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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler et al. in 2007 (doi:10.1086/511864
). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package."><title>Determine First Isolates — first_isolate • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="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 --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Determine First Isolates — first_isolate"><meta property="og:description" content="Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler et al. in 2007 (doi:10.1086/511864
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). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package."><meta property="og:description" content="Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler et al. in 2007 (doi:10.1086/511864
). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"></head><body>
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<img src="../logo.svg" class="logo" alt=""><h1>Determine First Isolates</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/first_isolate.R" class="external-link"><code>R/first_isolate.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/first_isolate.R" class="external-link"><code>R/first_isolate.R</code></a></small>
<div class="d-none name"><code>first_isolate.Rd</code></div>
</div>
@@ -209,91 +103,91 @@
</ul></div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing isolates. Can be left blank for automatic determination, see <em>Examples</em>.</p></dd>
<dt>col_date</dt>
<dt id="arg-col-date">col_date<a class="anchor" aria-label="anchor" href="#arg-col-date"></a></dt>
<dd><p>column name of the result date (or date that is was received on the lab) - the default is the first column with a date class</p></dd>
<dt>col_patient_id</dt>
<dt id="arg-col-patient-id">col_patient_id<a class="anchor" aria-label="anchor" href="#arg-col-patient-id"></a></dt>
<dd><p>column name of the unique IDs of the patients - the default is the first column that starts with 'patient' or 'patid' (case insensitive)</p></dd>
<dt>col_mo</dt>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>col_testcode</dt>
<dt id="arg-col-testcode">col_testcode<a class="anchor" aria-label="anchor" href="#arg-col-testcode"></a></dt>
<dd><p>column name of the test codes. Use <code>col_testcode = NULL</code> to <strong>not</strong> exclude certain test codes (such as test codes for screening). In that case <code>testcodes_exclude</code> will be ignored.</p></dd>
<dt>col_specimen</dt>
<dt id="arg-col-specimen">col_specimen<a class="anchor" aria-label="anchor" href="#arg-col-specimen"></a></dt>
<dd><p>column name of the specimen type or group</p></dd>
<dt>col_icu</dt>
<dt id="arg-col-icu">col_icu<a class="anchor" aria-label="anchor" href="#arg-col-icu"></a></dt>
<dd><p>column name of the logicals (<code>TRUE</code>/<code>FALSE</code>) whether a ward or department is an Intensive Care Unit (ICU). This can also be a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector with the same length as rows in <code>x</code>.</p></dd>
<dt>col_keyantimicrobials</dt>
<dt id="arg-col-keyantimicrobials">col_keyantimicrobials<a class="anchor" aria-label="anchor" href="#arg-col-keyantimicrobials"></a></dt>
<dd><p>(only useful when <code>method = "phenotype-based"</code>) column name of the key antimicrobials to determine first isolates, see <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code>. The default is the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use <code>col_keyantimicrobials = FALSE</code> to prevent this. Can also be the output of <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code>.</p></dd>
<dt>episode_days</dt>
<dt id="arg-episode-days">episode_days<a class="anchor" aria-label="anchor" href="#arg-episode-days"></a></dt>
<dd><p>episode in days after which a genus/species combination will be determined as 'first isolate' again. The default of 365 days is based on the guideline by CLSI, see <em>Source</em>.</p></dd>
<dt>testcodes_exclude</dt>
<dt id="arg-testcodes-exclude">testcodes_exclude<a class="anchor" aria-label="anchor" href="#arg-testcodes-exclude"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector with test codes that should be excluded (case-insensitive)</p></dd>
<dt>icu_exclude</dt>
<dt id="arg-icu-exclude">icu_exclude<a class="anchor" aria-label="anchor" href="#arg-icu-exclude"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether ICU isolates should be excluded (rows with value <code>TRUE</code> in the column set with <code>col_icu</code>)</p></dd>
<dt>specimen_group</dt>
<dt id="arg-specimen-group">specimen_group<a class="anchor" aria-label="anchor" href="#arg-specimen-group"></a></dt>
<dd><p>value in the column set with <code>col_specimen</code> to filter on</p></dd>
<dt>type</dt>
<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
<dd><p>type to determine weighed isolates; can be <code>"keyantimicrobials"</code> or <code>"points"</code>, see <em>Details</em></p></dd>
<dt>method</dt>
<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
<dd><p>the method to apply, either <code>"phenotype-based"</code>, <code>"episode-based"</code>, <code>"patient-based"</code> or <code>"isolate-based"</code> (can be abbreviated), see <em>Details</em>. The default is <code>"phenotype-based"</code> if antimicrobial test results are present in the data, and <code>"episode-based"</code> otherwise.</p></dd>
<dt>ignore_I</dt>
<dt id="arg-ignore-i">ignore_I<a class="anchor" aria-label="anchor" href="#arg-ignore-i"></a></dt>
<dd><p><a href="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>
<dt id="arg-points-threshold">points_threshold<a class="anchor" aria-label="anchor" href="#arg-points-threshold"></a></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>
<dt>info</dt>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dt>include_unknown</dt>
<dt id="arg-include-unknown">include_unknown<a class="anchor" aria-label="anchor" href="#arg-include-unknown"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code <code>"UNKNOWN"</code>, which defaults to <code>FALSE</code>. For WHONET users, this means that all records with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default. Isolates with a microbial ID of <code>NA</code> will always be excluded as first isolate.</p></dd>
<dt>include_untested_sir</dt>
<dt id="arg-include-untested-sir">include_untested_sir<a class="anchor" aria-label="anchor" href="#arg-include-untested-sir"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use <code>include_untested_sir = FALSE</code> to always return <code>FALSE</code> for such rows. This checks the data set for columns of class <code>sir</code> and consequently requires transforming columns with antibiotic results using <code><a href="as.sir.html">as.sir()</a></code> first.</p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>arguments passed on to <code>first_isolate()</code> when using <code>filter_first_isolate()</code>, otherwise arguments passed on to <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code> (such as <code>universal</code>, <code>gram_negative</code>, <code>gram_positive</code>)</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector</p>
<p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -507,7 +401,7 @@
<span class="r-in"><span><span class="co"># }</span></span></span>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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