="st">"R"</span><span class="op">)</span>,</span>
<span> ampi <span class="op">=</span> <span class="fu"><a href="../reference/as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span>,</span>
<span> cipro <span class="op">=</span> <span class="fu"><a href="../reference/as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span><span class="op">)</span></span>
<span> TZP <span class="op">=</span> <span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="st">"R"</span><span class="op">)</span>,</span>
<span> ampi <span class="op">=</span> <span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span>,</span>
<span> cipro <span class="op">=</span> <span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="va">df</span></span>
<span><span class="co">#&gt; mo TZP ampi cipro</span></span>
<span><span class="co">#&gt; 1 Escherichia coli R S S</span></span>