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<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
<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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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<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="">2.1.1.9246</small>
<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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@ -92,7 +92,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 19 April 2025.</p>
generated on 20 April 2025.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -148,21 +148,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2025-04-19</td>
<td align="center">2025-04-20</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2025-04-19</td>
<td align="center">2025-04-20</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2025-04-19</td>
<td align="center">2025-04-20</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

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@ -31,7 +31,7 @@
<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="">2.1.1.9246</small>
<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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@ -81,7 +81,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">19 April 2025</h4>
<h4 data-toc-skip class="date">20 April 2025</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -418,14 +418,14 @@ all SNOMED codes as comma separated values.</p>
<h2 id="antimicrobials-antibiotic-and-antifungal-drugs">
<code>antimicrobials</code>: Antibiotic and Antifungal Drugs<a class="anchor" aria-label="anchor" href="#antimicrobials-antibiotic-and-antifungal-drugs"></a>
</h2>
<p>A data set with 496 rows and 14 columns, containing the following
<p>A data set with 497 rows and 14 columns, containing the following
column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antimicrobials</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 19 March 2025 15:05:24 UTC. Find more info
<p>It was last updated on 20 April 2025 10:55:31 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
@ -596,38 +596,38 @@ inhibitors</td>
<code>clinical_breakpoints</code>: Interpretation from MIC values
&amp; disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
</h2>
<p>A data set with 34 376 rows and 14 columns, containing the following
<p>A data set with 40 217 rows and 14 columns, containing the following
column names:<br><em>guideline</em>, <em>type</em>, <em>host</em>, <em>method</em>,
<em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>,
<em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>,
<em>breakpoint_R</em>, <em>uti</em>, and <em>is_SDD</em>.</p>
<p>This data set is in R available as <code>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 13 March 2025 14:38:39 UTC. Find more info
<p>It was last updated on 20 April 2025 10:55:31 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/clinical_breakpoints.html">data
set here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.rds" class="external-link">original
R Data Structure (RDS) file</a> (76 kB)<br>
R Data Structure (RDS) file</a> (88 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.txt" class="external-link">tab-separated
text file</a> (3.1 MB)<br>
text file</a> (3.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.xlsx" class="external-link">Microsoft
Excel workbook</a> (2 MB)<br>
Excel workbook</a> (2.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.feather" class="external-link">Apache
Feather file</a> (1.5 MB)<br>
Feather file</a> (1.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.parquet" class="external-link">Apache
Parquet file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.sav" class="external-link">IBM
SPSS Statistics data file</a> (5.6 MB)<br>
SPSS Statistics data file</a> (6.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.dta" class="external-link">Stata
DTA file</a> (9.6 MB)</li>
DTA file</a> (11.1 MB)</li>
</ul>
<p><strong>Example content</strong></p>
<table class="table">
@ -643,7 +643,7 @@ DTA file</a> (9.6 MB)</li>
<col width="2%">
<col width="14%">
<col width="8%">
<col width="9%">
<col width="7%">
<col width="6%">
<col width="6%">
<col width="3%">
@ -669,7 +669,7 @@ DTA file</a> (9.6 MB)</li>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">EUCAST 2024</td>
<td align="center">EUCAST 2025</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@ -687,7 +687,7 @@ DTA file</a> (9.6 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2024</td>
<td align="center">EUCAST 2025</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@ -705,7 +705,7 @@ DTA file</a> (9.6 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2024</td>
<td align="center">EUCAST 2025</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@ -716,14 +716,14 @@ DTA file</a> (9.6 MB)</li>
<td align="center">SXT</td>
<td align="center">Trimethoprim/sulfamethoxazole</td>
<td align="center">A. xylosoxidans</td>
<td align="center">1.25 mcg/23.75 mcg</td>
<td align="center">1.25/23.75 mcg</td>
<td align="center">26.000</td>
<td align="center">26.000</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2024</td>
<td align="center">EUCAST 2025</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@ -741,7 +741,7 @@ DTA file</a> (9.6 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2024</td>
<td align="center">EUCAST 2025</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@ -752,14 +752,14 @@ DTA file</a> (9.6 MB)</li>
<td align="center">TZP</td>
<td align="center">Piperacillin/tazobactam</td>
<td align="center">A. xylosoxidans</td>
<td align="center">30 mcg/6 mcg</td>
<td align="center">30/6 mcg</td>
<td align="center">26.000</td>
<td align="center">26.000</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2024</td>
<td align="center">EUCAST 2025</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@ -1151,37 +1151,37 @@ DTA file</a> (22.6 MB)</li>
<h2 id="dosage-dosage-guidelines-from-eucast">
<code>dosage</code>: Dosage Guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-dosage-guidelines-from-eucast"></a>
</h2>
<p>A data set with 503 rows and 9 columns, containing the following
<p>A data set with 759 rows and 9 columns, containing the following
column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
<em>dose_times</em>, <em>administration</em>, <em>notes</em>,
<em>original_txt</em>, and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 22 June 2023 13:10:59 UTC. Find more info
<p>It was last updated on 20 April 2025 10:55:31 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/dosage.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.rds" class="external-link">original
R Data Structure (RDS) file</a> (3 kB)<br>
R Data Structure (RDS) file</a> (4 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.txt" class="external-link">tab-separated
text file</a> (43 kB)<br>
text file</a> (66 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.xlsx" class="external-link">Microsoft
Excel workbook</a> (25 kB)<br>
Excel workbook</a> (37 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.feather" class="external-link">Apache
Feather file</a> (21 kB)<br>
Feather file</a> (28 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.parquet" class="external-link">Apache
Parquet file</a> (9 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.sav" class="external-link">IBM
SPSS Statistics data file</a> (64 kB)<br>
SPSS Statistics data file</a> (97 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.dta" class="external-link">Stata
DTA file</a> (0.1 MB)</li>
DTA file</a> (0.2 MB)</li>
</ul>
<p><strong>Example content</strong></p>
<table class="table">
@ -1217,7 +1217,7 @@ DTA file</a> (0.1 MB)</li>
<td align="center">iv</td>
<td align="center"></td>
<td align="center">25-30 mg/kg x 1 iv</td>
<td align="center">13</td>
<td align="center">15</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
@ -1228,7 +1228,7 @@ DTA file</a> (0.1 MB)</li>
<td align="center">iv</td>
<td align="center"></td>
<td align="center">2 g x 6 iv</td>
<td align="center">13</td>
<td align="center">15</td>
</tr>
<tr class="odd">
<td align="center">AMX</td>
@ -1239,7 +1239,7 @@ DTA file</a> (0.1 MB)</li>
<td align="center">iv</td>
<td align="center"></td>
<td align="center">1 g x 3-4 iv</td>
<td align="center">13</td>
<td align="center">15</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
@ -1250,7 +1250,7 @@ DTA file</a> (0.1 MB)</li>
<td align="center">oral</td>
<td align="center"></td>
<td align="center">0.75-1 g x 3 oral</td>
<td align="center">13</td>
<td align="center">15</td>
</tr>
<tr class="odd">
<td align="center">AMX</td>
@ -1261,7 +1261,7 @@ DTA file</a> (0.1 MB)</li>
<td align="center">oral</td>
<td align="center"></td>
<td align="center">0.5 g x 3 oral</td>
<td align="center">13</td>
<td align="center">15</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
@ -1272,7 +1272,7 @@ DTA file</a> (0.1 MB)</li>
<td align="center">oral</td>
<td align="center"></td>
<td align="center">0.5 g x 3 oral</td>
<td align="center">13</td>
<td align="center">15</td>
</tr>
</tbody>
</table>
@ -1795,29 +1795,29 @@ set here</a>.</p>
<h2 id="microorganisms-codes-common-laboratory-codes">
<code>microorganisms.codes</code>: Common Laboratory Codes<a class="anchor" aria-label="anchor" href="#microorganisms-codes-common-laboratory-codes"></a>
</h2>
<p>A data set with 4 971 rows and 2 columns, containing the following
<p>A data set with 5 063 rows and 2 columns, containing the following
column names:<br><em>code</em> and <em>mo</em>.</p>
<p>This data set is in R available as <code>microorganisms.codes</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 September 2024 20:17:56 UTC. Find more info
<p>It was last updated on 20 April 2025 10:55:31 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.codes.html">data
set here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.rds" class="external-link">original
R Data Structure (RDS) file</a> (22 kB)<br>
R Data Structure (RDS) file</a> (23 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.txt" class="external-link">tab-separated
text file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.xlsx" class="external-link">Microsoft
Excel workbook</a> (82 kB)<br>
Excel workbook</a> (84 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.feather" class="external-link">Apache
Feather file</a> (85 kB)<br>
Feather file</a> (87 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.parquet" class="external-link">Apache
Parquet file</a> (56 kB)<br>
Parquet file</a> (59 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.sav" class="external-link">IBM
SPSS Statistics data file</a> (0.1 MB)<br>

2
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@ -7,7 +7,7 @@
<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="">2.1.1.9246</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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@ -31,7 +31,7 @@
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<div class="section level3">
<h3 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h3>
<p>The <code>AMR</code> package is a peer-reviewed, <a href="#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. <a href="./authors.html">Many different researchers</a> from around the globe are continually helping us to make this a successful and durable project!</p>
<p>The <code>AMR</code> package is a peer-reviewed, <a href="#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of <a href="./authors.html">many different researchers</a> from around the globe to make this a successful and durable project!</p>
<p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>).</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~79,000 distinct microbial species</strong></a> (updated June 2024) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<div class="section level5">

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9246" id="amr-2119246">AMR 2.1.1.9246<a class="anchor" aria-label="anchor" href="#amr-2119246"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9247" id="amr-2119247">AMR 2.1.1.9247<a class="anchor" aria-label="anchor" href="#amr-2119247"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://amr-for-r.org/#get-this-package">the instructions here</a>.)</em></p>
<div class="section level5">
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9246">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9246"></a></h5>
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9247">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9247"></a></h5>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
</div>
<div class="section level3">
<h3 id="breaking-2-1-1-9246">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9246"></a></h3>
<h3 id="breaking-2-1-1-9247">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9247"></a></h3>
<ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li>
<li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over two years ago.</li>
<li>Functions <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> and <code><a href="../reference/resistance_predict.html">sir_predict()</a></code> is now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a basic introduction</a>.</li>
</ul></div>
<div class="section level3">
<h3 id="new-2-1-1-9246">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9246"></a></h3>
<h3 id="new-2-1-1-9247">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9247"></a></h3>
<ul><li>
<strong>One Health implementation</strong>
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
@ -87,12 +87,13 @@
</ul></li>
<li>
<strong>Updated clinical breakpoints</strong>
<ul><li>EUCAST 2024 and CLSI 2024 are now supported, by adding all of their over 4,000 new clinical breakpoints to the <code>clinical_breakpoints</code> data set for usage in <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2024 is now the new default guideline for all MIC and disk diffusion interpretations.</li>
<ul><li>Breakpoint of 2024 and 2025 of both CLSI and EUCAST are now supported, by adding all of their over 10,000 new clinical breakpoints to the <code>clinical_breakpoints</code> data set for usage in <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2025 is now the new default guideline for all MIC and disk diffusion interpretations.</li>
<li>Added all Expected Resistant Phenotypes from EUCAST (v1.2). The default <code>rules</code> for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> are now: <code>c("breakpoints", "expected_phenotypes")</code>.</li>
<li>Updated the <code>intrinsic_resistant</code> data set, which is now based on EUCAST Expected Resistant Phenotypes v1.2</li>
<li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> now brings additional factor levels: “NI” for non-interpretable and “SDD” for susceptible dose-dependent. Currently, the <code>clinical_breakpoints</code> data set contains 24 breakpoints that can return the value “SDD” instead of “I”.</li>
<li>EUCAST interpretive rules (using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>) are now available for EUCAST 12 (2022), 13 (2023), and 14 (2024).</li>
<li>EUCAST interpretive rules (using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>) are now available for EUCAST 12 (2022), 13 (2023), 14 (2024), and 15 (2025).</li>
<li>EUCAST dosage tables (<code>dosage</code> data set) are now available for EUCAST 13 (2023), 14 (2024), and 15 (2025).</li>
</ul></li>
<li>
<strong>New advanced ggplot2 extensions for MIC and SIR plotting and transforming</strong>
@ -116,7 +117,7 @@
</ul></li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9246">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9246"></a></h3>
<h3 id="changed-2-1-1-9247">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9247"></a></h3>
<ul><li>SIR interpretation
<ul><li>It is now possible to use column names for arguments <code>guideline</code>, <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
@ -148,10 +149,11 @@
<code>antimicrobials</code> data set
<ul><li>Added agents used for screening, with an ID all ending with <code>-S</code>: benzylpenicillin screening test (<code>PEN-S</code>), beta-lactamase screening test (<code>BLA-S</code>), cefotaxime screening test (<code>CTX-S</code>), clindamycin inducible screening test (<code>CLI-S</code>), nalidixic acid screening test (<code>NAL-S</code>), norfloxacin screening test (<code>NOR-S</code>), oxacillin screening test (<code>OXA-S</code>), pefloxacin screening test (<code>PEF-S</code>), and tetracycline screening test (<code>TCY-S</code>). The ID of cefoxitin screening was renamed from <code>FOX1</code> to <code>FOX-S</code>, while the old code remains to work.</li>
<li>For this reason, the antimicrobial selectors <code><a href="../reference/antimicrobial_selectors.html">cephalosporins()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">cephalosporins_3rd()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">lincosamides()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">isoxazolylpenicillins()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">quinolones()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">fluoroquinolones()</a></code>, and <code><a href="../reference/antimicrobial_selectors.html">tetracyclines()</a></code> now contain the argument <code>only_treatable = TRUE</code> (similar to other antimicrobial selectors that contain non-treatable drugs)</li>
<li>Added amorolfine (<code>AMO</code>, D01AE16), which is now also part of the <code><a href="../reference/antimicrobial_selectors.html">antifungals()</a></code> selector</li>
<li>Added efflux (<code>EFF</code>), to allow mapping to AMRFinderPlus</li>
<li>Added amorolfine (<code>AMO</code>, D01AE16), an antimycotic, which is now also part of the <code><a href="../reference/antimicrobial_selectors.html">antifungals()</a></code> selector</li>
<li>Added cefepime/enmetazobactam (<code>FPE</code>), a 4th gen cephalosporin</li>
<li>Added tigemonam (<code>TNM</code>), a monobactam</li>
<li>Added bleomycin (<code>BLM</code>), a glycopeptide</li>
<li>Added efflux (<code>EFF</code>), to allow mapping to AMRFinderPlus</li>
<li>Updated all ATC codes, trade names, and DDDs</li>
</ul></li>
<li>MICs
@ -196,7 +198,7 @@
<li>Added console colours support of <code>sir</code> class for Positron</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9246">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9246"></a></h3>
<h3 id="other-2-1-1-9247">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9247"></a></h3>
<ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old domain (<a href="http://amr-for-r.org" class="external-link uri">http://amr-for-r.org</a>) will remain to work.</li>
<li>Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way</li>
<li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
@ -206,7 +208,7 @@
<li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
</ul></div>
<div class="section level3">
<h3 id="older-versions-2-1-1-9246">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9246"></a></h3>
<h3 id="older-versions-2-1-1-9247">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9247"></a></h3>
<p>This changelog only contains changes from AMR v3.0 (March 2025) and later.</p>
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>

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PCA: PCA.html
welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html
last_built: 2025-04-19T14:26Z
last_built: 2025-04-20T11:00Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 496 rows and 14 columns.</p>
<p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 497 rows and 14 columns.</p>
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<li><p><code>AMR_custom_ab</code> <br> A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li>
<li><p><code>AMR_custom_mo</code> <br> A file location to an RDS file, to use custom microorganisms with this package. This is explained in <code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code>.</p></li>
<li><p><code>AMR_eucastrules</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default types of rules for <code><a href="eucast_rules.html">eucast_rules()</a></code> function, must be one or more of: <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expert")</code>.</p></li>
<li><p><code>AMR_guideline</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default guideline for interpreting MIC values and disk diffusion diameters with <code><a href="as.sir.html">as.sir()</a></code>. Can be only the guideline name (e.g., <code>"CLSI"</code>) or the name with a year (e.g. <code>"CLSI 2019"</code>). The default to the latest implemented EUCAST guideline, currently <code>"EUCAST 2024"</code>. Supported guideline are currently EUCAST (2011-2024) and CLSI (2011-2024).</p></li>
<li><p><code>AMR_guideline</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default guideline for interpreting MIC values and disk diffusion diameters with <code><a href="as.sir.html">as.sir()</a></code>. Can be only the guideline name (e.g., <code>"CLSI"</code>) or the name with a year (e.g. <code>"CLSI 2019"</code>). The default to the latest implemented EUCAST guideline, currently <code>"EUCAST 2025"</code>. Supported guideline are currently EUCAST (2011-2025) and CLSI (2011-2025).</p></li>
<li><p><code>AMR_ignore_pattern</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to ignore (i.e., make <code>NA</code>) any match given in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions.</p></li>
<li><p><code>AMR_include_PKPD</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>.</p></li>
<li><p><code>AMR_substitute_missing_r_breakpoint</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that missing R breakpoints must be substituted with <code>"R"</code> - the default is <code>FALSE</code>.</p></li>

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reference/age.html
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@ -7,7 +7,7 @@
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@ -112,16 +112,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 25 25.80274 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.21918 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.36986 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.13425 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.46301 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.17534 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.16164 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.27123 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.64384 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.22740 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 25 25.80548 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.22192 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.37260 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.13699 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.46575 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.17808 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.16438 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.27397 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.64658 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.23014 21</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

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reference/antibiogram.html
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@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
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reference/antimicrobial_selectors.html
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@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
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@ -217,14 +217,14 @@ my_data_with_all_these_columns %&amp;gt;%
<li><p><code>aminopenicillins()</code> can select: <br> amoxicillin (AMX) and ampicillin (AMP)</p></li>
<li><p><code>antifungals()</code> can select: <br> amorolfine (AMO), amphotericin B (AMB), amphotericin B-high (AMH), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), and voriconazole (VOR)</p></li>
<li><p><code>antimycobacterials()</code> can select: <br> 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)</p></li>
<li><p><code>betalactams()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), carumonam (CAR), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC), and tigemonam (TMN)</p></li>
<li><p><code>betalactams_with_inhibitor()</code> can select: <br> amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>betalactams()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), carumonam (CAR), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC), and tigemonam (TMN)</p></li>
<li><p><code>betalactams_with_inhibitor()</code> can select: <br> amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>carbapenems()</code> can select: <br> biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), and tebipenem (TBP)</p></li>
<li><p><code>cephalosporins()</code> can select: <br> cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)</p></li>
<li><p><code>cephalosporins()</code> can select: <br> cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)</p></li>
<li><p><code>cephalosporins_1st()</code> can select: <br> cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), and cephradine (CED)</p></li>
<li><p><code>cephalosporins_2nd()</code> can select: <br> cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA), and loracarbef (LOR)</p></li>
<li><p><code>cephalosporins_3rd()</code> can select: <br> cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), and latamoxef (LTM)</p></li>
<li><p><code>cephalosporins_4th()</code> can select: <br> cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO), and cefquinome (CEQ)</p></li>
<li><p><code>cephalosporins_4th()</code> can select: <br> cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO), and cefquinome (CEQ)</p></li>
<li><p><code>cephalosporins_5th()</code> can select: <br> ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)</p></li>
<li><p><code>fluoroquinolones()</code> can select: <br> besifloxacin (BES), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)</p></li>
<li><p><code>glycopeptides()</code> can select: <br> avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), and vancomycin-macromethod (VAM)</p></li>

12
reference/antimicrobials.html
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<img src="../logo.svg" class="logo" alt=""><h1>Data Sets with 616 Antimicrobial Drugs</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Data Sets with 617 Antimicrobial Drugs</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="d-none name"><code>antimicrobials.Rd</code></div>
</div>
@ -64,7 +64,7 @@
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<div class="section">
<h3 id="for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-">For the antimicrobials data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 496 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-"></a></h3>
<h3 id="for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-">For the antimicrobials data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 497 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-"></a></h3>
<ul><li><p><code>ab</code><br> antimicrobial ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>cid</code><br> Compound ID as found in PubChem. <em><strong>This is a unique identifier.</strong></em></p></li>
@ -137,7 +137,7 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">antimicrobials</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 496 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 497 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab cid name group atc atc_group1 atc_group2 abbreviations synonyms</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lis&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;list&gt;</span> <span style="color: #949494; font-style: italic;">&lt;named &gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> AMA <span style="text-decoration: underline;">4</span>649 4-ami… Anti… <span style="color: #949494;">&lt;chr&gt;</span> Drugs for… Aminosali… <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
@ -150,7 +150,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> AMX <span style="text-decoration: underline;">33</span>613 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Penicilli… <span style="color: #949494;">&lt;chr [3]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> AMC 23<span style="text-decoration: underline;">665</span>637 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Combinati… <span style="color: #949494;">&lt;chr [5]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> AXS <span style="text-decoration: underline;">465</span>441 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 486 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 487 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5 more variables: oral_ddd &lt;dbl&gt;, oral_units &lt;chr&gt;, iv_ddd &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># iv_units &lt;chr&gt;, loinc &lt;list&gt;</span></span>
<span class="r-in"><span><span class="va">antivirals</span></span></span>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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="">2.1.1.9247</small>
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@ -132,7 +132,7 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">ampicillin</span><span style="color: #0000BB;">' (AMP), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">ampicillin</span><span style="color: #0000BB;">' (AMP), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
@ -144,16 +144,16 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: column '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: column '</span><span style="color: #0000BB; font-weight: bold;">CIP</span><span style="color: #0000BB;">' (ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: column '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">' (tobramycin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism AMP CIP GEN TOB</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S &lt;NA&gt; S S</span>

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reference/as.mic.html
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@ -7,7 +7,7 @@
<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="">2.1.1.9246</small>
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@ -105,7 +105,7 @@
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>To interpret MIC values as SIR values, use <code><a href="as.sir.html">as.sir()</a></code> on MIC values. It supports guidelines from EUCAST (2011-2024) and CLSI (2011-2024).</p>
<p>To interpret MIC values as SIR values, use <code><a href="as.sir.html">as.sir()</a></code> on MIC values. It supports guidelines from EUCAST (2011-2025) and CLSI (2011-2025).</p>
<p>This class for MIC values is a quite a special data type: formally it is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with valid MIC values as <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a>x <span class="ot">&lt;-</span> <span class="fu">random_mic</span>(<span class="dv">10</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a>x</span>
@ -187,9 +187,9 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">amoxicillin (AMX)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Streptococcus pneumoniae</span><span style="color: #080808;"> - assuming body site 'Meningitis'.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">amoxicillin (AMX)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Streptococcus pneumoniae</span><span style="color: #080808;"> - assuming body site 'Meningitis, Endocarditis'.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
<span class="r-in"><span><span class="fu"><a href="as.sir.html">as.sir</a></span><span class="op">(</span></span></span>
@ -202,9 +202,9 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">amoxicillin (AMX)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Streptococcus pneumoniae</span><span style="color: #080808;"> - assuming body site 'Meningitis'.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">amoxicillin (AMX)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Streptococcus pneumoniae</span><span style="color: #080808;"> - assuming body site 'Meningitis, Endocarditis'.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R R R</span>
<span class="r-in"><span></span></span>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -1,16 +1,16 @@
<!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>Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data — as.sir • 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="Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data — as.sir"><meta name="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.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2012-2024 and CLSI 2022-2024.
For clinical microbiology: EUCAST 2011-2025 and CLSI 2011-2025;
For veterinary microbiology: EUCAST 2021-2025 and CLSI 2019-2025;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
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.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2012-2024 and CLSI 2022-2024.
For clinical microbiology: EUCAST 2011-2025 and CLSI 2011-2025;
For veterinary microbiology: EUCAST 2021-2025 and CLSI 2019-2025;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
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>
@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<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="">2.1.1.9246</small>
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@ -65,9 +65,9 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<div class="ref-description section level2">
<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/r/base/factor.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>
<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2024 and CLSI 2011-2024;</p></li>
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2024 and CLSI 2019-2024;</p></li>
<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2012-2024 and CLSI 2022-2024.</p></li>
<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2025 and CLSI 2011-2025;</p></li>
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2025 and CLSI 2019-2025;</p></li>
<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.</p></li>
</ul><p>All breakpoints used for interpretation are available in our <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set.</p>
</div>
@ -125,11 +125,11 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<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>, 2011-2024, <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>
<li><p><strong>CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2024, <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>
<li><p><strong>CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals</strong>, 2019-2024, <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>
<li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2024, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/clinical_breakpoints" class="external-link">https://www.eucast.org/clinical_breakpoints</a>.</p></li>
<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>), 1989-2024, <em>WHO Collaborating Centre for Surveillance of Antimicrobial Resistance</em>. <a href="https://whonet.org/" class="external-link">https://whonet.org/</a>.</p></li>
<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>
<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>
<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>
<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/clinical_breakpoints" class="external-link">https://www.eucast.org/clinical_breakpoints</a>.</p></li>
<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>
</ul></div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
@ -164,7 +164,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
<dd><p>A guideline name (or column name) to use for SIR interpretation. Defaults to EUCAST 2024 (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 (2011-2024) and CLSI (2011-2024), 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>
<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>
<dt id="arg-uti">uti<a class="anchor" aria-label="anchor" href="#arg-uti"></a></dt>
@ -267,8 +267,10 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<h3 id="supported-guidelines">Supported Guidelines<a class="anchor" aria-label="anchor" href="#supported-guidelines"></a></h3>
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for <strong>clinical microbiology</strong>: EUCAST 2011-2024 and CLSI 2011-2024, and for <strong>veterinary microbiology</strong>: EUCAST 2021-2024 and CLSI 2019-2024.</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2024"</code> or <code>"CLSI 2024"</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, which must be analysed in the context of, for example, different years.</p>
<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>
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2025 and CLSI 2019-2025;</p></li>
<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.</p></li>
</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>
<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>
<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>
<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>
@ -579,11 +581,11 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX) based on column</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for amoxicillin (AMX) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Intravenous'. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin) based on column</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
@ -591,19 +593,19 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX) based on column</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for amoxicillin (AMX) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Intravenous'. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin) based on column</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin) based on</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">column '</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">column '</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for tobramycin (TOB) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming an unspecified body site. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin) based on</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">column '</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">column '</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for gentamicin (GEN) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming an unspecified body site. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
@ -611,11 +613,11 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX) based on column</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for amoxicillin (AMX) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Intravenous'. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin) based on column</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
@ -623,15 +625,15 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX) based on column</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for amoxicillin (AMX) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Intravenous'. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin) based on column</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin) based on</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">column '</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">column '</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for tobramycin (TOB) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming an unspecified body site. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
@ -639,15 +641,15 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX) based on column</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for amoxicillin (AMX) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Intravenous'. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin) based on column</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin) based on</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">column '</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">column '</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for tobramycin (TOB) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming an unspecified body site. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
@ -665,7 +667,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX), '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin),</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), and '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin) based on column</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
@ -676,11 +678,11 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span>
@ -691,11 +693,11 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
@ -710,7 +712,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX), '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin),</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), and '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin) based on column</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `mics = (function (x, ...) ...`.</span>
@ -725,7 +727,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX), '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin),</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), and '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin) based on column</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
@ -739,15 +741,15 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Assuming </span><span style="color: #0000BB; background-color: #EEEEEE;">breakpoint_type = "animal"</span><span style="color: #0000BB;">, since </span><span style="color: #0000BB; background-color: #EEEEEE;">host</span><span style="color: #0000BB;"> is set.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (ASP, acetylspiramycin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (ASP, acetylspiramycin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFAFAF;"> WARNING </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • No MIC breakpoints available for acetylspiramycin (ASP).</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (ASP, acetylspiramycin),</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFAFAF;"> WARNING </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • No DISK breakpoints available for acetylspiramycin (ASP).</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (ASP, acetylspiramycin),</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFAFAF;"> WARNING </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • No DISK breakpoints available for acetylspiramycin (ASP).</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 2 warnings in `mutate()`.</span>
@ -763,11 +765,11 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Assuming </span><span style="color: #0000BB; background-color: #EEEEEE;">breakpoint_type = "animal"</span><span style="color: #0000BB;">, since </span><span style="color: #0000BB; background-color: #EEEEEE;">host</span><span style="color: #0000BB;"> is set.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 2 warnings in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
@ -780,7 +782,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: column '</span><span style="color: #0000BB; font-weight: bold;">nitrofuratoin</span><span style="color: #0000BB;">' (NIT,</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">nitrofurantoin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">nitrofurantoin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Assuming value "urine" in column '</span><span style="color: #0000BB; font-weight: bold;">specimen</span><span style="color: #0000BB;">' reflects a urinary tract</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> infection.</span></span>
@ -790,19 +792,19 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: column '</span><span style="color: #0000BB; font-weight: bold;">nitrofuratoin</span><span style="color: #0000BB;">' (NIT,</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">nitrofurantoin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">nitrofurantoin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism amoxicillin cipro tobra genta ERY</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli 8 &lt;NA&gt; S S R</span>
@ -815,19 +817,19 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: column '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: column '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for amoxicillin (AMX) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Intravenous'. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: column '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: column '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for tobramycin (TOB) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming an unspecified body site. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: column '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for gentamicin (GEN) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming an unspecified body site. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Assigning class 'sir' to already clean column '</span><span style="color: #0000BB; font-weight: bold;">ERY</span><span style="color: #0000BB;">' (erythromycin)...</span></span>
@ -840,16 +842,16 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 65 × 17</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-04-19 <span style="color: #949494;">14:26:49</span> 1 DISK ampicillin Strep pneu human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-04-19 <span style="color: #949494;">14:26:49</span> 1 DISK AMP Escherich… human 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-04-19 <span style="color: #949494;">14:26:49</span> 1 DISK AMP Escherich… human 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-04-20 <span style="color: #949494;">11:00:51</span> 1 DISK ampicillin Strep pneu human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-04-20 <span style="color: #949494;">11:00:51</span> 1 DISK AMP Escherich… human 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-04-20 <span style="color: #949494;">11:00:51</span> 1 DISK AMP Escherich… human 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-04-19 <span style="color: #949494;">14:26:50</span> 1 DISK GEN Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-04-19 <span style="color: #949494;">14:26:50</span> 1 DISK TOB Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-04-19 <span style="color: #949494;">14:26:51</span> 1 MIC AMX B_STRPT_P… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-04-19 <span style="color: #949494;">14:26:51</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-04-19 <span style="color: #949494;">14:26:51</span> 2 MIC AMX B_STRPT_P… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-04-19 <span style="color: #949494;">14:26:51</span> 3 MIC AMX B_STRPT_P… human 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-04-20 <span style="color: #949494;">11:00:52</span> 1 DISK GEN Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-04-20 <span style="color: #949494;">11:00:52</span> 1 DISK TOB Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-04-20 <span style="color: #949494;">11:00:53</span> 1 MIC AMX B_STRPT_P… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-04-20 <span style="color: #949494;">11:00:53</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-04-20 <span style="color: #949494;">11:00:53</span> 2 MIC AMX B_STRPT_P… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-04-20 <span style="color: #949494;">11:00:53</span> 3 MIC AMX B_STRPT_P… human 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 55 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 10 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
@ -866,9 +868,9 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ampicillin (AMP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Streptococcus pneumoniae</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ampicillin (AMP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Streptococcus pneumoniae</span><span style="color: #080808;"> - assuming body site 'Non-meningitis, Non-endocarditis'.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
<span class="r-in"><span></span></span>
@ -882,7 +884,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">ampicillin</span><span style="color: #0000BB;">' (AMP), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">ampicillin</span><span style="color: #0000BB;">' (AMP), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>

2
reference/atc_online.html
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@ -7,7 +7,7 @@
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reference/clinical_breakpoints.html
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@ -1,16 +1,16 @@
<!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>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.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2012-2024 and CLSI 2022-2024.
For clinical microbiology: EUCAST 2011-2025 and CLSI 2011-2025;
For veterinary microbiology: EUCAST 2021-2025 and CLSI 2019-2025;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
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.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2012-2024 and CLSI 2022-2024.
For clinical microbiology: EUCAST 2011-2025 and CLSI 2011-2025;
For veterinary microbiology: EUCAST 2021-2025 and CLSI 2019-2025;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
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>
@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<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="">2.1.1.9246</small>
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@ -65,9 +65,9 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<div class="ref-description section level2">
<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>
<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2024 and CLSI 2011-2024;</p></li>
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2024 and CLSI 2019-2024;</p></li>
<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2012-2024 and CLSI 2022-2024.</p></li>
<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2025 and CLSI 2011-2025;</p></li>
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2025 and CLSI 2019-2025;</p></li>
<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.</p></li>
</ul><p>Use <code><a href="as.sir.html">as.sir()</a></code> to transform MICs or disks measurements to SIR values.</p>
</div>
@ -78,7 +78,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<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>
<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>
<li><p><code>type</code><br> Breakpoint type, either "ECOFF", "animal", or "human"</p></li>
<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>
<li><p><code>method</code><br> Testing method, either "DISK" or "MIC"</p></li>
@ -91,7 +91,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<li><p><code>breakpoint_S</code><br> Lowest MIC value or highest number of millimetres that leads to "S"</p></li>
<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>
<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>
<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>
<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>
</ul></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@ -143,20 +143,20 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">clinical_breakpoints</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 34,376 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 40,217 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> guideline type host method site mo rank_index ab ref_tbl </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2024 human human DISK Uncomp… <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EUCAST 2024 human human MIC Uncomp… <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 34,366 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2025 human human DISK Uncomp… <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EUCAST 2025 human human MIC Uncomp… <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 40,207 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5 more variables: disk_dose &lt;chr&gt;, breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># uti &lt;lgl&gt;, is_SDD &lt;lgl&gt;</span></span>
</code></pre></div>

2
reference/count.html
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@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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reference/custom_eucast_rules.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -140,16 +140,16 @@
<li><p>aminopenicillins<br>(amoxicillin and ampicillin)</p></li>
<li><p>antifungals<br>(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
<li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>
<li><p>betalactams<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)</p></li>
<li><p>betalactams_with_inhibitor<br>(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)</p></li>
<li><p>betalactams<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)</p></li>
<li><p>betalactams_with_inhibitor<br>(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)</p></li>
<li><p>carbapenems<br>(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem)</p></li>
<li><p>cephalosporins<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>cephalosporins<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>cephalosporins_1st<br>(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine)</p></li>
<li><p>cephalosporins_2nd<br>(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening test, cefprozil, cefuroxime, cefuroxime axetil, and loracarbef)</p></li>
<li><p>cephalosporins_3rd<br>(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef)</p></li>
<li><p>cephalosporins_4th<br>(cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)</p></li>
<li><p>cephalosporins_4th<br>(cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)</p></li>
<li><p>cephalosporins_5th<br>(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam)</p></li>
<li><p>cephalosporins_except_caz<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>cephalosporins_except_caz<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>fluoroquinolones<br>(besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>glycopeptides<br>(avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod)</p></li>
<li><p>glycopeptides_except_lipo<br>(avoparcin, bleomycin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, and vancomycin-macromethod)</p></li>

32
reference/dosage.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9246</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9247</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -60,15 +60,15 @@
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 503 observations and 9 variables:</p><ul><li><p><code>ab</code><br> Antimicrobial ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 759 observations and 9 variables:</p><ul><li><p><code>ab</code><br> Antimicrobial ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>name</code><br> Official name of the antimicrobial drug as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>type</code><br> Type of the dosage, either "high_dosage", "standard_dosage", or "uncomplicated_uti"</p></li>
<li><p><code>dose</code><br> Dose, such as "2 g" or "25 mg/kg"</p></li>
<li><p><code>dose_times</code><br> Number of times a dose must be administered</p></li>
<li><p><code>administration</code><br> Route of administration, either "im", "iv", or "oral"</p></li>
<li><p><code>administration</code><br> Route of administration, either "", "im", "iv", or "oral"</p></li>
<li><p><code>notes</code><br> Additional dosage notes</p></li>
<li><p><code>original_txt</code><br> Original text in the PDF file of EUCAST</p></li>
<li><p><code>eucast_version</code><br> Version number of the EUCAST Clinical Breakpoints guideline to which these dosages apply, either 13, 12, or 11</p></li>
<li><p><code>eucast_version</code><br> Version number of the EUCAST Clinical Breakpoints guideline to which these dosages apply, either 15, 14, 13.1, 12, or 11</p></li>
</ul></div>
<div class="section level2">
<h2 id="download-our-reference-data">Download Our Reference Data<a class="anchor" aria-label="anchor" href="#download-our-reference-data"></a></h2>
@ -82,20 +82,20 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dosage</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 503 × 9</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 759 × 9</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab name type dose dose_times administration notes original_txt</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> AMK Amikacin stan… 25-3… 1 iv <span style="color: #949494;">""</span> 25-30 mg/kg…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> AMX Amoxicillin high… 2 g 6 iv <span style="color: #949494;">""</span> 2 g x 6 iv </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> AMX Amoxicillin stan… 1 g 3 iv <span style="color: #949494;">""</span> 1 g x 3-4 iv</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> AMX Amoxicillin high… 0.75… 3 oral <span style="color: #949494;">""</span> 0.75-1 g x …</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> AMX Amoxicillin stan… 0.5 g 3 oral <span style="color: #949494;">""</span> 0.5 g x 3 o…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> AMX Amoxicillin unco… 0.5 g 3 oral <span style="color: #949494;">""</span> 0.5 g x 3 o…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> AMC Amoxicillin/cl… high… 2 g … 3 iv <span style="color: #949494;">""</span> (2 g amoxic…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> AMC Amoxicillin/cl… stan… 1 g … 3 iv <span style="color: #949494;">""</span> (1 g amoxic…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> AMC Amoxicillin/cl… high… 0.87… 3 oral <span style="color: #949494;">""</span> (0.875 g am…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> AMC Amoxicillin/cl… stan… 0.5 … 3 oral <span style="color: #949494;">""</span> (0.5 g amox…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 493 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> AMK Amikacin stan… 25-3… 1 iv <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>25-30 mg/k…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> AMX Amoxicillin high… 2 g 6 iv <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>2 g x 6 iv<span style="color: #949494;">"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> AMX Amoxicillin stan… 1 g 3 iv <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>1 g x 3-4 …</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> AMX Amoxicillin high… 0.75… 3 oral <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>0.75-1 g x…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> AMX Amoxicillin stan… 0.5 g 3 oral <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>0.5 g x 3 …</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> AMX Amoxicillin unco… 0.5 g 3 oral <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>0.5 g x 3 …</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> AMC Amoxicillin/cl… high… 2 g … 3 iv <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>(2 g amoxi…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> AMC Amoxicillin/cl… stan… 1 g … 3 iv <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>(1 g amoxi…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> AMC Amoxicillin/cl… high… 0.87… 3 oral <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>(0.875 g a…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> AMC Amoxicillin/cl… stan… 0.5 … 3 oral <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>(0.5 g amo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 749 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: eucast_version &lt;dbl&gt;</span></span>
</code></pre></div>
</div>

16
reference/eucast_rules.html
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@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<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="">2.1.1.9246</small>
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@ -60,12 +60,12 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<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">eucast_rules</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> rules <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_eucastrules"</span>, default <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"breakpoints"</span>,</span>
<span> <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, version_breakpoints <span class="op">=</span> <span class="fl">14</span>,</span>
<span> <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, version_breakpoints <span class="op">=</span> <span class="fl">15</span>,</span>
<span> version_expected_phenotypes <span class="op">=</span> <span class="fl">1.2</span>, version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,</span>
<span> ampc_cephalosporin_resistance <span class="op">=</span> <span class="cn">NA</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> custom_rules <span class="op">=</span> <span class="cn">NULL</span>, overwrite <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="va">ab</span>, administration <span class="op">=</span> <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">12</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="va">ab</span>, administration <span class="op">=</span> <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">15</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
@ -106,7 +106,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt id="arg-version-breakpoints">version_breakpoints<a class="anchor" aria-label="anchor" href="#arg-version-breakpoints"></a></dt>
<dd><p>The version number to use for the EUCAST Clinical Breakpoints guideline. Can be "14.0", "13.1", "12.0", "11.0", or "10.0".</p></dd>
<dd><p>The version number to use for the EUCAST Clinical Breakpoints guideline. Can be "15.0", "14.0", "13.1", "12.0", "11.0", or "10.0".</p></dd>
<dt id="arg-version-expected-phenotypes">version_expected_phenotypes<a class="anchor" aria-label="anchor" href="#arg-version-expected-phenotypes"></a></dt>
@ -142,7 +142,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt id="arg-administration">administration<a class="anchor" aria-label="anchor" href="#arg-administration"></a></dt>
<dd><p>Route of administration, either "im", "iv", or "oral".</p></dd>
<dd><p>Route of administration, either "", "im", "iv", or "oral".</p></dd>
</dl></div>
<div class="section level2">
@ -262,8 +262,8 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 Table 4: Expected resistant phenotype in gram-positive bacteria</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 Table 4: Expected resistant phenotype in gram-positive bacteria</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> rule_source</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 'EUCAST Clinical Breakpoint Tables' v14.0, 2024</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 'EUCAST Clinical Breakpoint Tables' v14.0, 2024</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 'EUCAST Clinical Breakpoint Tables' v15.0, 2025</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 'EUCAST Clinical Breakpoint Tables' v15.0, 2025</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 'EUCAST Expected Resistant Phenotypes' v1.2, 2023</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 'EUCAST Expected Resistant Phenotypes' v1.2, 2023</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 'EUCAST Expected Resistant Phenotypes' v1.2, 2023</span>
@ -274,7 +274,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> Tables' v12.0 (2022). </span><span style="color: #BB0000;">This note will be shown once per session.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> Tables' v15.0 (2025). </span><span style="color: #BB0000;">This note will be shown once per session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab name standard_dosage high_dosage </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>

2
reference/example_isolates.html
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@ -7,7 +7,7 @@
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reference/example_isolates_unclean.html
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@ -7,7 +7,7 @@
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2
reference/export_ncbi_biosample.html
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@ -7,7 +7,7 @@
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2
reference/first_isolate.html
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@ -9,7 +9,7 @@
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2
reference/g.test.html
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@ -7,7 +7,7 @@
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2
reference/get_episode.html
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@ -7,7 +7,7 @@
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reference/ggplot_pca.html
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2
reference/ggplot_sir.html
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@ -7,7 +7,7 @@
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2
reference/guess_ab_col.html
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@ -7,7 +7,7 @@
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6
reference/index.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9246</small>
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@ -367,7 +367,7 @@
<code><a href="antimicrobials.html">antimicrobials</a></code> <code><a href="antimicrobials.html">antivirals</a></code>
</dt>
<dd>Data Sets with 616 Antimicrobial Drugs</dd>
<dd>Data Sets with 617 Antimicrobial Drugs</dd>
</dl><dl><dt>
<code><a href="clinical_breakpoints.html">clinical_breakpoints</a></code>
@ -385,7 +385,7 @@
<code><a href="microorganisms.codes.html">microorganisms.codes</a></code>
</dt>
<dd>Data Set with 4 971 Common Microorganism Codes</dd>
<dd>Data Set with 5 063 Common Microorganism Codes</dd>
</dl><dl><dt>
<code><a href="microorganisms.groups.html">microorganisms.groups</a></code>

2
reference/intrinsic_resistant.html
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@ -7,7 +7,7 @@
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2
reference/like.html
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2
reference/mdro.html
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reference/microorganisms.codes.html
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@ -7,7 +7,7 @@
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@ -44,7 +44,7 @@
</nav><div class="container template-reference-topic">
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 4 971 Common Microorganism Codes</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 5 063 Common Microorganism Codes</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="d-none name"><code>microorganisms.codes.Rd</code></div>
</div>
@ -60,7 +60,7 @@
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 4 971 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism. <em><strong>This is a unique identifier.</strong></em></p></li>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 5 063 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</p></li>
</ul></div>
<div class="section level2">
@ -79,7 +79,7 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms.codes</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4,971 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5,063 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> code mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 1011 <span style="color: #949494;">B_</span>GRAMP </span>
@ -92,7 +92,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 1100 <span style="color: #949494;">B_</span>STRPT </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 1101 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>VIRI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 1102 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>HAEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 4,961 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5,053 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># 'ECO' or 'eco' is the WHONET code for E. coli:</span></span></span>
<span class="r-in"><span><span class="va">microorganisms.codes</span><span class="op">[</span><span class="va">microorganisms.codes</span><span class="op">$</span><span class="va">code</span> <span class="op">==</span> <span class="st">"ECO"</span>, <span class="op">]</span></span></span>

2
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@ -7,7 +7,7 @@
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@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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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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@ -267,7 +267,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<h3 id="the-scale-mic-functions">The <code>scale_*_mic()</code> Functions<a class="anchor" aria-label="anchor" href="#the-scale-mic-functions"></a></h3>
<p>The functions <code>scale_x_mic()</code>, <code>scale_y_mic()</code>, <code>scale_colour_mic()</code>, and <code>scale_fill_mic()</code> functions allow to plot the <a href="as.mic.html">mic</a> class (MIC values) on a continuous, logarithmic scale. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the signs in MIC values if desired. Missing intermediate log2 levels will be plotted too.</p>
<p>The functions <code>scale_x_mic()</code>, <code>scale_y_mic()</code>, <code>scale_colour_mic()</code>, and <code>scale_fill_mic()</code> functions allow to plot the <a href="as.mic.html">mic</a> class (MIC values) on a continuous, logarithmic scale. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the operators in MIC values (such as <code>&gt;=</code>) if desired. Missing intermediate log2 levels will be plotted too.</p>
</div>
<div class="section">
@ -287,7 +287,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<li><p><code>theme_sir()</code> is a <a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">ggplot2 theme</a> with minimal distraction.</p></li>
<li><p><code>labels_sir_count()</code> print datalabels on the bars with percentage and number of isolates, using <code><a href="https://ggplot2.tidyverse.org/reference/geom_text.html" class="external-link">ggplot2::geom_text()</a></code>.</p></li>
</ul><p>The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.</p>
<p>For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2024, unless the package option <code><a href="AMR-options.html">AMR_guideline</a></code> is set. See <code><a href="as.sir.html">as.sir()</a></code> for more information.</p>
<p>For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2025, unless the package option <code><a href="AMR-options.html">AMR_guideline</a></code> is set. See <code><a href="as.sir.html">as.sir()</a></code> for more information.</p>
</div>
</div>
@ -429,7 +429,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
<span class="r-plt img"><img src="plot-12.png" alt="" width="700" height="433"></span>

2
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@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -7,7 +7,7 @@
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@ -93,7 +93,7 @@
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The base <span style="R">R</span> function <code><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample()</a></code> is used for generating values.</p>
<p>Generated values are based on the EUCAST 2024 guideline as implemented in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. To create specific generated values per bug or drug, set the <code>mo</code> and/or <code>ab</code> argument.</p>
<p>Generated values are based on the EUCAST 2025 guideline as implemented in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. To create specific generated values per bug or drug, set the <code>mo</code> and/or <code>ab</code> argument.</p>
</div>
<div class="section level2">

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reference/resistance_predict.html
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reference/skewness.html
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reference/translate.html
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