<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><metaname="description"content="These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see first_isolate()). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes."><title>(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials • AMR (for R)</title><!-- favicons --><linkrel="icon"type="image/png"sizes="16x16"href="../favicon-16x16.png"><linkrel="icon"type="image/png"sizes="32x32"href="../favicon-32x32.png"><linkrel="apple-touch-icon"type="image/png"sizes="180x180"href="../apple-touch-icon.png"><linkrel="apple-touch-icon"type="image/png"sizes="120x120"href="../apple-touch-icon-120x120.png"><linkrel="apple-touch-icon"type="image/png"sizes="76x76"href="../apple-touch-icon-76x76.png"><linkrel="apple-touch-icon"type="image/png"sizes="60x60"href="../apple-touch-icon-60x60.png"><scriptsrc="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><linkhref="../deps/bootstrap-5.1.3/bootstrap.min.css"rel="stylesheet"><scriptsrc="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><linkhref="../deps/Fira_Code-0.4.4/font.css"rel="stylesheet"><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- bootstrap-toc --><scriptsrc="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- search --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js"integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js"integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js"integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww=="crossorigin="anonymous"></script><!-- pkgdown --><scriptsrc="../pkgdown.js"></script><linkhref="../extra.css"rel="stylesheet"><scriptsrc="../extra.js"></script><metaproperty="og:title"content="(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials"><metaproperty="og:description"content="These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see first_isolate()). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes."><metaproperty="og:image"content="https://msberends.github.io/AMR/logo.svg"><metaname="twitter:card"content="summary_l
<p>These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see <code><ahref="first_isolate.html">first_isolate()</a></code>). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes.</p>
<span> type <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/c.html"class="external-link">c</a></span><spanclass="op">(</span><spanclass="st">"points"</span>, <spanclass="st">"keyantimicrobials"</span><spanclass="op">)</span>,</span>
<dd><p>a <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a> with antibiotics columns, like <code>AMX</code> or <code>amox</code>. Can be left blank to determine automatically</p></dd>
<dt>col_mo</dt>
<dd><p>column name of the IDs of the microorganisms (see <code><ahref="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><ahref="as.mo.html">mo</a></code>. Values will be coerced using <code><ahref="as.mo.html">as.mo()</a></code>.</p></dd>
<dd><p>names of <strong>broad-spectrum</strong> antimicrobial drugs, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antimicrobial drugs</p></dd>
<dd><p>names of antibiotic drugs for <strong>Gram-positives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antibiotic drugs</p></dd>
<dd><p>names of antibiotic drugs for <strong>Gram-negatives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antibiotic drugs</p></dd>
<dd><p>names of antifungal drugs for <strong>fungi</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antifungal drugs</p></dd>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to indicate whether only columns must be included that were transformed to class <code>rsi</code> (see <code><ahref="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
<dd><p>ignored, only in place to allow future extensions</p></dd>
<dt>y, z</dt>
<dd><p><ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> vectors to compare</p></dd>
<dt>type</dt>
<dd><p>type to determine weighed isolates; can be <code>"keyantimicrobials"</code> or <code>"points"</code>, see <em>Details</em></p></dd>
<dt>ignore_I</dt>
<dd><p><ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em></p></dd>
<dt>points_threshold</dt>
<dd><p>minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em></p></dd>
<p>The <code>key_antimicrobials()</code> and <code>all_antimicrobials()</code> functions are context-aware. This means that the <code>x</code> argument can be left blank if used inside a <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a> call, see <em>Examples</em>.</p>
<p>The function <code>key_antimicrobials()</code> returns a <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> vector with 12 antimicrobial results for every isolate. The function <code>all_antimicrobials()</code> returns a <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> vector with all antimicrobial drug results for every isolate. These vectors can then be compared using <code>antimicrobials_equal()</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>) by <code>key_antimicrobials()</code> and ignored by <code>antimicrobials_equal()</code>.</p>
<p>Please see the <code><ahref="first_isolate.html">first_isolate()</a></code> function how these important functions enable the 'phenotype-based' method for determination of first isolates.</p>
</ul><p>The default antimicrobial drugs used for <strong>Gram-negative bacteria</strong> (set in <code>gram_negative</code>) are:</p><ul><li><p>Cefotaxime</p></li>
</ul><p>The default antimicrobial drugs used for <strong>Gram-positive bacteria</strong> (set in <code>gram_positive</code>) are:</p><ul><li><p>Erythromycin</p></li>
<divclass="sourceCode"><preclass="sourceCode r"><code><spanclass="r-in"><span><spanclass="co"># `example_isolates` is a data set available in the AMR package.</span></span></span>
<spanclass="r-in"><span><spanclass="co"># See ?example_isolates.</span></span></span>
<spanclass="r-in"><span></span></span>
<spanclass="r-in"><span><spanclass="co"># output of the `key_antimicrobials()` function could be like this:</span></span></span>
<spanclass="r-in"><span><spanclass="co"># those strings can be compared with:</span></span></span>
<spanclass="r-in"><span><spanclass="fu">antimicrobials_equal</span><spanclass="op">(</span><spanclass="va">strainA</span>, <spanclass="va">strainB</span>, type <spanclass="op">=</span><spanclass="st">"keyantimicrobials"</span><spanclass="op">)</span></span></span>
<spanclass="r-in"><span><spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/mutate.html"class="external-link">mutate</a></span><spanclass="op">(</span>keyab <spanclass="op">=</span><spanclass="fu">key_antimicrobials</span><spanclass="op">(</span>antifungal <spanclass="op">=</span><spanclass="cn">NULL</span><spanclass="op">)</span><spanclass="op">)</span><spanclass="op"><ahref="https://magrittr.tidyverse.org/reference/pipe.html"class="external-link">%>%</a></span><spanclass="co"># no need to define `x`</span></span></span>
<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <atarget="_blank"href="https://github.com/msberends/AMR/blob/main/LICENSE"class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <atarget="_blank"href="https://www.rug.nl"class="external-link">University of Groningen</a> and <atarget="_blank"href="https://www.umcg.nl"class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
