Built site for AMR@3.0.1.9061: 0c1709c

2026-06-24 12:16:22 +02:00 · 2026-06-23 18:00:14 +00:00
parent 9447e0f2c2
commit 2a7bfb9ffb
328 changed files with 5357 additions and 3687 deletions
--- a/reference/proportion.html
+++ b/reference/proportion.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate Antimicrobial Resistance — proportion • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Calculate Antimicrobial Resistance — proportion"><meta name="description" content="These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also support grouped variables, see Examples.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate Antimicrobial Resistance — proportion • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.8/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.8/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Calculate Antimicrobial Resistance — proportion"><meta name="description" content="These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also support grouped variables, see Examples.
 resistance() should be used to calculate resistance, susceptibility() should be used to calculate susceptibility."><meta property="og:description" content="These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also support grouped variables, see Examples.
 resistance() should be used to calculate resistance, susceptibility() should be used to calculate susceptibility."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be

    <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="">3.0.1.9057</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9061</small>


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@@ -58,46 +58,64 @@ resistance() should be used to calculate resistance, susceptibility() should be

    <div class="section level2">
    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">resistance</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, guideline <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_guideline"</span>,</span>
-<span>  <span class="st">"EUCAST"</span><span class="op">)</span><span class="op">)</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">resistance</span><span class="op">(</span></span>
+<span>  <span class="va">...</span>,</span>
+<span>  minimum <span class="op">=</span> <span class="fl">30</span>,</span>
+<span>  as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  guideline <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_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">susceptibility</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, guideline <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_guideline"</span>,</span>
-<span>  <span class="st">"EUCAST"</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="fu">susceptibility</span><span class="op">(</span></span>
+<span>  <span class="va">...</span>,</span>
+<span>  minimum <span class="op">=</span> <span class="fl">30</span>,</span>
+<span>  as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  guideline <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_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">sir_confidence_interval</span><span class="op">(</span><span class="va">...</span>, ab_result <span class="op">=</span> <span class="st">"R"</span>, minimum <span class="op">=</span> <span class="fl">30</span>,</span>
-<span>  as_percent <span class="op">=</span> <span class="cn">FALSE</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, confidence_level <span class="op">=</span> <span class="fl">0.95</span>,</span>
-<span>  side <span class="op">=</span> <span class="st">"both"</span>, collapse <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
+<span><span class="fu">sir_confidence_interval</span><span class="op">(</span></span>
+<span>  <span class="va">...</span>,</span>
+<span>  ab_result <span class="op">=</span> <span class="st">"R"</span>,</span>
+<span>  minimum <span class="op">=</span> <span class="fl">30</span>,</span>
+<span>  as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  confidence_level <span class="op">=</span> <span class="fl">0.95</span>,</span>
+<span>  side <span class="op">=</span> <span class="st">"both"</span>,</span>
+<span>  collapse <span class="op">=</span> <span class="cn">FALSE</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">proportion_R</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
+<span><span class="fu">proportion_R</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">proportion_IR</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
+<span><span class="fu">proportion_IR</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">proportion_I</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
+<span><span class="fu">proportion_I</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">proportion_SI</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
+<span><span class="fu">proportion_SI</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">proportion_S</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
+<span><span class="fu">proportion_S</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">proportion_df</span><span class="op">(</span><span class="va">data</span>, translate_ab <span class="op">=</span> <span class="st">"name"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  confidence_level <span class="op">=</span> <span class="fl">0.95</span><span class="op">)</span></span>
+<span><span class="fu">proportion_df</span><span class="op">(</span></span>
+<span>  <span class="va">data</span>,</span>
+<span>  translate_ab <span class="op">=</span> <span class="st">"name"</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  minimum <span class="op">=</span> <span class="fl">30</span>,</span>
+<span>  as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  confidence_level <span class="op">=</span> <span class="fl">0.95</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">sir_df</span><span class="op">(</span><span class="va">data</span>, translate_ab <span class="op">=</span> <span class="st">"name"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  confidence_level <span class="op">=</span> <span class="fl">0.95</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">sir_df</span><span class="op">(</span></span>
+<span>  <span class="va">data</span>,</span>
+<span>  translate_ab <span class="op">=</span> <span class="st">"name"</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  minimum <span class="op">=</span> <span class="fl">30</span>,</span>
+<span>  as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  confidence_level <span class="op">=</span> <span class="fl">0.95</span></span>
+<span><span class="op">)</span></span></code></pre></div>
    </div>

-    <div class="section level2">
-    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
-    <p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 5th Edition</strong>, 2022, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p>
-    </div>
    <div class="section level2">
    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>

@@ -204,6 +222,10 @@ resistance() should be used to calculate resistance, susceptibility() should be

 <p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/" class="external-link">https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/</a>).</p>
 <p>This AMR package follows insight; use <code>susceptibility()</code> (equal to <code>proportion_SI()</code>) to determine antimicrobial susceptibility and <code><a href="count.html">count_susceptible()</a></code> (equal to <code><a href="count.html">count_SI()</a></code>) to count susceptible isolates.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 5th Edition</strong>, 2022, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p>
    </div>
    <div class="section level2">
    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>