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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"><title>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir • 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"><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="Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir"><meta name="description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, NI.
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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"><title>Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data — as.sir • 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"><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="Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data — as.sir"><meta name="description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, NI.
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These breakpoints are currently implemented:
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For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
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For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
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@ -13,7 +13,7 @@ For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
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For ECOFFs (Epidemiological Cut-off Values): EUCAST 2012-2024 and CLSI 2022-2024.
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All breakpoints used for interpretation are available in our clinical_breakpoints data set."><meta property="og:image" content="https://msberends.github.io/AMR/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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All breakpoints used for interpretation are available in our clinical_breakpoints data set."><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 href="#main" class="visually-hidden-focusable">Skip to contents</a>
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@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9234</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -58,7 +58,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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</nav><div class="container template-reference-topic">
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<div class="row">
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data</h1>
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<img src="../logo.svg" class="logo" alt=""><h1>Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/sir.R" class="external-link"><code>R/sir.R</code></a></small>
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<div class="d-none name"><code>as.sir.Rd</code></div>
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</div>
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@ -129,7 +129,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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<li><p><strong>CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2024, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
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<li><p><strong>CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals</strong>, 2019-2024, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/veterinary-medicine/documents/vet01/" class="external-link">https://clsi.org/standards/products/veterinary-medicine/documents/vet01/</a>.</p></li>
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<li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2024, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/clinical_breakpoints" class="external-link">https://www.eucast.org/clinical_breakpoints</a>.</p></li>
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<li><p><strong>WHONET</strong> as a source for machine-reading the clinical breakpoints (<a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html#imported-from-whonet">read more here</a>), 1989-2024, <em>WHO Collaborating Centre for Surveillance of Antimicrobial Resistance</em>. <a href="https://whonet.org/" class="external-link">https://whonet.org/</a>.</p></li>
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<li><p><strong>WHONET</strong> as a source for machine-reading the clinical breakpoints (<a href="https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet">read more here</a>), 1989-2024, <em>WHO Collaborating Centre for Surveillance of Antimicrobial Resistance</em>. <a href="https://whonet.org/" class="external-link">https://whonet.org/</a>.</p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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@ -312,7 +312,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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<p>All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.</p>
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<p>For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.</p>
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<p>Visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for direct download links</a>, or explore the actual files in <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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<p>Visit <a href="https://amr-for-r.org/articles/datasets.html">our website for direct download links</a>, or explore the actual files in <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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</div>
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<div class="section level2">
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<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
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@ -842,16 +842,16 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 65 × 17</span></span>
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<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2025-04-07 <span style="color: #949494;">16:46:11</span> 1 DISK ampicillin Strep pneu human 18 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-04-07 <span style="color: #949494;">16:46:12</span> 1 DISK AMP Escherich… human 20 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2025-04-07 <span style="color: #949494;">16:46:12</span> 1 DISK AMP Escherich… human 20 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2025-04-08 <span style="color: #949494;">15:07:44</span> 1 DISK ampicillin Strep pneu human 18 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-04-08 <span style="color: #949494;">15:07:44</span> 1 DISK AMP Escherich… human 20 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2025-04-08 <span style="color: #949494;">15:07:44</span> 1 DISK AMP Escherich… human 20 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-04-07 <span style="color: #949494;">16:46:12</span> 1 DISK GEN Escherich… human 18 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-04-07 <span style="color: #949494;">16:46:12</span> 1 DISK TOB Escherich… human 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-04-07 <span style="color: #949494;">16:46:13</span> 1 MIC AMX B_STRPT_P… human 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-04-07 <span style="color: #949494;">16:46:13</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-04-07 <span style="color: #949494;">16:46:13</span> 2 MIC AMX B_STRPT_P… human 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-04-07 <span style="color: #949494;">16:46:13</span> 3 MIC AMX B_STRPT_P… human 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-04-08 <span style="color: #949494;">15:07:45</span> 1 DISK GEN Escherich… human 18 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-04-08 <span style="color: #949494;">15:07:45</span> 1 DISK TOB Escherich… human 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-04-08 <span style="color: #949494;">15:07:45</span> 1 MIC AMX B_STRPT_P… human 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-04-08 <span style="color: #949494;">15:07:46</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-04-08 <span style="color: #949494;">15:07:46</span> 2 MIC AMX B_STRPT_P… human 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-04-08 <span style="color: #949494;">15:07:46</span> 3 MIC AMX B_STRPT_P… human 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 55 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 10 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
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