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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints • 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-0.4.10/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="Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints"><meta name="description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
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These breakpoints are currently implemented:
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For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
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For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
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For ECOFFs (Epidemiological Cut-off Values): EUCAST 2012-2024 and CLSI 2022-2024.
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For clinical microbiology: EUCAST 2011-2025 and CLSI 2011-2025;
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For veterinary microbiology: EUCAST 2021-2025 and CLSI 2019-2025;
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For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
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Use as.sir() to transform MICs or disks measurements to SIR values."><meta property="og:description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
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These breakpoints are currently implemented:
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For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
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For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
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For ECOFFs (Epidemiological Cut-off Values): EUCAST 2012-2024 and CLSI 2022-2024.
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For clinical microbiology: EUCAST 2011-2025 and CLSI 2011-2025;
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For veterinary microbiology: EUCAST 2021-2025 and CLSI 2019-2025;
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For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
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Use as.sir() to transform MICs or disks measurements to SIR values."><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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@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9246</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9247</small>
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@ -65,9 +65,9 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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<div class="ref-description section level2">
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<p>Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.</p>
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<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>
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<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2012-2024 and CLSI 2022-2024.</p></li>
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<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2025 and CLSI 2011-2025;</p></li>
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<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2025 and CLSI 2019-2025;</p></li>
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<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.</p></li>
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</ul><p>Use <code><a href="as.sir.html">as.sir()</a></code> to transform MICs or disks measurements to SIR values.</p>
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</div>
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@ -78,7 +78,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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<div class="section level2">
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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
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<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 34 376 observations and 14 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
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<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 40 217 observations and 14 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
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<li><p><code>type</code><br> Breakpoint type, either "ECOFF", "animal", or "human"</p></li>
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<li><p><code>host</code><br> Host of infectious agent. This is mostly useful for veterinary breakpoints and is either "ECOFF", "aquatic", "cats", "cattle", "dogs", "horse", "human", "poultry", or "swine"</p></li>
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<li><p><code>method</code><br> Testing method, either "DISK" or "MIC"</p></li>
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@ -91,7 +91,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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<li><p><code>breakpoint_S</code><br> Lowest MIC value or highest number of millimetres that leads to "S"</p></li>
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<li><p><code>breakpoint_R</code><br> Highest MIC value or lowest number of millimetres that leads to "R", can be <code>NA</code></p></li>
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<li><p><code>uti</code><br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> value (<code>TRUE</code>/<code>FALSE</code>) to indicate whether the rule applies to a urinary tract infection (UTI)</p></li>
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<li><p><code>is_SDD</code><br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> value (<code>TRUE</code>/<code>FALSE</code>) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 24 breakpoints.</p></li>
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<li><p><code>is_SDD</code><br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> value (<code>TRUE</code>/<code>FALSE</code>) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 48 breakpoints.</p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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@ -143,20 +143,20 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">clinical_breakpoints</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 34,376 × 14</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 40,217 × 14</span></span>
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<span class="r-out co"><span class="r-pr">#></span> guideline type host method site mo rank_index ab ref_tbl </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2024 human human DISK <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS 2 MEM A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2024 human human MIC <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS 2 MEM A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2024 human human DISK <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS 2 SXT A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2024 human human MIC <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS 2 SXT A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2024 human human DISK <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS 2 TZP A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2024 human human MIC <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS 2 TZP A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2024 human human DISK <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2024 human human DISK Uncomp… <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2024 human human MIC <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> EUCAST 2024 human human MIC Uncomp… <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 34,366 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2025 human human DISK <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS 2 MEM A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2025 human human MIC <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS 2 MEM A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2025 human human DISK <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS 2 SXT A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2025 human human MIC <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS 2 SXT A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2025 human human DISK <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS 2 TZP A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2025 human human MIC <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS 2 TZP A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2025 human human DISK <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2025 human human DISK Uncomp… <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2025 human human MIC <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> EUCAST 2025 human human MIC Uncomp… <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 40,207 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 5 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># uti <lgl>, is_SDD <lgl></span></span>
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</code></pre></div>
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