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Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025, see Details. All breakpoints used for interpretation are available in our clinical_breakpoints data set."><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.
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Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025, see Details. All breakpoints used for interpretation are available in our clinical_breakpoints data set."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026, see Details. All breakpoints used for interpretation are available in our clinical_breakpoints data set."><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.
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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@@ -53,7 +53,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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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/pkg/data.table/man/fctr.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>
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<p>Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025, see <em>Details</em>. All breakpoints used for interpretation are available in our <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set.</p>
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<p>Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026, see <em>Details</em>. 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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<div class="section level2">
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@@ -118,11 +118,11 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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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>, 2011-2025, <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>, 2011-2025, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
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<li><p><strong>CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals</strong>, 2019-2025, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/veterinary-medicine/documents/vet01/" class="external-link">https://clsi.org/standards/products/veterinary-medicine/documents/vet01/</a>.</p></li>
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<li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2025, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" class="external-link">https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/</a>.</p></li>
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<li><p><strong>WHONET</strong> as a source for machine-reading the clinical breakpoints (<a href="https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet">read more here</a>), 1989-2025, <em>WHO Collaborating Centre for Surveillance of Antimicrobial Resistance</em>. <a href="https://whonet.org/" class="external-link">https://whonet.org/</a>.</p></li>
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<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>, 2011-2026, <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>, 2011-2026, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
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<li><p><strong>CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals</strong>, 2019-2026, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/veterinary-medicine/documents/vet01/" class="external-link">https://clsi.org/standards/products/veterinary-medicine/documents/vet01/</a>.</p></li>
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<li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2026, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" class="external-link">https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/</a>.</p></li>
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<li><p><strong>WHONET</strong> as a source for machine-reading the clinical breakpoints (<a href="https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet">read more here</a>), 1989-2026, <em>WHO Collaborating Centre for Surveillance of Antimicrobial Resistance</em>. <a href="https://whonet.org/" class="external-link">https://whonet.org/</a>.</p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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@@ -158,7 +158,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
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<dd><p>A guideline name (or column name) to use for SIR interpretation. Defaults to EUCAST 2025 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the package option <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2025) and CLSI (2011-2025), see <em>Details</em>. Using a column name allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.</p></dd>
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<dd><p>A guideline name (or column name) to use for SIR interpretation. Defaults to EUCAST 2026 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the package option <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2026) and CLSI (2011-2026), see <em>Details</em>. Using a column name allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.</p></dd>
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<dt id="arg-uti">uti<a class="anchor" aria-label="anchor" href="#arg-uti"></a></dt>
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@@ -283,10 +283,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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<h3 id="supported-guidelines">Supported Guidelines<a class="anchor" aria-label="anchor" href="#supported-guidelines"></a></h3>
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<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are:</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>The <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2025"</code> or <code>"CLSI 2025"</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. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data that must be analysed in the context of, for example, different years.</p>
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<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2026 and CLSI 2011-2026;</p></li>
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<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2026 and CLSI 2019-2026;</p></li>
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<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2020-2026 and CLSI 2022-2026.</p></li>
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</ul><p>The <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2026"</code> or <code>"CLSI 2026"</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. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data that must be analysed in the context of, for example, different years.</p>
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<p>You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
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<p>It is also possible to set the default guideline with the package option <code><a href="AMR-options.html">AMR_guideline</a></code> (e.g. in your <code>.Rprofile</code> file), such as:</p>
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<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>
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@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
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<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2026-03-24 <span style="color: #949494;">12:30:17</span> 1 MIC amoxicillin Escherich… human 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2026-03-24 <span style="color: #949494;">12:30:17</span> 1 MIC cipro Escherich… human 0.256 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2026-03-24 <span style="color: #949494;">12:30:18</span> 1 DISK tobra Escherich… human 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2026-03-24 <span style="color: #949494;">12:30:18</span> 1 DISK genta Escherich… human 18 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2026-03-30 <span style="color: #949494;">08:14:10</span> 1 MIC amoxicillin Escherich… human 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2026-03-30 <span style="color: #949494;">08:14:10</span> 1 MIC cipro Escherich… human 0.256 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2026-03-30 <span style="color: #949494;">08:14:10</span> 1 DISK tobra Escherich… human 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2026-03-30 <span style="color: #949494;">08:14:11</span> 1 DISK genta Escherich… human 18 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
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