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<h1>Antibiotic class selectors</h1>
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<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab_class_selectors.R'><code>R/ab_class_selectors.R</code></a></small>
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<div class="hidden name"><code>antibiotic_class_selectors.Rd</code></div>
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<div class="ref-description">
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<p>Use these selection helpers inside any function that allows <a href='https://tidyselect.r-lib.org/reference/language.html'>Tidyverse selections</a>, like <code><a href='https://dplyr.tidyverse.org/reference/select.html'>dplyr::select()</a></code> or <code><a href='https://tidyr.tidyverse.org/reference/pivot_longer.html'>tidyr::pivot_longer()</a></code>. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.</p>
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</div>
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<pre class="usage"><span class='fu'>ab_class</span>(<span class='kw'>ab_class</span>)
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<span class='fu'>aminoglycosides</span>()
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<span class='fu'>carbapenems</span>()
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<span class='fu'>cephalosporins</span>()
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<span class='fu'>cephalosporins_1st</span>()
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<span class='fu'>cephalosporins_2nd</span>()
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<span class='fu'>cephalosporins_3rd</span>()
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<span class='fu'>cephalosporins_4th</span>()
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<span class='fu'>cephalosporins_5th</span>()
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<span class='fu'>fluoroquinolones</span>()
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<span class='fu'>glycopeptides</span>()
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<span class='fu'>macrolides</span>()
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<span class='fu'>penicillins</span>()
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<span class='fu'>tetracyclines</span>()</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>ab_class</th>
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<td><p>an antimicrobial class, like <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched (case-insensitive) for this value.</p></td>
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</tr>
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</table>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a selector like e.g. <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
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<p>These functions only work if the <code>tidyselect</code> package is installed, that comes with the <code>dplyr</code> package. An error will be thrown if <code>tidyselect</code> package is not installed, or if the functions are used outside a function that allows Tidyverse selections like <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code> or <code>pivot_longer()</code>.</p>
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<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
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<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<div class='dont-index'><p><code><a href='filter_ab_class.html'>filter_ab_class()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> equivalent.</p></div>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'>if</span> (<span class='fl'>FALSE</span>) {
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<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
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<span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>carbapenems</span>())
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<span class='co'># this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>mo</span>, <span class='fu'>aminoglycosides</span>())
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<span class='co'># this will select columns 'mo' and all antimycobacterial drugs ('RIF'):</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>mo</span>, <span class='fu'>ab_class</span>(<span class='st'>"mycobact"</span>))
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<span class='co'># get bug/drug combinations for only macrolides in Gram-positives:</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='kw'>mo</span>) <span class='op'>%like%</span> <span class='st'>"pos"</span>) <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>mo</span>, <span class='fu'>macrolides</span>()) <span class='op'>%>%</span>
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<span class='fu'><a href='bug_drug_combinations.html'>bug_drug_combinations</a></span>() <span class='op'>%>%</span>
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<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>()
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<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(irrelevant = <span class='st'>"value"</span>,
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J01CA01 = <span class='st'>"S"</span>) <span class='op'>%>%</span> <span class='co'># ATC code of ampicillin</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>penicillins</span>()) <span class='co'># so the 'J01CA01' column is selected</span>
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}</pre>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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