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2
404.html
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@@ -31,7 +31,7 @@
<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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">

4
CLAUDE.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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -73,7 +73,7 @@
<span><span class="fu">pkgdown</span><span class="fu">::</span><span class="fu"><a href="https://pkgdown.r-lib.org/reference/build_site.html" class="external-link">build_site</a></span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Code coverage report</span></span>
<span><span class="fu">covr</span><span class="fu">::</span><span class="fu"><a href="http://covr.r-lib.org/reference/package_coverage.html" class="external-link">package_coverage</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">covr</span><span class="fu">::</span><span class="fu">package_coverage</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>From the shell:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="co"># CRAN check from parent directory</span></span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="ex">R</span> CMD check AMR</span></code></pre></div>

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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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">

14
articles/AMR.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -91,7 +91,7 @@
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 24 March 2026.</p>
generated on 30 March 2026.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2026-03-24</td>
<td align="center">2026-03-30</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">2026-03-24</td>
<td align="center">2026-03-30</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">2026-03-24</td>
<td align="center">2026-03-30</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -263,8 +263,8 @@ user input can be used:</p>
<p>Now we can thus clean our data:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Retrieved values from the `microorganisms.codes` data set for "ESCCOL",</span></span>
<span><span class="co">#&gt; "KLEPNE", "STAAUR", and "STRPNE".</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Retrieved values from the `microorganisms.codes` data set for <span style="color: #0000BB;">"ESCCOL"</span>,</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">"KLEPNE"</span>, <span style="color: #0000BB;">"STAAUR"</span>, and <span style="color: #0000BB;">"STRPNE"</span>.</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Microorganism translation was uncertain for four microorganisms. Run</span></span>
<span><span class="co">#&gt; `mo_uncertainties()` to review these uncertainties, or use</span></span>
<span><span class="co">#&gt; `add_custom_microorganisms()` to add custom entries.</span></span></code></pre></div>

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articles/AMR.md
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@@ -3,7 +3,7 @@
**Note:** values on this page will change with every website update
since they are based on randomly created values and the page was written
in [R Markdown](https://rmarkdown.rstudio.com/). However, the
methodology remains unchanged. This page was generated on 24 March 2026.
methodology remains unchanged. This page was generated on 30 March 2026.
## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-03-24 | abcd | Escherichia coli | S | S |
| 2026-03-24 | abcd | Escherichia coli | S | R |
| 2026-03-24 | efgh | Escherichia coli | R | S |
| 2026-03-30 | abcd | Escherichia coli | S | S |
| 2026-03-30 | abcd | Escherichia coli | S | R |
| 2026-03-30 | efgh | Escherichia coli | R | S |
### Needed R packages

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articles/AMR_for_Python.html
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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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">

2
articles/AMR_with_tidymodels.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">

2
articles/EUCAST.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">

2
articles/PCA.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">

2
articles/WHONET.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">

2
articles/WISCA.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">

42
articles/datasets.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -80,7 +80,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
<h4 data-toc-skip class="date">24 March 2026</h4>
<h4 data-toc-skip class="date">30 March 2026</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>
@@ -595,38 +595,38 @@ 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 40 217 rows and 14 columns, containing the following
<p>A data set with 45 797 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 20 April 2025 10:55:31 UTC. Find more info
<p>It was last updated on 30 March 2026 08:01:49 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> (88 kB)<br>
R Data Structure (RDS) file</a> (92 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> (3.7 MB)<br>
text file</a> (4.2 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> (2.4 MB)<br>
Excel workbook</a> (2.7 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> (1.8 MB)<br>
Feather file</a> (2 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> (6.6 MB)<br>
SPSS Statistics data file</a> (7.5 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> (11.1 MB)</li>
DTA file</a> (12.6 MB)</li>
</ul>
<p><strong>Example content</strong></p>
<table class="table">
@@ -668,7 +668,7 @@ DTA file</a> (11.1 MB)</li>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">EUCAST 2025</td>
<td align="center">EUCAST 2026</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@@ -686,7 +686,7 @@ DTA file</a> (11.1 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2025</td>
<td align="center">EUCAST 2026</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@@ -704,7 +704,7 @@ DTA file</a> (11.1 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2025</td>
<td align="center">EUCAST 2026</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@@ -722,7 +722,7 @@ DTA file</a> (11.1 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2025</td>
<td align="center">EUCAST 2026</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@@ -740,7 +740,7 @@ DTA file</a> (11.1 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2025</td>
<td align="center">EUCAST 2026</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@@ -758,7 +758,7 @@ DTA file</a> (11.1 MB)</li>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2025</td>
<td align="center">EUCAST 2026</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@@ -1794,17 +1794,17 @@ 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 6 036 rows and 2 columns, containing the following
<p>A data set with 6 050 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 4 May 2025 16:50:25 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
<p>It was last updated on 30 March 2026 08:01:49 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> (27 kB)<br>
R Data Structure (RDS) file</a> (28 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>
@@ -1816,7 +1816,7 @@ Excel workbook</a> (98 kB)<br>
Feather file</a> (0.1 MB)<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> (68 kB)<br>
Parquet file</a> (69 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> (0.2 MB)<br>

38
articles/datasets.md
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@@ -147,7 +147,7 @@ as comma separated values.
## `clinical_breakpoints`: Interpretation from MIC values & disk diameters to SIR
A data set with 40 217 rows and 14 columns, containing the following
A data set with 45 797 rows and 14 columns, containing the following
column names:
*guideline*, *type*, *host*, *method*, *site*, *mo*, *rank_index*, *ab*,
*ref_tbl*, *disk_dose*, *breakpoint_S*, *breakpoint_R*, *uti*, and
@@ -156,7 +156,7 @@ column names:
This data set is in R available as `clinical_breakpoints`, after you
load the `AMR` package.
It was last updated on 20 April 2025 10:55:31 UTC. Find more info about
It was last updated on 30 March 2026 08:01:49 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/clinical_breakpoints.html).
@@ -164,36 +164,36 @@ here](https://amr-for-r.org/reference/clinical_breakpoints.html).
- Download as [original R Data Structure (RDS)
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.rds)
(88 kB)
(92 kB)
- Download as [tab-separated text
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.txt)
(3.7 MB)
(4.2 MB)
- Download as [Microsoft Excel
workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.xlsx)
(2.4 MB)
(2.7 MB)
- Download as [Apache Feather
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.feather)
(1.8 MB)
(2 MB)
- Download as [Apache Parquet
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.parquet)
(0.1 MB)
- Download as [IBM SPSS Statistics data
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.sav)
(6.6 MB)
(7.5 MB)
- Download as [Stata DTA
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.dta)
(11.1 MB)
(12.6 MB)
**Example content**
| guideline | type | host | method | site | mo | mo_name | rank_index | ab | ab_name | ref_tbl | disk_dose | breakpoint_S | breakpoint_R | uti | is_SDD |
|:-----------:|:-----:|:-----:|:------:|:----:|:-------------:|:--------------------------:|:----------:|:---:|:-----------------------------:|:---------------:|:--------------:|:------------:|:------------:|:-----:|:------:|
| EUCAST 2025 | human | human | DISK | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | MEM | Meropenem | A. xylosoxidans | 10 mcg | 26.000 | 20.000 | FALSE | FALSE |
| EUCAST 2025 | human | human | MIC | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | MEM | Meropenem | A. xylosoxidans | | 1.000 | 4.000 | FALSE | FALSE |
| EUCAST 2025 | human | human | DISK | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | SXT | Trimethoprim/sulfamethoxazole | A. xylosoxidans | 1.25/23.75 mcg | 26.000 | 26.000 | FALSE | FALSE |
| EUCAST 2025 | human | human | MIC | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | SXT | Trimethoprim/sulfamethoxazole | A. xylosoxidans | | 0.125 | 0.125 | FALSE | FALSE |
| EUCAST 2025 | human | human | DISK | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | TZP | Piperacillin/tazobactam | A. xylosoxidans | 30/6 mcg | 26.000 | 26.000 | FALSE | FALSE |
| EUCAST 2025 | human | human | MIC | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | TZP | Piperacillin/tazobactam | A. xylosoxidans | | 4.000 | 4.000 | FALSE | FALSE |
| EUCAST 2026 | human | human | DISK | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | MEM | Meropenem | A. xylosoxidans | 10 mcg | 26.000 | 20.000 | FALSE | FALSE |
| EUCAST 2026 | human | human | MIC | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | MEM | Meropenem | A. xylosoxidans | | 1.000 | 4.000 | FALSE | FALSE |
| EUCAST 2026 | human | human | DISK | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | SXT | Trimethoprim/sulfamethoxazole | A. xylosoxidans | 1.25/23.75 mcg | 26.000 | 26.000 | FALSE | FALSE |
| EUCAST 2026 | human | human | MIC | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | SXT | Trimethoprim/sulfamethoxazole | A. xylosoxidans | | 0.125 | 0.125 | FALSE | FALSE |
| EUCAST 2026 | human | human | DISK | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | TZP | Piperacillin/tazobactam | A. xylosoxidans | 30/6 mcg | 26.000 | 26.000 | FALSE | FALSE |
| EUCAST 2026 | human | human | MIC | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | TZP | Piperacillin/tazobactam | A. xylosoxidans | | 4.000 | 4.000 | FALSE | FALSE |
------------------------------------------------------------------------
@@ -460,22 +460,22 @@ here](https://amr-for-r.org/reference/example_isolates_unclean.html).
## `microorganisms.codes`: Common Laboratory Codes
A data set with 6 036 rows and 2 columns, containing the following
A data set with 6 050 rows and 2 columns, containing the following
column names:
*code* and *mo*.
This data set is in R available as `microorganisms.codes`, after you
load the `AMR` package.
It was last updated on 4 May 2025 16:50:25 UTC. Find more info about the
contents, (scientific) source, and structure of this [data set
It was last updated on 30 March 2026 08:01:49 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/microorganisms.codes.html).
**Direct download links:**
- Download as [original R Data Structure (RDS)
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.rds)
(27 kB)
(28 kB)
- Download as [tab-separated text
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.txt)
(0.1 MB)
@@ -487,7 +487,7 @@ here](https://amr-for-r.org/reference/microorganisms.codes.html).
(0.1 MB)
- Download as [Apache Parquet
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.parquet)
(68 kB)
(69 kB)
- Download as [IBM SPSS Statistics data
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.sav)
(0.2 MB)

2
articles/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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">

2
authors.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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">

34
index.html
View File

@@ -33,7 +33,7 @@
<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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -87,7 +87,7 @@
<li>Peer-reviewed, used in over 175 countries, available in 28 languages</li>
<li>Generates <strong>antibiograms</strong> - traditional, combined, syndromic, and even WISCA</li>
<li>Provides the <strong>full microbiological taxonomy</strong> of ~79 000 distinct species and extensive info of ~620 antimicrobial drugs</li>
<li>Applies <strong>CLSI 2011-2025</strong> and <strong>EUCAST 2011-2025</strong> clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation</li>
<li>Applies <strong>CLSI 2011-2026</strong> and <strong>EUCAST 2011-2026</strong> clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation</li>
<li>Corrects for duplicate isolates, <strong>calculates</strong> and <strong>predicts</strong> AMR per antimicrobial class</li>
<li>Integrates with <strong>WHONET</strong>, ATC, <strong>EARS-Net</strong>, PubChem, <strong>LOINC</strong>, <strong>SNOMED CT</strong>, and <strong>NCBI</strong>
</li>
@@ -112,7 +112,7 @@
</h2>
<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 2011-2025 and EUCAST 2011-2025 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> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</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 2011-2026 and EUCAST 2011-2026 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> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<div class="section level3">
<h3 id="used-in-over-175-countries-available-in-28-languages">Used in over 175 countries, available in 28 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-available-in-28-languages"></a>
</h3>
@@ -142,14 +142,14 @@
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,</span>
<span> <span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ Using column 'mo' as input for `mo_fullname()`</span></span>
<span><span class="co">#&gt; ℹ Using column 'mo' as input for `mo_is_gram_negative()`</span></span>
<span><span class="co">#&gt; ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`</span></span>
<span><span class="co">#&gt; ℹ Using column mo as input for `mo_fullname()`</span></span>
<span><span class="co">#&gt; ℹ Using column mo as input for `mo_is_gram_negative()`</span></span>
<span><span class="co">#&gt; ℹ Using column mo as input for `mo_is_intrinsic_resistant()`</span></span>
<span><span class="co">#&gt; ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant</span></span>
<span><span class="co">#&gt; Phenotypes' v1.2 (2023). This note will be shown once per session.</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span></span>
<span><span class="co">#&gt; (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
<span><span class="co">#&gt; (amikacin), and KAN (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span>
<span><span class="co">#&gt; # A tibble: 35 × 7</span></span>
<span><span class="co">#&gt; bacteria GEN TOB AMK KAN IPM MEM </span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span></span>
@@ -174,9 +174,9 @@
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antimicrobials <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="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span></span>
<span><span class="co">#&gt; (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span></code></pre></div>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
<span><span class="co">#&gt; (amikacin), and KAN (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span></code></pre></div>
<table style="width:100%;" class="table">
<colgroup>
<col width="14%">
@@ -425,15 +425,15 @@
<span> <span class="co"># calculate AMR using resistance(), over all aminoglycosides and polymyxins:</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></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="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
<span> <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span></span>
<span><span class="co">#&gt; (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `polymyxins()` using column 'COL' (colistin)</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
<span><span class="co">#&gt; (amikacin), and KAN (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `polymyxins()` using column COL (colistin)</span></span>
<span><span class="co">#&gt; Warning: There was 1 warning in `summarise()`.</span></span>
<span><span class="co">#&gt; ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.</span></span>
<span><span class="co">#&gt; ℹ In group 3: `ward = "Outpatient"`.</span></span>
<span><span class="co">#&gt; Caused by warning:</span></span>
<span><span class="co">#&gt; ! Introducing NA: only 23 results available for KAN in group: ward =</span></span>
<span><span class="co">#&gt; "Outpatient" (`minimum` = 30).</span></span>
<span><span class="co">#&gt; ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient"</span></span>
<span><span class="co">#&gt; (whilst `minimum = 30`).</span></span>
<span><span class="va">out</span></span>
<span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
<span><span class="co">#&gt; ward GEN TOB AMK KAN COL</span></span>

32
index.md
View File

@@ -7,7 +7,7 @@
even WISCA
- Provides the **full microbiological taxonomy** of ~79 000 distinct
species and extensive info of ~620 antimicrobial drugs
- Applies **CLSI 2011-2025** and **EUCAST 2011-2025** clinical and
- Applies **CLSI 2011-2026** and **EUCAST 2011-2026** clinical and
veterinary breakpoints, and ECOFFs, for MIC and disk zone
interpretation
- Corrects for duplicate isolates, **calculates** and **predicts** AMR
@@ -55,7 +55,7 @@ June 2024) and all [**~620 antimicrobial and antiviral
drugs**](https://amr-for-r.org/reference/antimicrobials.md) 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 2011-2025 and EUCAST 2011-2025 are
breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 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
@@ -113,14 +113,14 @@ example_isolates %>%
select(bacteria,
aminoglycosides(),
carbapenems())
#> ℹ Using column 'mo' as input for `mo_fullname()`
#> ℹ Using column 'mo' as input for `mo_is_gram_negative()`
#> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`
#> ℹ Using column mo as input for `mo_fullname()`
#> ℹ Using column mo as input for `mo_is_gram_negative()`
#> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant
#> Phenotypes' v1.2 (2023). This note will be shown once per session.
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 35 × 7
#> bacteria GEN TOB AMK KAN IPM MEM
#> <chr> <sir> <sir> <sir> <sir> <sir> <sir>
@@ -163,9 +163,9 @@ output format automatically (such as markdown, LaTeX, HTML, etc.).
``` r
antibiogram(example_isolates,
antimicrobials = c(aminoglycosides(), carbapenems()))
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
```
| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
@@ -292,15 +292,15 @@ out <- example_isolates %>%
# calculate AMR using resistance(), over all aminoglycosides and polymyxins:
summarise(across(c(aminoglycosides(), polymyxins()),
resistance))
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `polymyxins()` using column 'COL' (colistin)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `polymyxins()` using column COL (colistin)
#> Warning: There was 1 warning in `summarise()`.
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
#> ℹ In group 3: `ward = "Outpatient"`.
#> Caused by warning:
#> ! Introducing NA: only 23 results available for KAN in group: ward =
#> "Outpatient" (`minimum` = 30).
#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient"
#> (whilst `minimum = 30`).
out
#> # A tibble: 3 × 6
#> ward GEN TOB AMK KAN COL

34
llms.txt
View File

@@ -7,7 +7,7 @@
even WISCA
- Provides the **full microbiological taxonomy** of ~79 000 distinct
species and extensive info of ~620 antimicrobial drugs
- Applies **CLSI 2011-2025** and **EUCAST 2011-2025** clinical and
- Applies **CLSI 2011-2026** and **EUCAST 2011-2026** clinical and
veterinary breakpoints, and ECOFFs, for MIC and disk zone
interpretation
- Corrects for duplicate isolates, **calculates** and **predicts** AMR
@@ -55,7 +55,7 @@ June 2024) and all [**~620 antimicrobial and antiviral
drugs**](https://amr-for-r.org/reference/antimicrobials.md) 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 2011-2025 and EUCAST 2011-2025 are
breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 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
@@ -113,14 +113,14 @@ example_isolates %>%
select(bacteria,
aminoglycosides(),
carbapenems())
#> ℹ Using column 'mo' as input for `mo_fullname()`
#> ℹ Using column 'mo' as input for `mo_is_gram_negative()`
#> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`
#> ℹ Using column mo as input for `mo_fullname()`
#> ℹ Using column mo as input for `mo_is_gram_negative()`
#> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant
#> Phenotypes' v1.2 (2023). This note will be shown once per session.
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 35 × 7
#> bacteria GEN TOB AMK KAN IPM MEM
#> <chr> <sir> <sir> <sir> <sir> <sir> <sir>
@@ -163,9 +163,9 @@ output format automatically (such as markdown, LaTeX, HTML, etc.).
``` r
antibiogram(example_isolates,
antimicrobials = c(aminoglycosides(), carbapenems()))
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
```
| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
@@ -292,15 +292,15 @@ out <- example_isolates %>%
# calculate AMR using resistance(), over all aminoglycosides and polymyxins:
summarise(across(c(aminoglycosides(), polymyxins()),
resistance))
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `polymyxins()` using column 'COL' (colistin)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `polymyxins()` using column COL (colistin)
#> Warning: There was 1 warning in `summarise()`.
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
#> ℹ In group 3: `ward = "Outpatient"`.
#> Caused by warning:
#> ! Introducing NA: only 23 results available for KAN in group: ward =
#> "Outpatient" (`minimum` = 30).
#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient"
#> (whilst `minimum = 30`).
out
#> # A tibble: 3 × 6
#> ward GEN TOB AMK KAN COL
@@ -874,7 +874,7 @@ information about how to work with functions in this package.
- [`esbl_isolates`](https://amr-for-r.org/reference/esbl_isolates.md) :
Data Set with 500 ESBL Isolates
- [`microorganisms.codes`](https://amr-for-r.org/reference/microorganisms.codes.md)
: Data Set with 6 036 Common Microorganism Codes
: Data Set with 6 050 Common Microorganism Codes
- [`microorganisms.groups`](https://amr-for-r.org/reference/microorganisms.groups.md)
: Data Set with 534 Microorganisms In Species Groups
- [`intrinsic_resistant`](https://amr-for-r.org/reference/intrinsic_resistant.md)

13
news/index.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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -49,10 +49,11 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9040" id="amr-3019040">AMR 3.0.1.9040<a class="anchor" aria-label="anchor" href="#amr-3019040"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9041" id="amr-3019041">AMR 3.0.1.9041<a class="anchor" aria-label="anchor" href="#amr-3019041"></a></h2>
<div class="section level4">
<h4 id="new-3-0-1-9040">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9040"></a></h4>
<ul><li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
<h4 id="new-3-0-1-9041">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9041"></a></h4>
<ul><li>Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 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 2026 is now the new default guideline for all MIC and disk diffusion interpretations.</li>
<li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
<ul><li>
<code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code> to transform <code>&lt;mic&gt;</code> columns with log2, and <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code> to convert <code>&lt;sir&gt;</code> columns to numeric</li>
<li>New <code>tidyselect</code> helpers:
@@ -83,7 +84,7 @@
<li>Function <code><a href="../reference/amr_course.html">amr_course()</a></code>, which allows for automated download and unpacking of a GitHub repository for e.g. webinar use</li>
</ul></div>
<div class="section level4">
<h4 id="fixes-3-0-1-9040">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9040"></a></h4>
<h4 id="fixes-3-0-1-9041">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9041"></a></h4>
<ul><li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where values that were purely numeric (e.g., <code>"1"</code>) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter</li>
<li>Fixed a bug in <code><a href="../reference/as.mic.html">as.mic()</a></code> where MIC values in scientific notation (e.g., <code>"1e-3"</code>) were incorrectly handled because the letter <code>e</code> was removed along with other Unicode letters; scientific notation <code>e</code> is now preserved</li>
<li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> where certain AB codes containing “PH” or “TH” (such as <code>ETH</code>, <code>MTH</code>, <code>PHE</code>, <code>PHN</code>, <code>STH</code>, <code>THA</code>, <code>THI1</code>) would incorrectly return <code>NA</code> when combined in a vector with any untranslatable value (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
@@ -98,7 +99,7 @@
<li>Fixed SIR and MIC coercion of combined values, e.g. <code>as.sir("&lt;= 0.002; S")</code> or <code>as.mic("S; 0.002")</code> (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li>
</ul></div>
<div class="section level4">
<h4 id="updates-3-0-1-9040">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9040"></a></h4>
<h4 id="updates-3-0-1-9041">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9041"></a></h4>
<ul><li>Extensive <code>cli</code> integration for better message handling and clickable links in messages and warnings (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li>
<li>
<code><a href="../reference/mdro.html">mdro()</a></code> now infers resistance for a <em>missing</em> base drug column from an <em>available</em> corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument <code>infer_from_combinations</code>, which defaults to <code>TRUE</code> (<a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a>). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).</li>

8
news/index.md
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@@ -1,9 +1,15 @@
# Changelog
## AMR 3.0.1.9040
## AMR 3.0.1.9041
#### New
- Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by
adding all of their over 5,700 new clinical breakpoints to the
`clinical_breakpoints` data set for usage in
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md). EUCAST 2026
is now the new default guideline for all MIC and disk diffusion
interpretations.
- Integration with the **tidymodels** framework to allow seamless use of
SIR, MIC and disk data in modelling pipelines via `recipes`
- [`step_mic_log2()`](https://amr-for-r.org/reference/amr-tidymodels.md)

2
pkgdown.yml
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@@ -10,7 +10,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2026-03-24T12:29Z
last_built: 2026-03-30T08:13Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles

2
reference/AMR-deprecated.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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">

8
reference/AMR-options.html
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@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -68,12 +68,12 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<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="interpretive_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 used throughout the <code>AMR</code> package wherever a <code>guideline</code> argument is available. This option is used as the default in e.g. <code><a href="as.sir.html">as.sir()</a></code>, <code><a href="proportion.html">resistance()</a></code>, <code><a href="proportion.html">susceptibility()</a></code>, <code><a href="interpretive_rules.html">interpretive_rules()</a></code> and many plotting functions. <strong>While unset</strong>, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2025).</p><ul><li><p>For <code><a href="as.sir.html">as.sir()</a></code>, this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., <code>"CLSI"</code> or <code>"EUCAST"</code>) or the name including a year (e.g., <code>"CLSI 2019"</code>). Supported guidelines are EUCAST 2011 to 2025, and CLSI 2011 to 2025.</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 used throughout the <code>AMR</code> package wherever a <code>guideline</code> argument is available. This option is used as the default in e.g. <code><a href="as.sir.html">as.sir()</a></code>, <code><a href="proportion.html">resistance()</a></code>, <code><a href="proportion.html">susceptibility()</a></code>, <code><a href="interpretive_rules.html">interpretive_rules()</a></code> and many plotting functions. <strong>While unset</strong>, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2026).</p><ul><li><p>For <code><a href="as.sir.html">as.sir()</a></code>, this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., <code>"CLSI"</code> or <code>"EUCAST"</code>) or the name including a year (e.g., <code>"CLSI 2019"</code>). Supported guidelines are EUCAST 2011 to 2026, and CLSI 2011 to 2026.</p></li>
<li><p>For <code><a href="proportion.html">resistance()</a></code> and <code><a href="proportion.html">susceptibility()</a></code>, this setting determines how the <code>"I"</code> (Intermediate / Increased exposure) category is handled in calculations. Under CLSI, <code>"I"</code> is considered <em>resistant</em> in susceptibility calculations; under EUCAST, <code>"I"</code> is considered <em>susceptible</em> in susceptibility calculations. Explicitly setting this option ensures reproducible AMR proportion estimates.</p></li>
<li><p>For <code><a href="interpretive_rules.html">interpretive_rules()</a></code>, this determines which guideline-specific interpretive (expert) rules are applied to antimicrobial test results, either EUCAST or CLSI.</p></li>
<li><p>For many plotting functions (e.g., for MIC or disk diffusion values), supplying <code>mo</code> and <code>ab</code> enables automatic SIR-based interpretative colouring. These colours are derived from <code><a href="as.sir.html">as.sir()</a></code> in the background and therefore depend on the active <code>guideline</code> setting, which again uses EUCAST 2025 if not set explicitly.</p></li>
<li><p>For many plotting functions (e.g., for MIC or disk diffusion values), supplying <code>mo</code> and <code>ab</code> enables automatic SIR-based interpretative colouring. These colours are derived from <code><a href="as.sir.html">as.sir()</a></code> in the background and therefore depend on the active <code>guideline</code> setting, which again uses EUCAST 2026 if not set explicitly.</p></li>
</ul></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_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 2026"</code>. Supported guideline are currently EUCAST (2011-2026) and CLSI (2011-2026).</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>

10
reference/AMR-options.md
View File

@@ -63,14 +63,14 @@ the `AMR` package. Set them using the
[`susceptibility()`](https://amr-for-r.org/reference/proportion.md),
[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
and many plotting functions. **While unset**, the AMR package uses the
latest implemented EUCAST guideline (currently EUCAST 2025).
latest implemented EUCAST guideline (currently EUCAST 2026).
- For [`as.sir()`](https://amr-for-r.org/reference/as.sir.md), this
determines which clinical breakpoint guideline is used to interpret
MIC values and disk diffusion diameters. It can be either the
guideline name (e.g., `"CLSI"` or `"EUCAST"`) or the name including
a year (e.g., `"CLSI 2019"`). Supported guidelines are EUCAST 2011
to 2025, and CLSI 2011 to 2025.
to 2026, and CLSI 2011 to 2026.
- For [`resistance()`](https://amr-for-r.org/reference/proportion.md)
and
@@ -92,7 +92,7 @@ the `AMR` package. Set them using the
interpretative colouring. These colours are derived from
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) in the
background and therefore depend on the active `guideline` setting,
which again uses EUCAST 2025 if not set explicitly.
which again uses EUCAST 2026 if not set explicitly.
- `AMR_guideline`
A [character](https://rdrr.io/r/base/character.html) to set the
@@ -101,8 +101,8 @@ the `AMR` package. Set them using the
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md). Can be only
the guideline name (e.g., `"CLSI"`) or the name with a year (e.g.
`"CLSI 2019"`). The default to the latest implemented EUCAST
guideline, currently `"EUCAST 2025"`. Supported guideline are
currently EUCAST (2011-2025) and CLSI (2011-2025).
guideline, currently `"EUCAST 2026"`. Supported guideline are
currently EUCAST (2011-2026) and CLSI (2011-2026).
- `AMR_ignore_pattern`
A [regular expression](https://rdrr.io/r/base/regex.html) to ignore

8
reference/AMR.html
View File

@@ -5,14 +5,14 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~79 000 distinct microbial species (updated June 2024) and all ~620 antimicrobial and antiviral drugs 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 2011-2025 and EUCAST 2011-2025 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). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
After installing this package, R knows ~79 000 distinct microbial species (updated June 2024) and all ~620 antimicrobial and antiviral drugs 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 2011-2026 and EUCAST 2011-2026 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). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:description" content="Welcome to the AMR package.
The AMR package is a peer-reviewed, free and open-source R package with zero dependencies 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. Our aim is to provide a standard 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 many different researchers from around the globe to make this a successful and durable project!
This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~79 000 distinct microbial species (updated June 2024) and all ~620 antimicrobial and antiviral drugs 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 2011-2025 and EUCAST 2011-2025 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). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
After installing this package, R knows ~79 000 distinct microbial species (updated June 2024) and all ~620 antimicrobial and antiviral drugs 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 2011-2026 and EUCAST 2011-2026 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). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><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>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<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="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -70,7 +70,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
) 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="https://amr-for-r.org/reference/microorganisms.html"><strong>~79 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="https://amr-for-r.org/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 2011-2025 and EUCAST 2011-2025 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> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<p>After installing this package, R knows <a href="https://amr-for-r.org/reference/microorganisms.html"><strong>~79 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="https://amr-for-r.org/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 2011-2026 and EUCAST 2011-2026 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> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<p>The <code>AMR</code> package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
</div>

2
reference/AMR.md
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@@ -29,7 +29,7 @@ June 2024) and all [**~620 antimicrobial and antiviral
drugs**](https://amr-for-r.org/reference/antimicrobials.html) 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 2011-2025 and EUCAST 2011-2025 are
breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 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

2
reference/WHOCC.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="">3.0.1.9040</small>
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2
reference/WHONET.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="">3.0.1.9040</small>
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2
reference/ab_from_text.html
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@@ -7,7 +7,7 @@
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2
reference/ab_property.html
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@@ -7,7 +7,7 @@
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2
reference/add_custom_antimicrobials.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="">3.0.1.9040</small>
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2
reference/add_custom_microorganisms.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="">3.0.1.9040</small>
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22
reference/age.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="">3.0.1.9040</small>
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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 26 26.73151 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.14795 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.29863 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.06301 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.39178 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.10411 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.09041 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.20000 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.57260 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.15616 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 26 26.74795 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.16438 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.31507 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.07945 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.40822 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.12055 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.10685 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.21644 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.58904 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.17260 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>

20
reference/age.md
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@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
df
#> birth_date age age_exact age_at_y2k
#> 1 1999-06-30 26 26.73151 0
#> 2 1968-01-29 58 58.14795 31
#> 3 1965-12-05 60 60.29863 34
#> 4 1980-03-01 46 46.06301 19
#> 5 1949-11-01 76 76.39178 50
#> 6 1947-02-14 79 79.10411 52
#> 7 1940-02-19 86 86.09041 59
#> 8 1988-01-10 38 38.20000 11
#> 9 1997-08-27 28 28.57260 2
#> 10 1978-01-26 48 48.15616 21
#> 1 1999-06-30 26 26.74795 0
#> 2 1968-01-29 58 58.16438 31
#> 3 1965-12-05 60 60.31507 34
#> 4 1980-03-01 46 46.07945 19
#> 5 1949-11-01 76 76.40822 50
#> 6 1947-02-14 79 79.12055 52
#> 7 1940-02-19 86 86.10685 59
#> 8 1988-01-10 38 38.21644 11
#> 9 1997-08-27 28 28.58904 2
#> 10 1978-01-26 48 48.17260 21
```

2
reference/age_groups.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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@@ -7,7 +7,7 @@
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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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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
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@@ -7,7 +7,7 @@
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@@ -7,7 +7,7 @@
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@@ -7,7 +7,7 @@
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4
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>
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@@ -111,7 +111,7 @@
</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 (2011-2025) and CLSI (2011-2025).</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 (2011-2026) and CLSI (2011-2026).</p>
<p>This class for MIC values is a quite a special data type: formally it is an ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> with valid MIC values as <a href="https://rdrr.io/pkg/data.table/man/fctr.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>

2
reference/as.mic.md
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@@ -85,7 +85,7 @@ the outcome of any mathematical operation on MICs will return a
To interpret MIC values as SIR values, use
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) on MIC values.
It supports guidelines from EUCAST (2011-2025) and CLSI (2011-2025).
It supports guidelines from EUCAST (2011-2026) and CLSI (2011-2026).
This class for MIC values is a quite a special data type: formally it is
an ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with

2
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@@ -7,7 +7,7 @@
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36
reference/as.sir.html
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@@ -1,7 +1,7 @@
<!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="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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.
Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025, see Details. All breakpoints used for interpretation are available in our clinical_breakpoints data set."><meta property="og:description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, NI.
Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025, see Details. All breakpoints used for interpretation are available in our clinical_breakpoints data set."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026, see Details. All breakpoints used for interpretation are available in our clinical_breakpoints data set."><meta property="og:description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, NI.
Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026, see Details. All breakpoints used for interpretation are available in our clinical_breakpoints data set."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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@@ -53,7 +53,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<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/pkg/data.table/man/fctr.html" class="external-link">factor</a> containing the levels <code>S</code>, <code>SDD</code>, <code>I</code>, <code>R</code>, <code>NI</code>.</p>
<p>Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025, see <em>Details</em>. All breakpoints used for interpretation are available in our <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set.</p>
<p>Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026, see <em>Details</em>. All breakpoints used for interpretation are available in our <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set.</p>
</div>
<div class="section level2">
@@ -118,11 +118,11 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<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>, 2011-2025, <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/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" class="external-link">https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/</a>.</p></li>
<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>
<p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2011-2026, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
<li><p><strong>CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2026, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
<li><p><strong>CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals</strong>, 2019-2026, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/veterinary-medicine/documents/vet01/" class="external-link">https://clsi.org/standards/products/veterinary-medicine/documents/vet01/</a>.</p></li>
<li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2026, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" class="external-link">https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/</a>.</p></li>
<li><p><strong>WHONET</strong> as a source for machine-reading the clinical breakpoints (<a href="https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet">read more here</a>), 1989-2026, <em>WHO Collaborating Centre for Surveillance of Antimicrobial Resistance</em>. <a href="https://whonet.org/" class="external-link">https://whonet.org/</a>.</p></li>
</ul></div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
@@ -158,7 +158,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<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 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>
<dd><p>A guideline name (or column name) to use for SIR interpretation. Defaults to EUCAST 2026 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the package option <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2026) and CLSI (2011-2026), see <em>Details</em>. Using a column name allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.</p></dd>
<dt id="arg-uti">uti<a class="anchor" aria-label="anchor" href="#arg-uti"></a></dt>
@@ -283,10 +283,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<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:</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>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2026 and CLSI 2011-2026;</p></li>
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2026 and CLSI 2019-2026;</p></li>
<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2020-2026 and CLSI 2022-2026.</p></li>
</ul><p>The <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2026"</code> or <code>"CLSI 2026"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data that must be analysed in the context of, for example, different years.</p>
<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>
@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</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> 2026-03-24 <span style="color: #949494;">12:30:17</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-03-24 <span style="color: #949494;">12:30:17</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-03-24 <span style="color: #949494;">12:30:18</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-03-24 <span style="color: #949494;">12:30:18</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-03-30 <span style="color: #949494;">08:14:10</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-03-30 <span style="color: #949494;">08:14:10</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-03-30 <span style="color: #949494;">08:14:10</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-03-30 <span style="color: #949494;">08:14:11</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>

38
reference/as.sir.md
View File

@@ -7,8 +7,8 @@ which is an ordered
[factor](https://rdrr.io/pkg/data.table/man/fctr.html) containing the
levels `S`, `SDD`, `I`, `R`, `NI`.
Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI
2011-2025, see *Details*. All breakpoints used for interpretation are
Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI
2011-2026, see *Details*. All breakpoints used for interpretation are
available in our
[clinical_breakpoints](https://amr-for-r.org/reference/clinical_breakpoints.md)
data set.
@@ -80,29 +80,29 @@ For interpretations of minimum inhibitory concentration (MIC) values and
disk diffusion diameters:
- **CLSI M39: Analysis and Presentation of Cumulative Antimicrobial
Susceptibility Test Data**, 2011-2025, *Clinical and Laboratory
Susceptibility Test Data**, 2011-2026, *Clinical and Laboratory
Standards Institute* (CLSI).
<https://clsi.org/standards/products/microbiology/documents/m39/>.
- **CLSI M100: Performance Standard for Antimicrobial Susceptibility
Testing**, 2011-2025, *Clinical and Laboratory Standards Institute*
Testing**, 2011-2026, *Clinical and Laboratory Standards Institute*
(CLSI).
<https://clsi.org/standards/products/microbiology/documents/m100/>.
- **CLSI VET01: Performance Standards for Antimicrobial Disk and
Dilution Susceptibility Tests for Bacteria Isolated From Animals**,
2019-2025, *Clinical and Laboratory Standards Institute* (CLSI).
2019-2026, *Clinical and Laboratory Standards Institute* (CLSI).
<https://clsi.org/standards/products/veterinary-medicine/documents/vet01/>.
- **EUCAST Breakpoint tables for interpretation of MICs and zone
diameters**, 2011-2025, *European Committee on Antimicrobial
diameters**, 2011-2026, *European Committee on Antimicrobial
Susceptibility Testing* (EUCAST).
<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/>.
- **WHONET** as a source for machine-reading the clinical breakpoints
([read more
here](https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet)),
1989-2025, *WHO Collaborating Centre for Surveillance of Antimicrobial
1989-2026, *WHO Collaborating Centre for Surveillance of Antimicrobial
Resistance*. <https://whonet.org/>.
## Arguments
@@ -162,12 +162,12 @@ disk diffusion diameters:
- guideline:
A guideline name (or column name) to use for SIR interpretation.
Defaults to EUCAST 2025 (the latest implemented EUCAST guideline in
Defaults to EUCAST 2026 (the latest implemented EUCAST guideline in
the
[clinical_breakpoints](https://amr-for-r.org/reference/clinical_breakpoints.md)
data set), but can be set with the package option
[`AMR_guideline`](https://amr-for-r.org/reference/AMR-options.md).
Currently supports EUCAST (2011-2025) and CLSI (2011-2025), see
Currently supports EUCAST (2011-2026) and CLSI (2011-2026), see
*Details*. Using a column name allows for straightforward
interpretation of historical data, which must be analysed in the
context of, for example, different years.
@@ -457,15 +457,15 @@ interpretation, and the exact input and output values.
For interpreting MIC values as well as disk diffusion diameters,
currently implemented guidelines are:
- For **clinical microbiology**: EUCAST 2011-2025 and CLSI 2011-2025;
- For **clinical microbiology**: EUCAST 2011-2026 and CLSI 2011-2026;
- For **veterinary microbiology**: EUCAST 2021-2025 and CLSI 2019-2025;
- For **veterinary microbiology**: EUCAST 2021-2026 and CLSI 2019-2026;
- For **ECOFFs** (Epidemiological Cut-off Values): EUCAST 2020-2025 and
CLSI 2022-2025.
- For **ECOFFs** (Epidemiological Cut-off Values): EUCAST 2020-2026 and
CLSI 2022-2026.
The `guideline` argument must be set to e.g., `"EUCAST 2025"` or
`"CLSI 2025"`. By simply using `"EUCAST"` (the default) or `"CLSI"` as
The `guideline` argument must be set to e.g., `"EUCAST 2026"` or
`"CLSI 2026"`. By simply using `"EUCAST"` (the default) or `"CLSI"` 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
@@ -660,10 +660,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2026-03-24 12:30:17 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-24 12:30:17 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-24 12:30:18 1 DISK tobra Escherich… human 16
#> 4 2026-03-24 12:30:18 1 DISK genta Escherich… human 18
#> 1 2026-03-30 08:14:10 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-30 08:14:10 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-30 08:14:10 1 DISK tobra Escherich… human 16
#> 4 2026-03-30 08:14:11 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr>

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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="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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 data set contains breakpoints for humans, 7 different animal groups, and ECOFFs.
These breakpoints are currently implemented:
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.
For clinical microbiology: EUCAST 2011-2026 and CLSI 2011-2026;
For veterinary microbiology: EUCAST 2021-2026 and CLSI 2019-2026;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2026 and CLSI 2022-2026.
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 data set contains breakpoints for humans, 7 different animal groups, and ECOFFs.
These breakpoints are currently implemented:
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.
For clinical microbiology: EUCAST 2011-2026 and CLSI 2011-2026;
For veterinary microbiology: EUCAST 2021-2026 and CLSI 2019-2026;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2026 and CLSI 2022-2026.
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
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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 data set contains 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 2011-2025 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>
<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2026 and CLSI 2011-2026;</p></li>
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2026 and CLSI 2019-2026;</p></li>
<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2020-2026 and CLSI 2022-2026.</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 40 217 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 45 797 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 48 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 72 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: 40,217 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 45,797 × 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 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: #BCBCBC;"> 1</span> EUCAST 2026 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 2026 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 2026 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 2026 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 2026 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 2026 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 2026 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 2026 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 2026 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 2026 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 45,787 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>

38
reference/clinical_breakpoints.md
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@@ -7,12 +7,12 @@ ECOFFs.
These breakpoints are currently implemented:
- For **clinical microbiology**: EUCAST 2011-2025 and CLSI 2011-2025;
- For **clinical microbiology**: EUCAST 2011-2026 and CLSI 2011-2026;
- For **veterinary microbiology**: EUCAST 2021-2025 and CLSI 2019-2025;
- For **veterinary microbiology**: EUCAST 2021-2026 and CLSI 2019-2026;
- For **ECOFFs** (Epidemiological Cut-off Values): EUCAST 2020-2025 and
CLSI 2022-2025.
- For **ECOFFs** (Epidemiological Cut-off Values): EUCAST 2020-2026 and
CLSI 2022-2026.
Use [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) to transform
MICs or disks measurements to SIR values.
@@ -25,8 +25,8 @@ clinical_breakpoints
## Format
A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 40
217 observations and 14 variables:
A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 45
797 observations and 14 variables:
- `guideline`
Name of the guideline
@@ -80,7 +80,7 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 40
A [logical](https://rdrr.io/r/base/logical.html) value
(`TRUE`/`FALSE`) to indicate whether the intermediate range between
"S" and "R" should be interpreted as "SDD", instead of "I". This
currently applies to 48 breakpoints.
currently applies to 72 breakpoints.
## Details
@@ -154,20 +154,20 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
``` r
clinical_breakpoints
#> # A tibble: 40,217 × 14
#> # A tibble: 45,797 × 14
#> guideline type host method site mo rank_index ab ref_tbl
#> <chr> <chr> <chr> <chr> <chr> <mo> <dbl> <ab> <chr>
#> 1 EUCAST 2025 human human DISK NA B_ACHRMB_XYLS 2 MEM A. xylo…
#> 2 EUCAST 2025 human human MIC NA B_ACHRMB_XYLS 2 MEM A. xylo…
#> 3 EUCAST 2025 human human DISK NA B_ACHRMB_XYLS 2 SXT A. xylo…
#> 4 EUCAST 2025 human human MIC NA B_ACHRMB_XYLS 2 SXT A. xylo…
#> 5 EUCAST 2025 human human DISK NA B_ACHRMB_XYLS 2 TZP A. xylo…
#> 6 EUCAST 2025 human human MIC NA B_ACHRMB_XYLS 2 TZP A. xylo…
#> 7 EUCAST 2025 human human DISK NA B_ACNTB 3 AMK Acineto…
#> 8 EUCAST 2025 human human DISK Uncomp… B_ACNTB 3 AMK Acineto…
#> 9 EUCAST 2025 human human MIC NA B_ACNTB 3 AMK Acineto…
#> 10 EUCAST 2025 human human MIC Uncomp… B_ACNTB 3 AMK Acineto…
#> # ℹ 40,207 more rows
#> 1 EUCAST 2026 human human DISK NA B_ACHRMB_XYLS 2 MEM A. xylo…
#> 2 EUCAST 2026 human human MIC NA B_ACHRMB_XYLS 2 MEM A. xylo…
#> 3 EUCAST 2026 human human DISK NA B_ACHRMB_XYLS 2 SXT A. xylo…
#> 4 EUCAST 2026 human human MIC NA B_ACHRMB_XYLS 2 SXT A. xylo…
#> 5 EUCAST 2026 human human DISK NA B_ACHRMB_XYLS 2 TZP A. xylo…
#> 6 EUCAST 2026 human human MIC NA B_ACHRMB_XYLS 2 TZP A. xylo…
#> 7 EUCAST 2026 human human DISK NA B_ACNTB 3 AMK Acineto…
#> 8 EUCAST 2026 human human DISK Uncomp… B_ACNTB 3 AMK Acineto…
#> 9 EUCAST 2026 human human MIC NA B_ACNTB 3 AMK Acineto…
#> 10 EUCAST 2026 human human MIC Uncomp… B_ACNTB 3 AMK Acineto…
#> # ℹ 45,787 more rows
#> # ℹ 5 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>,
#> # uti <lgl>, is_SDD <lgl>
```

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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -421,7 +421,7 @@
<code><a href="microorganisms.codes.html">microorganisms.codes</a></code>
</dt>
<dd>Data Set with 6 036 Common Microorganism Codes</dd>
<dd>Data Set with 6 050 Common Microorganism Codes</dd>
<dt>

2
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@@ -402,7 +402,7 @@ information about how to work with functions in this package.
- [`esbl_isolates`](https://amr-for-r.org/reference/esbl_isolates.md) :
Data Set with 500 ESBL Isolates
- [`microorganisms.codes`](https://amr-for-r.org/reference/microorganisms.codes.md)
: Data Set with 6 036 Common Microorganism Codes
: Data Set with 6 050 Common Microorganism Codes
- [`microorganisms.groups`](https://amr-for-r.org/reference/microorganisms.groups.md)
: Data Set with 534 Microorganisms In Species Groups
- [`intrinsic_resistant`](https://amr-for-r.org/reference/intrinsic_resistant.md)

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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
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<!DOCTYPE html>
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@@ -7,7 +7,7 @@
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@@ -44,7 +44,7 @@
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<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 6 036 Common Microorganism Codes</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 6 050 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 6 036 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 6 050 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: 6,036 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 6,050 × 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 6,026 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6,040 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>

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reference/microorganisms.codes.md
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@@ -1,4 +1,4 @@
# Data Set with 6 036 Common Microorganism Codes
# Data Set with 6 050 Common Microorganism Codes
A data set containing commonly used codes for microorganisms, from
laboratory systems and [WHONET](https://whonet.org). Define your own
@@ -17,7 +17,7 @@ microorganisms.codes
## Format
A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 6
036 observations and 2 variables:
050 observations and 2 variables:
- `code`
Commonly used code of a microorganism. ***This is a unique
@@ -53,7 +53,7 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
``` r
microorganisms.codes
#> # A tibble: 6,036 × 2
#> # A tibble: 6,050 × 2
#> code mo
#> <chr> <mo>
#> 1 1011 B_GRAMP
@@ -66,7 +66,7 @@ microorganisms.codes
#> 8 1100 B_STRPT
#> 9 1101 B_STRPT_VIRI
#> 10 1102 B_STRPT_HAEM
#> # ℹ 6,026 more rows
#> # ℹ 6,040 more rows
# 'ECO' or 'eco' is the WHONET code for E. coli:
microorganisms.codes[microorganisms.codes$code == "ECO", ]

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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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@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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reference/pca.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/plot.html
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<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="">3.0.1.9040</small>
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@@ -291,7 +291,7 @@ 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 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>
<p>For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2026, 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>
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reference/plot.md
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@@ -336,7 +336,7 @@ EUCAST guidelines since 2019, and will be named "Intermediate" in all
other cases.
For interpreting MIC values as well as disk diffusion diameters, the
default guideline is EUCAST 2025, unless the package option
default guideline is EUCAST 2026, unless the package option
[`AMR_guideline`](https://amr-for-r.org/reference/AMR-options.md) is
set. See [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) for
more information.

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reference/proportion.html
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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