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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"><meta name="description" content='Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing SIR values. This transforms the input to a new class sir, which is an ordered factor with levels S &amp;lt; I &amp;lt; R.
Currently available breakpoint guidelines are EUCAST 2011-2023 and CLSI 2011-2023, and available breakpoint types are "".
Currently available breakpoint guidelines are EUCAST 2011-2023 and CLSI 2011-2023, and available breakpoint types are "ECOFF", "animal", and "human".
All breakpoints used for interpretation are publicly available in the clinical_breakpoints data set.'><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-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.6/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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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="Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir"><meta property="og:description" content='Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing SIR values. This transforms the input to a new class sir, which is an ordered factor with levels S &amp;lt; I &amp;lt; R.
Currently available breakpoint guidelines are EUCAST 2011-2023 and CLSI 2011-2023, and available breakpoint types are "".
Currently available breakpoint guidelines are EUCAST 2011-2023 and CLSI 2011-2023, and available breakpoint types are "ECOFF", "animal", and "human".
All breakpoints used for interpretation are publicly available in the clinical_breakpoints data set.'><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"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@ -14,7 +14,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9026</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9028</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -165,7 +165,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<div class="ref-description section level2">
<p>Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing SIR values. This transforms the input to a new class <code>sir</code>, which is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with levels <code>S &lt; I &lt; R</code>.</p>
<p>Currently available <strong>breakpoint guidelines</strong> are EUCAST 2011-2023 and CLSI 2011-2023, and available <strong>breakpoint types</strong> are "".</p>
<p>Currently available <strong>breakpoint guidelines</strong> are EUCAST 2011-2023 and CLSI 2011-2023, and available <strong>breakpoint types</strong> are "ECOFF", "animal", and "human".</p>
<p>All breakpoints used for interpretation are publicly available in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set.</p>
</div>
@ -191,7 +191,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<span> reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
<span> include_screening <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
@ -206,7 +206,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<span> reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
<span> include_screening <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
@ -222,7 +222,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<span> reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
<span> include_screening <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="cn">FALSE</span><span class="op">)</span></span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">sir_interpretation_history</span><span class="op">(</span>clean <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
@ -289,7 +289,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<dt>breakpoint_type</dt>
<dd><p>the type of breakpoints to use, either "". ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>.</p></dd>
<dd><p>the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>.</p></dd>
<dt>col_mo</dt>
@ -310,8 +310,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<div class="section">
<p><em>Note: The clinical breakpoints in this package were validated through and imported from <a href="https://whonet.org" class="external-link">WHONET</a> and the public use of this <code>AMR</code> package has been endorsed by CLSI and EUCAST, please see <a href="clinical_breakpoints.html">clinical_breakpoints</a> for more information.</em></p><div class="section">
<h3 id="how-it-works">How it Works<a class="anchor" aria-label="anchor" href="#how-it-works"></a></h3>
@ -354,7 +353,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<h3 id="machine-readable-clinical-breakpoints">Machine-Readable Clinical Breakpoints<a class="anchor" aria-label="anchor" href="#machine-readable-clinical-breakpoints"></a></h3>
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 42 599 rows and 12 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 28 454 rows and 12 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
</div>
<div class="section">
@ -533,29 +532,26 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span> ERY <span class="op">=</span> <span class="st">"R"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'AMP' (ampicillin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'AMP' (ampicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'AMP' (ampicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for ampicillin (AMP) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'CIP' (ciprofloxacin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ampicillin (AMP) in Escherichia coli -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming body site 'Intravenous'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'CIP' (ciprofloxacin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'CIP' (ciprofloxacin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of column 'GEN' (gentamicin) according</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of column 'TOB' (tobramycin) according</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'GEN' (gentamicin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'GEN' (gentamicin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'TOB' (tobramycin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'TOB' (tobramycin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Assigning class 'sir' to already clean column 'ERY' (erythromycin)...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism AMP CIP GEN TOB ERY</span>
@ -563,20 +559,20 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span>
<span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 49 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_guideline mo_input mo_guideline </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-06-26 <span style="color: #949494;">11:57:13</span> 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-06-26 <span style="color: #949494;">11:57:13</span> 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-06-26 <span style="color: #949494;">11:57:12</span> 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-06-26 <span style="color: #949494;">11:57:12</span> 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-06-26 <span style="color: #949494;">11:57:06</span> 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-06-26 <span style="color: #949494;">11:57:06</span> 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-06-26 <span style="color: #949494;">11:57:06</span> 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-06-26 <span style="color: #949494;">11:57:06</span> 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-06-26 <span style="color: #949494;">11:57:06</span> 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-06-26 <span style="color: #949494;">11:57:06</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 40 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-07-08 <span style="color: #949494;">19:07:23</span> 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-07-08 <span style="color: #949494;">19:07:22</span> 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-07-08 <span style="color: #949494;">19:07:22</span> 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-07-08 <span style="color: #949494;">19:07:21</span> 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-07-08 <span style="color: #949494;">19:07:14</span> 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-07-08 <span style="color: #949494;">19:07:14</span> 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-07-08 <span style="color: #949494;">19:07:14</span> 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-07-08 <span style="color: #949494;">19:07:14</span> 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-07-08 <span style="color: #949494;">19:07:14</span> 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-07-08 <span style="color: #949494;">19:07:14</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 39 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6 more variables: guideline &lt;chr&gt;, ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;sir&gt;, breakpoint_S_R &lt;chr&gt;</span></span>
<span class="r-in"><span></span></span>
@ -587,8 +583,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMP"</span>,</span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ampicillin (AMP) in Streptococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> pneumoniae - assuming body site 'Non-meningitis'.</span>
@ -601,8 +597,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span></span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'ampicillin' (AMP) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
@ -637,151 +633,151 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for ampicillin (AMP) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ampicillin (AMP) in Escherichia coli -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming body site 'Intravenous'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for ampicillin (AMP) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ampicillin (AMP) in Escherichia coli -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming body site 'Intravenous'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for ampicillin (AMP) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ampicillin (AMP) in Escherichia coli -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming body site 'Intravenous'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for ampicillin (AMP) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ampicillin (AMP) in Escherichia coli -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming body site 'Intravenous'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for ampicillin (AMP) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ampicillin (AMP) in Escherichia coli -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming body site 'Intravenous'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for ampicillin (AMP) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ampicillin (AMP) in Escherichia coli -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming body site 'Intravenous'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2023...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming uti = TRUE. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * WARNING *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> infection.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use as.sir(uti = FALSE) to prevent this.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2023...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming uti = TRUE. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * WARNING *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism AMP CIP GEN TOB ERY</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S I S S R</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism AMP CIP GEN TOB ERY</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S &lt;NA&gt; S S R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># For CLEANING existing SIR values ------------------------------------</span></span></span>
<span class="r-in"><span></span></span>