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2026-02-08 22:40:23 +00:00
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reference/antimicrobial_selectors.html
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %>%
<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="">3.0.1.9018</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</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">
@@ -211,7 +211,7 @@ my_data_with_all_these_columns %&amp;gt;%
<p>The <code>amr_class()</code> function can be used to filter/select on a manually defined antimicrobial class. It searches for results in the <a href="antimicrobials.html">antimicrobials</a> data set within the columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code>.</p>
<p>The <code>administrable_per_os()</code> and <code>administrable_iv()</code> functions also rely on the <a href="antimicrobials.html">antimicrobials</a> data set - antimicrobials will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the <a href="antimicrobials.html">antimicrobials</a> data set.</p>
<p>The <code>amr_selector()</code> function can be used to internally filter the <a href="antimicrobials.html">antimicrobials</a> data set on any results, see <em>Examples</em>. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.</p>
<p>The <code>not_intrinsic_resistant()</code> function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of <em>E. coli</em> and <em>K. pneumoniae</em> and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023) to determine intrinsic resistance, using the <code><a href="eucast_rules.html">eucast_rules()</a></code> function internally. Because of this determination, this function is quite slow in terms of performance.</p>
<p>The <code>not_intrinsic_resistant()</code> function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of <em>E. coli</em> and <em>K. pneumoniae</em> and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023) to determine intrinsic resistance, using the <code><a href="interpretive_rules.html">eucast_rules()</a></code> function internally. Because of this determination, this function is quite slow in terms of performance.</p>
</div>
<div class="section level2">
<h2 id="full-list-of-supported-antimicrobial-classes">Full list of supported (antimicrobial) classes<a class="anchor" aria-label="anchor" href="#full-list-of-supported-antimicrobial-classes"></a></h2>
@@ -668,7 +668,7 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-in"><span><span class="co"># base R, but add `with = FALSE` if using a single AB selector.</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">dt</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdatatable.gitlab.io/data.table/reference/as.data.table.html" class="external-link">as.data.table</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="va">dt</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/data.table/man/as.data.table.html" class="external-link">as.data.table</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># this does not work, it returns column *names*</span></span></span>
<span class="r-in"><span> <span class="va">dt</span><span class="op">[</span>, <span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>