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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>
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<div class="ref-description">
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<p>These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. <strong>
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</strong></p>
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</div>
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<pre class="usage"><span class='fu'>ab_class</span><span class='op'>(</span><span class='va'>ab_class</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>aminoglycosides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>carbapenems</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>cephalosporins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>cephalosporins_1st</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>cephalosporins_2nd</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>cephalosporins_3rd</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>cephalosporins_4th</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>cephalosporins_5th</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>fluoroquinolones</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>glycopeptides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>macrolides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>oxazolidinones</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>penicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='fu'>tetracyclines</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</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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<tr>
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<th>only_rsi_columns</th>
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<td><p>a logical to indicate whether only columns of class <a href='[rsi]'><code><rsi></code></a> must be selected (defaults to <code>FALSE</code>)</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><strong>
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</strong></p>
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<p>All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the <a href='antibiotics.html'>antibiotics</a> data set. 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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<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
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<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
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The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
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<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
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<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
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<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href='https://msberends.github.io/AMR/articles/datasets.html'>all download links on our website</a>, which is automatically updated with every code change.</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 data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> 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'># `example_isolates` is a data set available in the AMR package.</span>
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<span class='co'># See ?example_isolates.</span>
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<span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
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<span class='va'>example_isolates</span><span class='op'>[</span>, <span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span><span class='op'>]</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='va'>example_isolates</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'>"mo"</span>, <span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span><span class='op'>]</span>
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<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
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<span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
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<span class='va'>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='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</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='va'>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='op'>(</span><span class='va'>mo</span>, <span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</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='va'>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='op'>(</span><span class='va'>mo</span>, <span class='fu'>ab_class</span><span class='op'>(</span><span class='st'>"mycobact"</span><span class='op'>)</span><span class='op'>)</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='va'>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='op'>(</span><span class='fu'><a href='mo_property.html'>mo_is_gram_positive</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</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='op'>(</span><span class='va'>mo</span>, <span class='fu'>macrolides</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</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><span class='op'>)</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>some_column <span class='op'>=</span> <span class='st'>"some_value"</span>,
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J01CA01 <span class='op'>=</span> <span class='st'>"S"</span><span class='op'>)</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='op'>(</span><span class='fu'>penicillins</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># only the 'J01CA01' column will be selected</span>
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<span class='co'># with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:</span>
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<span class='co'># (though the row names on the first are more correct)</span>
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='filter_ab_class.html'>filter_carbapenems</a></span><span class='op'>(</span><span class='st'>"R"</span>, <span class='st'>"all"</span><span class='op'>)</span>
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>~</span><span class='va'>.</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
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<span class='op'>}</span>
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</pre>
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