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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="">2.0.0.9023</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</small>
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</div>
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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. Currently implemented guidelines are EUCAST (2013-2022) and CLSI (2013-2022). 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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<p>Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2023) and CLSI (2011-2023). 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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<div class="section level2">
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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 18 271 observations and 11 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 42 599 observations and 12 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
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<li><p><code>method</code><br> Either "DISK" or "MIC"</p></li>
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<li><p><code>site</code><br> Body site, e.g. "Oral" or "Respiratory"</p></li>
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<li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
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@ -180,11 +180,13 @@
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<li><p><code>disk_dose</code><br> Dose of the used disk diffusion method</p></li>
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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>ecoff</code><br> Epidemiological cut-off (ECOFF) value, used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi (use <code><a href="as.sir.html">as.sir(..., ecoff = TRUE)</a></code> to interpret raw data using ECOFF values)</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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</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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<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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<p>Clinical breakpoints are validated through <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on <a href="https://whonet.org" class="external-link">their website</a>.</p>
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<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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<p>They <strong>allow for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI.</p>
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</div>
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<div class="section level2">
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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: 18,271 × 11</span></span>
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<span class="r-out co"><span class="r-pr">#></span> guideline method site mo rank_index ab ref_tbl disk_dose</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;"><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 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 2022 MIC <span style="color: #BB0000;">NA</span> F_ASPRG_MGTS 2 AMB Aspergil… <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_ASPRG_NIGR 2 AMB Aspergil… <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_CANDD_ALBC 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_CANDD_DBLN 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_CANDD_GLBR 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_CANDD_KRUS 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_CANDD_PRPS 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_CANDD_TRPC 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_CRYPT_NFRM 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> EUCAST 2022 DISK <span style="color: #BB0000;">NA</span> B_[ORD]_ENTRBCTR 5 AMC Enteroba… 20ug/10ug</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 18,261 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 3 more variables: breakpoint_S <dbl>, breakpoint_R <dbl>, uti <lgl></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 42,599 × 12</span></span>
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<span class="r-out co"><span class="r-pr">#></span> guideline method site mo rank_index ab ref_tbl disk_dose</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;"><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 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 2023 MIC <span style="color: #BB0000;">NA</span> F_ASPRG_MGTS 2 AMB Aspergillus <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_ASPRG_NIGR 2 AMB Aspergillus <span style="color: #BB0000;">NA</span> </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_CANDD_ALBC 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_CANDD_DBLN 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_CANDD_GLBR 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_CANDD_KRUS 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_CANDD_PRPS 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_CANDD_TRPC 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> F_CRYPT_NFRM 2 AMB Candida <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> EUCAST 2023 MIC <span style="color: #BB0000;">NA</span> B_ANAER-NEG 6 AMC Gram-negativ… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 42,589 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 4 more variables: breakpoint_S <dbl>, breakpoint_R <dbl>, ecoff <dbl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># uti <lgl></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
Reference in New Issue
Block a user