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@ -16,7 +16,7 @@ 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="">2.1.1.9059</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9060</small>
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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">
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@ -179,7 +179,7 @@ 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 34 085 observations and 13 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 34 063 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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@ -192,6 +192,7 @@ 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"</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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</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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@ -235,7 +236,7 @@ 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="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: 34,085 × 13</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 34,063 × 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> B_ACHRMB_XYLS 2 MEM A. xylo…</span>
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@ -248,9 +249,9 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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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… B_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> B_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… B_ACNTB 3 AMK Acineto…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 34,075 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 4 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></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 34,053 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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</div>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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