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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="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, N.
|
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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="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.
|
||||
These breakpoints are currently implemented:
|
||||
For clinical microbiology: EUCAST 2011-2023 and CLSI 2011-2023;
|
||||
For veterinary microbiology: EUCAST 2021-2023 and CLSI 2019-2023;
|
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ECOFFs (Epidemiological cut-off values): EUCAST 2020-2023 and CLSI 2022-2023.
|
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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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ECOFFs (Epidemiological cut-off values): EUCAST 2020-2024 and CLSI 2022-2024.
|
||||
|
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|
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All breakpoints used for interpretation are available in our 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-5.3.1/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="Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir"><meta property="og: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, N.
|
||||
All breakpoints used for interpretation are available in our 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-5.3.1/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="Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir"><meta property="og: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.
|
||||
These breakpoints are currently implemented:
|
||||
For clinical microbiology: EUCAST 2011-2023 and CLSI 2011-2023;
|
||||
For veterinary microbiology: EUCAST 2021-2023 and CLSI 2019-2023;
|
||||
ECOFFs (Epidemiological cut-off values): EUCAST 2020-2023 and CLSI 2022-2023.
|
||||
For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
|
||||
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
|
||||
ECOFFs (Epidemiological cut-off values): EUCAST 2020-2024 and CLSI 2022-2024.
|
||||
|
||||
|
||||
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"><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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@ -24,7 +24,7 @@ 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>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9048</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
|
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|
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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">
|
||||
@ -174,10 +174,10 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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</div>
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|
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<div class="ref-description section level2">
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<p>Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. <code>as.sir()</code> 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> containing the levels <code>S</code>, <code>SDD</code>, <code>I</code>, <code>R</code>, <code>N</code>.</p>
|
||||
<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2023 and CLSI 2011-2023;</p></li>
|
||||
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2023 and CLSI 2019-2023;</p></li>
|
||||
<li><p>ECOFFs (Epidemiological cut-off values): EUCAST 2020-2023 and CLSI 2022-2023.</p></li>
|
||||
<p>Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. <code>as.sir()</code> 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> containing the levels <code>S</code>, <code>SDD</code>, <code>I</code>, <code>R</code>, <code>NI</code>.</p>
|
||||
<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2024 and CLSI 2011-2024;</p></li>
|
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<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2024 and CLSI 2019-2024;</p></li>
|
||||
<li><p>ECOFFs (Epidemiological cut-off values): EUCAST 2020-2024 and CLSI 2022-2024.</p></li>
|
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</ul><p>All breakpoints used for interpretation are available in our <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set.</p>
|
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</div>
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||||
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@ -197,7 +197,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
|
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<span> S <span class="op">=</span> <span class="st">"^(S|U)+$"</span>,</span>
|
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<span> I <span class="op">=</span> <span class="st">"^(I)+$"</span>,</span>
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<span> R <span class="op">=</span> <span class="st">"^(R)+$"</span>,</span>
|
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<span> N <span class="op">=</span> <span class="st">"^(N|V)+$"</span>,</span>
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<span> NI <span class="op">=</span> <span class="st">"^(N|NI|V)+$"</span>,</span>
|
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<span> SDD <span class="op">=</span> <span class="st">"^(SDD|D|H)+$"</span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span>
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@ -256,10 +256,10 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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<div class="section level2">
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<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
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<p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2011-2023, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
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<li><p><strong>CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2023, <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>
|
||||
<li><p><strong>CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals</strong>, 2019-2023, <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>
|
||||
<li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2023, <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>
|
||||
<p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2011-2024, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <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><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>
|
||||
<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>
|
||||
<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>
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
|
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@ -275,7 +275,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
|
||||
<dd><p>maximum fraction of invalid antimicrobial interpretations of <code>x</code>, see <em>Examples</em></p></dd>
|
||||
|
||||
|
||||
<dt>S, I, R, N, SDD</dt>
|
||||
<dt>S, I, R, NI, SDD</dt>
|
||||
<dd><p>a case-independent <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to translate input to this result. This regular expression will be run <em>after</em> all non-letters and whitespaces are removed from the input.</p></dd>
|
||||
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|
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@ -288,7 +288,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
|
||||
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<dt>guideline</dt>
|
||||
<dd><p>defaults to EUCAST 2023 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2023) and CLSI (2011-2023), see <em>Details</em>.</p></dd>
|
||||
<dd><p>defaults to EUCAST 2024 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2024) and CLSI (2011-2024), see <em>Details</em>.</p></dd>
|
||||
|
||||
|
||||
<dt>uti</dt>
|
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@ -345,7 +345,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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<h3 id="how-it-works">How it Works<a class="anchor" aria-label="anchor" href="#how-it-works"></a></h3>
|
||||
|
||||
|
||||
<p>The <code>as.sir()</code> function can work in four ways:</p><ol><li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain valid values, namely: <strong>S</strong> for susceptible, <strong>I</strong> for intermediate or 'susceptible, increased exposure', <strong>R</strong> for resistant, <strong>N</strong> for non-interpretable, and <strong>SDD</strong> for susceptible dose-dependent. Each of these can be set using a <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a>. Furthermore, <code>as.sir()</code> will try its best to clean with some intelligence. For example, mixed values with SIR interpretations and MIC values such as <code>"<0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is invalid.</p></li>
|
||||
<p>The <code>as.sir()</code> function can work in four ways:</p><ol><li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain valid values, namely: <strong>S</strong> for susceptible, <strong>I</strong> for intermediate or 'susceptible, increased exposure', <strong>R</strong> for resistant, <strong>NI</strong> for non-interpretable, and <strong>SDD</strong> for susceptible dose-dependent. Each of these can be set using a <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a>. Furthermore, <code>as.sir()</code> will try its best to clean with some intelligence. For example, mixed values with SIR interpretations and MIC values such as <code>"<0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is invalid.</p></li>
|
||||
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href="as.mic.html">as.mic()</a></code>, that also gives your columns the new data class <code><a href="as.mic.html">mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Using <code>dplyr</code>, SIR interpretation can be done very easily with either:</p>
|
||||
<p></p><div class="sourceCode r"><pre><code><span><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span><span class="op">)</span></span>
|
||||
<span><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span>
|
||||
@ -373,8 +373,8 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
|
||||
<h3 id="supported-guidelines">Supported Guidelines<a class="anchor" aria-label="anchor" href="#supported-guidelines"></a></h3>
|
||||
|
||||
|
||||
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for <strong>clinical microbiology</strong>: EUCAST 2011-2023 and CLSI 2011-2023, and for <strong>veterinary microbiology</strong>: EUCAST 2021-2023 and CLSI 2019-2023.</p>
|
||||
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2023"</code> or <code>"CLSI 2023"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
|
||||
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for <strong>clinical microbiology</strong>: EUCAST 2011-2024 and CLSI 2011-2024, and for <strong>veterinary microbiology</strong>: EUCAST 2021-2024 and CLSI 2019-2024.</p>
|
||||
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2024"</code> or <code>"CLSI 2024"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
|
||||
<p>You can set the default guideline with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code> (e.g. in your <code>.Rprofile</code> file), such as:</p>
|
||||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI"</span>)</span>
|
||||
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI 2018"</span>)</span>
|
||||
@ -397,7 +397,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
|
||||
<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 29 883 rows and 13 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 34 085 rows and 13 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">
|
||||
@ -406,7 +406,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
|
||||
|
||||
<p>The function <code>is.sir()</code> detects if the input contains class <code>sir</code>. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
|
||||
<p>The base R function <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> can be used to retrieve quantitative values from a <code>sir</code> object: <code>"S"</code> = 1, <code>"I"</code>/<code>"SDD"</code> = 2, <code>"R"</code> = 3. All other values are rendered <code>NA</code> . <strong>Note:</strong> Do not use <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code>, since that (because of how R works internally) will return the factor level indices, and not these aforementioned quantitative values.</p>
|
||||
<p>The function <code>is_sir_eligible()</code> returns <code>TRUE</code> when a column contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R and/or N and/or SDD), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
|
||||
<p>The function <code>is_sir_eligible()</code> returns <code>TRUE</code> when a column contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R and/or NI and/or SDD), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
|
||||
</div>
|
||||
|
||||
<p><code>NA_sir_</code> is a missing value of the new <code>sir</code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
|
||||
@ -472,98 +472,98 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-out co"><span class="r-pr">#></span> Mode :character Unique:90 %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #1 :B_ESCHR_COLI %I : 0.7% (n=11) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #2 :B_STPHY_CONS %R :73.7% (n=1201) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #3 :B_STPHY_AURS %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #3 :B_STPHY_AURS %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :68.8% (n=251) %S :70.5% (n=665) %S :40.2% (n=543) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.2% (n=3) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :31.2% (n=114) %R :29.5% (n=278) %R :59.6% (n=804) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMC AMP TZP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :71.4% (n=1342) %S :40.2% (n=543) %S :86.1% (n=862) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 4.8% (n=91) %I : 0.2% (n=3) %I : 1.3% (n=13) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :23.7% (n=446) %R :59.6% (n=804) %R :12.6% (n=126) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CZO FEP CXM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :54.9% (n=245) %S :85.6% (n=620) %S :72.5% (n=1297) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.4% (n=2) %I : 0.1% (n=1) %I : 1.2% (n=22) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :44.6% (n=199) %R :14.2% (n=103) %R :26.3% (n=470) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FOX CTX CAZ </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :71.6% (n=586) %S :84.4% (n=796) %S :33.5% (n=607) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 1.0% (n=8) %I : 0.1% (n=1) %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :27.4% (n=224) %R :15.5% (n=146) %R :66.5% (n=1204) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CRO GEN TOB </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :84.4% (n=796) %S :74.0% (n=1372) %S :65.1% (n=879) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.1% (n=1) %I : 1.5% (n=27) %I : 0.5% (n=7) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :15.5% (n=146) %R :24.6% (n=456) %R :34.4% (n=465) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMK KAN TMP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :36.3% (n=251) %S : 0.0% (n=0) %S :61.2% (n=918) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.7% (n=10) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :63.7% (n=441) %R :100.0% (n=471) %R :38.1% (n=571) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> SXT NIT FOS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :79.1% (n=1392) %S :76.0% (n=565) %S :57.8% (n=203) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.3% (n=6) %I : 6.9% (n=51) %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :20.5% (n=361) %R :17.1% (n=127) %R :42.2% (n=148) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> LNZ CIP MFX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :30.7% (n=314) %S :78.9% (n=1112) %S :64.5% (n=136) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 4.9% (n=69) %I : 1.9% (n=4) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :69.3% (n=709) %R :16.2% (n=228) %R :33.6% (n=71) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> VAN TEC TCY </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :61.7% (n=1149) %S :24.3% (n=237) %S :68.3% (n=820) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 1.9% (n=23) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :38.3% (n=712) %R :75.7% (n=739) %R :29.8% (n=357) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TGC DOX ERY </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :87.3% (n=697) %S :71.7% (n=814) %S :42.3% (n=801) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.6% (n=7) %I : 0.5% (n=9) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :12.7% (n=101) %R :27.7% (n=315) %R :57.2% (n=1084) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CLI AZM IPM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :38.6% (n=586) %S :42.3% (n=801) %S :92.7% (n=824) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.3% (n=4) %I : 0.5% (n=9) %I : 1.1% (n=10) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :61.2% (n=930) %R :57.2% (n=1084) %R : 6.2% (n=55) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MEM MTR CHL </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :94.1% (n=780) %S :85.3% (n=29) %S :78.6% (n=121) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R : 5.9% (n=49) %R :14.7% (n=5) %R :21.4% (n=33) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> COL MUP RIF </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :18.8% (n=309) %S :93.0% (n=251) %S :30.2% (n=303) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 1.1% (n=3) %I : 0.2% (n=2) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :81.2% (n=1331) %R : 5.9% (n=16) %R :69.6% (n=698) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
@ -580,18 +580,18 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'AMP' (ampicillin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'AMP' (ampicillin), EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'CIP' (ciprofloxacin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'CIP' (ciprofloxacin), EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'GEN' (gentamicin), EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'TOB' (tobramycin), EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Assigning class 'sir' to already clean column 'ERY' (erythromycin)...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
@ -603,19 +603,19 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 13 × 14</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_user mo_user ab mo input</span>
|
||||
<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;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-06-13 <span style="color: #949494;">18:59:07</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-06-13 <span style="color: #949494;">18:59:07</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-06-13 <span style="color: #949494;">18:59:07</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-06-13 <span style="color: #949494;">18:59:07</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-06-13 <span style="color: #949494;">18:59:02</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-06-13 <span style="color: #949494;">18:59:02</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-06-13 <span style="color: #949494;">18:59:02</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-06-13 <span style="color: #949494;">18:59:02</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-06-13 <span style="color: #949494;">18:59:02</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-06-13 <span style="color: #949494;">18:59:01</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> 2024-06-13 <span style="color: #949494;">18:59:01</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> 2024-06-13 <span style="color: #949494;">18:59:01</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> 2024-06-13 <span style="color: #949494;">18:59:01</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-06-14 <span style="color: #949494;">20:46:45</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-06-14 <span style="color: #949494;">20:46:45</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-06-14 <span style="color: #949494;">20:46:45</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-06-14 <span style="color: #949494;">20:46:45</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> 2024-06-14 <span style="color: #949494;">20:46:39</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> 2024-06-14 <span style="color: #949494;">20:46:39</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 7 more variables: outcome <sir>, method <chr>, breakpoint_S_R <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># guideline <chr>, host <chr>, ref_table <chr>, uti <lgl></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
@ -629,8 +629,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ampicillin (AMP) in Streptococcus</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> pneumoniae - assuming body site 'Non-meningitis'.</span>
|
||||
@ -646,8 +646,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
|
||||
@ -685,104 +685,104 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2024...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> thus assuming uti = TRUE. See ?as.sir.</span>
|
||||
@ -793,8 +793,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2024...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></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">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> thus assuming uti = TRUE. See ?as.sir.</span>
|
||||
@ -802,25 +802,25 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin), EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'GEN' (gentamicin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'GEN' (gentamicin), EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin), EUCAST 2023...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin), EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism AMP CIP GEN TOB ERY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S <NA> 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>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><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">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"N"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><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">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.sir(): 3 results in column '24' truncated (38%) that were invalid</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> antimicrobial interpretations: "A", "B", and "C"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S SDD I R N <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S SDD I R NI <NA> <NA> <NA></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="st">"<= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S</span>
|
||||
@ -833,10 +833,10 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-plt img"><img src="as.sir-2.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># as common in R, you can use as.integer() to return factor indices:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fu">as.sir</span><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">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"N"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fu">as.sir</span><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">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2 3 4 5 NA</span>
|
||||
<span class="r-in"><span><span class="co"># but for computational use, as.double() will return 1 for S, 2 for I/SDD, and 3 for R:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double</a></span><span class="op">(</span><span class="fu">as.sir</span><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">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"N"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double</a></span><span class="op">(</span><span class="fu">as.sir</span><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">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2 2 3 NA NA</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># the dplyr way</span></span></span>
|
||||
|
||||
Reference in New Issue
Block a user