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<!DOCTYPE html>
<!-- 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"><title>Determine First Isolates — first_isolate • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></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 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
<!-- 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"><title>Determine First Isolates — first_isolate • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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-5.3.8/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.8/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></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 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."><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://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">first_isolate</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, col_date <span class="op">=</span> <span class="cn">NULL</span>, col_patient_id <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>, col_testcode <span class="op">=</span> <span class="cn">NULL</span>, col_specimen <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_icu <span class="op">=</span> <span class="cn">NULL</span>, col_keyantimicrobials <span class="op">=</span> <span class="cn">NULL</span>, episode_days <span class="op">=</span> <span class="fl">365</span>,</span>
<span> testcodes_exclude <span class="op">=</span> <span class="cn">NULL</span>, icu_exclude <span class="op">=</span> <span class="cn">FALSE</span>, specimen_group <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> type <span class="op">=</span> <span class="st">"points"</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"phenotype-based"</span>, <span class="st">"episode-based"</span>,</span>
<span> <span class="st">"patient-based"</span>, <span class="st">"isolate-based"</span><span class="op">)</span>, ignore_I <span class="op">=</span> <span class="cn">TRUE</span>, points_threshold <span class="op">=</span> <span class="fl">2</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, include_unknown <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> include_untested_sir <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">first_isolate</span><span class="op">(</span></span>
<span> x <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_date <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_patient_id <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_testcode <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_specimen <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_icu <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_keyantimicrobials <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> episode_days <span class="op">=</span> <span class="fl">365</span>,</span>
<span> testcodes_exclude <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> icu_exclude <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> specimen_group <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> type <span class="op">=</span> <span class="st">"points"</span>,</span>
<span> method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"phenotype-based"</span>, <span class="st">"episode-based"</span>, <span class="st">"patient-based"</span>, <span class="st">"isolate-based"</span><span class="op">)</span>,</span>
<span> ignore_I <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> points_threshold <span class="op">=</span> <span class="fl">2</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> include_unknown <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> include_untested_sir <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">filter_first_isolate</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, col_date <span class="op">=</span> <span class="cn">NULL</span>, col_patient_id <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>, episode_days <span class="op">=</span> <span class="fl">365</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"phenotype-based"</span>,</span>
<span> <span class="st">"episode-based"</span>, <span class="st">"patient-based"</span>, <span class="st">"isolate-based"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">filter_first_isolate</span><span class="op">(</span></span>
<span> x <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_date <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_patient_id <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> episode_days <span class="op">=</span> <span class="fl">365</span>,</span>
<span> method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"phenotype-based"</span>, <span class="st">"episode-based"</span>, <span class="st">"patient-based"</span>, <span class="st">"isolate-based"</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<p>Methodology of these functions is strictly based on:</p><ul><li><p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 5th Edition</strong>, 2022, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
<li><p>Hindler JF and Stelling J (2007). <strong>Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.</strong> Clinical Infectious Diseases, 44(6), 867-873. <a href="https://doi.org/10.1086/511864" class="external-link">doi:10.1086/511864</a></p></li>
</ul></div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
@@ -199,6 +214,11 @@
</div>
</div>
<div class="section level2">
<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
<p>Methodology of these functions is strictly based on:</p><ul><li><p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 5th Edition</strong>, 2022, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
<li><p>Hindler JF and Stelling J (2007). <strong>Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.</strong> Clinical Infectious Diseases, 44(6), 867-873. <a href="https://doi.org/10.1086/511864" class="external-link">doi:10.1086/511864</a></p></li>
</ul></div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p><code><a href="key_antimicrobials.html">key_antimicrobials()</a></code></p></div>