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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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@@ -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">package_coverage</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"><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>
<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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<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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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@@ -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 30 April 2026.</p>
generated on 02 May 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">2026-04-30</td>
<td align="center">2026-05-02</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">2026-04-30</td>
<td align="center">2026-05-02</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">2026-04-30</td>
<td align="center">2026-05-02</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

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**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 30 April 2026.
methodology remains unchanged. This page was generated on 02 May 2026.
## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-04-30 | abcd | Escherichia coli | S | S |
| 2026-04-30 | abcd | Escherichia coli | S | R |
| 2026-04-30 | efgh | Escherichia coli | R | S |
| 2026-05-02 | abcd | Escherichia coli | S | S |
| 2026-05-02 | abcd | Escherichia coli | S | R |
| 2026-05-02 | efgh | Escherichia coli | R | S |
### Needed R packages

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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="">3.0.1.9055</small>
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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="">3.0.1.9055</small>
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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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@@ -200,7 +200,7 @@ function:</p>
<span><span class="co">#&gt; [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co">#&gt; Importance of components:</span></span>
<span><span class="co">#&gt; PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
<span><span class="co">#&gt; Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co">#&gt; Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>

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@@ -123,7 +123,7 @@ summary(pca_result)
#> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"
#> Importance of components:
#> PC1 PC2 PC3 PC4 PC5 PC6 PC7
#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16
#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17
#> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00
#> Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00
```

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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="">3.0.1.9055</small>
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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="">3.0.1.9055</small>
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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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@@ -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">30 April 2026</h4>
<h4 data-toc-skip class="date">02 May 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>
@@ -424,8 +424,8 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antimicrobials</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 4 April 2026 09:51:50 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
<p>It was last updated on 2 May 2026 12:56:26 UTC. Find more info about
the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>

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@@ -100,8 +100,8 @@ names:
This data set is in R available as `antimicrobials`, after you load the
`AMR` package.
It was last updated on 4 April 2026 09:51:50 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
It was last updated on 2 May 2026 12:56:26 UTC. Find more info about the
contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/antimicrobials.html).
**Direct download links:**

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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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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="">3.0.1.9055</small>
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@@ -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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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@@ -606,7 +606,7 @@ from clinical text records, using
[`clear_custom_antimicrobials()`](https://amr-for-r.org/reference/add_custom_antimicrobials.md)
: Add Custom Antimicrobials
## Preparing data: antimicrobial results
## Interpreting data: antimicrobial results
With [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) and
[`as.disk()`](https://amr-for-r.org/reference/as.disk.md) you can
@@ -615,10 +615,10 @@ transform your raw input to valid MIC or disk diffusion values. Use
data to let it only contain “R”, “I” and “S”, or to interpret MIC or
disk diffusion values as SIR based on the lastest EUCAST and CLSI
guidelines. Afterwards, you can extend antibiotic interpretations by
applying [EUCAST
rules](https://www.eucast.org/expert_rules_and_intrinsic_resistance/)
applying interpretive rules, for example [from
EUCAST](https://www.eucast.org/expert_rules_and_intrinsic_resistance/)
with
[`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md).
[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md).
- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
[`NA_sir_`](https://amr-for-r.org/reference/as.sir.md)
@@ -643,8 +643,8 @@ with
[`clsi_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
[`eucast_dosage()`](https://amr-for-r.org/reference/interpretive_rules.md)
: Apply Interpretive Rules
- [`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md)
: Define Custom EUCAST Rules
- [`custom_interpretive_rules()`](https://amr-for-r.org/reference/custom_interpretive_rules.md)
: Define Custom Interpretive Rules
## Analysing data
@@ -955,8 +955,8 @@ and other utilities. Especially the ‘like’ function can be useful:
## Other: statistical tests
Some statistical tests or methods are not part of base R and were added
to this package for convenience.
Some statistical tests or methods usable for AMR analyses are not part
of base R and were added to this package for convenience.
- [`g.test()`](https://amr-for-r.org/reference/g.test.md) :
@@ -973,7 +973,8 @@ to this package for convenience.
These objects are deprecated, meaning that they will still work but show
a warning that they will be removed in a future version.
- [`ab_class()`](https://amr-for-r.org/reference/AMR-deprecated.md)
- [`custom_eucast_rules()`](https://amr-for-r.org/reference/AMR-deprecated.md)
[`ab_class()`](https://amr-for-r.org/reference/AMR-deprecated.md)
[`ab_selector()`](https://amr-for-r.org/reference/AMR-deprecated.md) :
Deprecated Functions, Arguments, or Datasets

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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">
@@ -49,96 +49,50 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9055" id="amr-3019055">AMR 3.0.1.9055<a class="anchor" aria-label="anchor" href="#amr-3019055"></a></h2>
<p>This will become release v3.1.0, intended for launch end of May.</p>
<h2 class="pkg-version" data-toc-text="3.0.1.9057" id="amr-3019057">AMR 3.0.1.9057<a class="anchor" aria-label="anchor" href="#amr-3019057"></a></h2>
<p>Planned as v3.1.0, May 2026.</p>
<div class="section level4">
<h4 id="new-3-0-1-9055">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9055"></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>Support for the <a href="https://future.futureverse.org" class="external-link"><code>future</code></a> package and its framework, as the previous implementation of parallel computing was slow
<ul><li>
<strong>Breaking change</strong>: <code><a href="../reference/as.sir.html">as.sir()</a></code> with <code>parallel = TRUE</code> now requires a non-sequential <code><a href="https://future.futureverse.org/reference/plan.html" class="external-link">future::plan()</a></code> to be active before the call — e.g., <code>future::plan(future::multisession)</code> — and throws an informative error if none is set.</li>
<li>New all-core usage setup: when the number of AB columns is smaller than the number of available cores, rows are now split into batches so all cores stay active (row-batch mode). Previously, a 6-column dataset on a 16-core machine would only use 6 cores; now all 16 are used, with each worker processing a smaller row slice (lower per-worker memory pressure and processing time)</li>
<h4 id="new-3-0-1-9057">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9057"></a></h4>
<ul><li>EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the <code>clinical_breakpoints</code> data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations</li>
<li>Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting <code>breakpoint_type = "ECOFF"</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code>; WT/NWT results are fully supported in all resistance/susceptibility functions and plots (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li>
<li>Faster parallel computing via the <code>future</code> package; <strong>breaking change</strong>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>; <code><a href="../reference/antibiogram.html">antibiogram()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code> now also support <code>parallel = TRUE</code> (<a href="https://github.com/msberends/AMR/issues/281" class="external-link">#281</a>)</li>
<li>
<code><a href="../reference/antibiogram.html">antibiogram()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code> gained a <code>parallel</code> argument using the same <code>future</code>/<code>future.apply</code> pattern: for WISCA, Monte Carlo simulations are split into <code>(group, chunk)</code> job pairs distributed across workers; for grouped antibiograms, each group is processed by a separate worker (<a href="https://github.com/msberends/AMR/issues/281" class="external-link">#281</a>)</li>
</ul></li>
<li>Integration with the <em>tidymodels</em> 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:
<ul><li>
<code><a href="../reference/amr-tidymodels.html">all_sir()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_sir_predictors()</a></code>
<em>tidymodels</em> integration for using SIR, MIC and disk data in modelling pipelines: <code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code>, <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code>, and new column selectors <code><a href="../reference/amr-tidymodels.html">all_sir()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_mic()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_disk()</a></code>
</li>
<li>
<code><a href="../reference/amr-tidymodels.html">all_mic()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_mic_predictors()</a></code>
<li>New <code>esbl_isolates</code> data set for practising AMR modelling</li>
<li>New antimicrobial selectors: <code><a href="../reference/antimicrobial_selectors.html">ionophores()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">peptides()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">phosphonics()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">spiropyrimidinetriones()</a></code>
</li>
<li>
<code><a href="../reference/amr-tidymodels.html">all_disk()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_disk_predictors()</a></code>
</li>
</ul></li>
</ul></li>
<li>Data set <code>esbl_isolates</code> to practise with AMR modelling</li>
<li>AMR selectors <code><a href="../reference/antimicrobial_selectors.html">ionophores()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">peptides()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">phosphonics()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">spiropyrimidinetriones()</a></code>
</li>
<li>Support for Wildtype (WT) / Non-wildtype (NWT) in <code><a href="../reference/as.sir.html">as.sir()</a></code>, all plotting functions, and all susceptibility/resistance functions.
<ul><li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> gained an argument <code>as_wt_nwt</code>, which defaults to <code>TRUE</code> only when <code>breakpoint_type = "ECOFF"</code> (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li>
<li>This transforms the output from S/R to WT/NWT</li>
<li>Functions such as <code><a href="../reference/proportion.html">susceptibility()</a></code> count WT as S and NWT as R</li>
</ul></li>
<li>Function <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, which allows future implementation of CLSI interpretive rules (<a href="https://github.com/msberends/AMR/issues/235" class="external-link">#235</a>)
<ul><li>
<code><a href="../reference/interpretive_rules.html">eucast_rules()</a></code> has become a wrapper around that function</li>
<li>Gained argument <code>add_if_missing</code> (default: <code>TRUE</code>). When set to <code>FALSE</code>, rules are only applied to cells that already contain an SIR value; <code>NA</code> cells are left untouched. This is useful with <code>overwrite = TRUE</code> to update reported results without imputing values for drugs that were not tested (<a href="https://github.com/msberends/AMR/issues/259" class="external-link">#259</a>)</li>
</ul></li>
<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>
<li>Two new <code>NA</code> objects, <code>NA_ab_</code> and <code>NA_mo_</code>, analogous to base R’s <code>NA_character_</code> and <code>NA_integer_</code>, for use in pipelines that require typed missing values</li>
<li>New <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, a unified function for EUCAST and CLSI interpretive rules; <code><a href="../reference/interpretive_rules.html">eucast_rules()</a></code> is now a wrapper around it (<a href="https://github.com/msberends/AMR/issues/235" class="external-link">#235</a>, <a href="https://github.com/msberends/AMR/issues/259" class="external-link">#259</a>)</li>
<li>New <code><a href="../reference/amr_course.html">amr_course()</a></code> to download and unpack course or webinar materials from GitHub in one call</li>
<li>Typed missing value constants <code>NA_ab_</code> and <code>NA_mo_</code>, for use in pipelines that need missing values of a specific class</li>
</ul></div>
<div class="section level4">
<h4 id="fixes-3-0-1-9055">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9055"></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>
<li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li>
<li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where for numeric input the arguments <code>S</code>, <code>I</code>, and <code>R</code> would not be considered (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
<li>Fixed a bug in plotting MIC values when <code>keep_operators = "all"</code>
</li>
<li>Fixed some foreign translations of antimicrobial drugs</li>
<li>Fixed a bug for printing column names to the console when using <code>mutate_at(vars(...), as.mic)</code> (<a href="https://github.com/msberends/AMR/issues/249" class="external-link">#249</a>)</li>
<li>Fixed a bug to disregard <code>NI</code> for susceptibility proportion functions</li>
<li>Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (<a href="https://github.com/msberends/AMR/issues/256" class="external-link">#256</a>)</li>
<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>
<li>Fixed translation of foreign languages in <code><a href="../reference/proportion.html">sir_df()</a></code> (<a href="https://github.com/msberends/AMR/issues/272" class="external-link">#272</a>)</li>
<li>Fixed BRMO classification by including bacterial complexes (<a href="https://github.com/msberends/AMR/issues/275" class="external-link">#275</a>)</li>
<li>Fixed <code><a href="../reference/as.sir.html">as.sir()</a></code> for data frames silently deleting columns whose AB class was already <code>&lt;sir&gt;</code> when called a second time (re-running on already-converted data) (<a href="https://github.com/msberends/AMR/issues/278" class="external-link">#278</a>)</li>
<li>Fixed <code><a href="../reference/as.sir.html">as.sir()</a></code> for data frames incorrectly treating metadata columns (e.g. <code>patient</code>, <code>ward</code>) as antibiotic columns when their names coincidentally matched an antibiotic code; column content is now validated against AMR data patterns before inclusion</li>
<li>Fixed <code><a href="../reference/as.sir.html">as.sir()</a></code> ignoring <code>info = FALSE</code> for columns with no breakpoints (e.g. cefoxitin against <em>E. coli</em>)</li>
<h4 id="fixes-3-0-1-9057">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9057"></a></h4>
<ul><li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> on data frames: already-converted SIR columns no longer dropped on re-run (<a href="https://github.com/msberends/AMR/issues/278" class="external-link">#278</a>); metadata columns (e.g. <code>patient</code>, <code>ward</code>) no longer misidentified as antibiotic columns; <code>info = FALSE</code> now suppresses all messages, including for columns without breakpoints</li>
<li>
<code><a href="../reference/as.mic.html">as.mic()</a></code>: values in scientific notation (e.g. <code>1e-3</code>) now handled correctly</li>
<li>
<code><a href="../reference/as.ab.html">as.ab()</a></code>: codes containing “PH” or “TH” (e.g. <code>ETH</code>, <code>PHE</code>) no longer return <code>NA</code> when mixed with unrecognised input (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
<li>Combined MIC/SIR input values (e.g. <code>"&lt;= 0.002; S"</code> or <code>"S; 0.002"</code>) now parsed correctly (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li>
<li>BRMO classification now includes bacterial complexes (<a href="https://github.com/msberends/AMR/issues/275" class="external-link">#275</a>)</li>
<li>Translation fixes for Italian CoNS/CoPS names (<a href="https://github.com/msberends/AMR/issues/256" class="external-link">#256</a>), Dutch antimicrobials, and <code><a href="../reference/proportion.html">sir_df()</a></code> foreign-language output (<a href="https://github.com/msberends/AMR/issues/272" class="external-link">#272</a>)</li>
</ul></div>
<div class="section level4">
<h4 id="updates-3-0-1-9055">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9055"></a></h4>
<h4 id="updates-3-0-1-9057">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9057"></a></h4>
<ul><li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> with <code>reference_data</code>: custom guideline names now correctly classify values as R using EUCAST convention (<code>&gt; breakpoint_R</code> for MIC, <code>&lt; breakpoint_R</code> for disk); custom breakpoints with <code>host = NA</code> now serve as a host-agnostic fallback when no host-specific row matches (<a href="https://github.com/msberends/AMR/issues/239" class="external-link">#239</a>)</li>
<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>
<code><a href="../reference/AMR-deprecated.html">custom_eucast_rules()</a></code> renamed to <code><a href="../reference/custom_interpretive_rules.html">custom_interpretive_rules()</a></code>; old name deprecated but still works (<a href="https://github.com/msberends/AMR/issues/268" class="external-link">#268</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>
<code><a href="../reference/mdro.html">mdro()</a></code> can now infer resistance from a drug+inhibitor combination when the base drug column is absent (e.g. piperacillin inferred from piperacillin/tazobactam); controlled via new <code>infer_from_combinations</code> argument (default <code>TRUE</code>) (<a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a>)</li>
<li>
<code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> gained the argument <code>guideline</code>, which defaults to EUCAST, for interpreting the ‘I’ category correctly.</li>
<li>Added to the <code>antimicrobials</code> data set: cefepime/taniborbactam (<code>FTA</code>), ceftibuten/avibactam (<code>CTA</code>), clorobiocin (<code>CLB</code>), kasugamycin (<code>KAS</code>), ostreogrycin (<code>OST</code>), taniborbactam (<code>TAN</code>), thiostrepton (<code>THS</code>), xeruborbactam (<code>XER</code>), and zorbamycin (<code>ZOR</code>)</li>
<code><a href="../reference/proportion.html">susceptibility()</a></code> / <code><a href="../reference/proportion.html">resistance()</a></code>: new <code>guideline</code> argument (default EUCAST) to ensure the ‘I’ category is interpreted correctly per guideline</li>
<li>Capped MIC handling in <code><a href="../reference/as.sir.html">as.sir()</a></code> reworked into four clearly defined options: <code>"none"</code>, <code>"conservative"</code> (new default), <code>"standard"</code>, <code>"lenient"</code> (<a href="https://github.com/msberends/AMR/issues/243" class="external-link">#243</a>)</li>
<li>
<code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.mic.html">rescale_mic()</a></code> gained the argument <code>round_to_next_log2</code>, which can be set to <code>TRUE</code> to round all values up to the nearest next log2 level (<a href="https://github.com/msberends/AMR/issues/255" class="external-link">#255</a>)</li>
<code><a href="../reference/as.mic.html">as.mic()</a></code> / <code><a href="../reference/as.mic.html">rescale_mic()</a></code>: new <code>round_to_next_log2</code> argument to round values up to the nearest log2 dilution level (<a href="https://github.com/msberends/AMR/issues/255" class="external-link">#255</a>)</li>
<li>
<code>antimicrobials$group</code> is now a <code>list</code> instead of a <code>character</code>, to contain any group the drug is in (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<li>
<code><a href="../reference/ab_property.html">ab_group()</a></code> gained an argument <code>all_groups</code> to return all groups the antimicrobial drug is in (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<li>Added explaining message to <code><a href="../reference/as.sir.html">as.sir()</a></code> when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
<li>Updated handling of capped MIC values (<code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, <code>&gt;=</code>) in <code><a href="../reference/as.sir.html">as.sir()</a></code> in the argument <code>capped_mic_handling</code>: (<a href="https://github.com/msberends/AMR/issues/243" class="external-link">#243</a>)
<ul><li>Introduced four clearly defined options: <code>"none"</code>, <code>"conservative"</code> (default), <code>"standard"</code>, and <code>"lenient"</code>
</li>
<li>Interpretation of capped MIC values now consistently returns <code>"NI"</code> (non-interpretable) when the true MIC could be at either side of a breakpoint, depending on the selected handling mode</li>
<li>This results in more reliable behaviour compared to previous versions for capped MIC values</li>
<li>Removed the <code>"inverse"</code> option, which has now become redundant</li>
</ul></li>
<li>
<code><a href="../reference/ab_property.html">ab_group()</a></code> now returns values consist with the AMR selectors (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<code>antimicrobials$group</code> now a <code>list</code>, so drugs belonging to multiple groups are fully represented; use <code>ab_group(all_groups = TRUE)</code> to retrieve all groups for a drug (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<li>New antimicrobials added: cefepime/taniborbactam (<code>FTA</code>), ceftibuten/avibactam (<code>CTA</code>), clorobiocin (<code>CLB</code>), kasugamycin (<code>KAS</code>), ostreogrycin (<code>OST</code>), taniborbactam (<code>TAN</code>), thiostrepton (<code>THS</code>), xeruborbactam (<code>XER</code>), zorbamycin (<code>ZOR</code>)</li>
<li>Improved console messages with clickable links throughout, powered by <code>cli</code> (<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>
</ul></div>
</div>
<div class="section level2">
@@ -300,7 +254,7 @@
<li>Disks of 0 to 5 mm are now allowed, the newly allowed range for disk diffusion (<code><a href="../reference/as.disk.html">as.disk()</a></code>) is now between 0 and 50 mm</li>
<li>Updated <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to support HTML output</li>
<li>
<code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> now supports multiple antimicrobials and antimicrobial groups to be affected by a single rule</li>
<code><a href="../reference/AMR-deprecated.html">custom_eucast_rules()</a></code> now supports multiple antimicrobials and antimicrobial groups to be affected by a single rule</li>
<li>
<code><a href="../reference/mo_property.html">mo_info()</a></code> now contains an extra element <code>rank</code> and <code>group_members</code> (with the contents of the new <code><a href="../reference/mo_property.html">mo_group_members()</a></code> function)</li>
<li>Updated all ATC codes from WHOCC</li>

269
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@@ -1,201 +1,116 @@
# Changelog
## AMR 3.0.1.9055
## AMR 3.0.1.9057
This will become release v3.1.0, intended for launch end of May.
Planned as v3.1.0, May 2026.
#### 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.
- Support for the [`future`](https://future.futureverse.org) package and
its framework, as the previous implementation of parallel computing
was slow
- **Breaking change**:
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) with
`parallel = TRUE` now requires a non-sequential
[`future::plan()`](https://future.futureverse.org/reference/plan.html)
to be active before the call — e.g.,
`future::plan(future::multisession)` — and throws an informative
error if none is set.
- New all-core usage setup: when the number of AB columns is smaller
than the number of available cores, rows are now split into batches
so all cores stay active (row-batch mode). Previously, a 6-column
dataset on a 16-core machine would only use 6 cores; now all 16 are
used, with each worker processing a smaller row slice (lower
per-worker memory pressure and processing time)
- [`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md)
and [`wisca()`](https://amr-for-r.org/reference/antibiogram.md)
gained a `parallel` argument using the same `future`/`future.apply`
pattern: for WISCA, Monte Carlo simulations are split into
`(group, chunk)` job pairs distributed across workers; for grouped
antibiograms, each group is processed by a separate worker
- EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints
added to the `clinical_breakpoints` data set; EUCAST 2026 is now the
default for all MIC and disk diffusion interpretations
- Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based
interpretation, by setting `breakpoint_type = "ECOFF"` in
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md); WT/NWT
results are fully supported in all resistance/susceptibility functions
and plots ([\#254](https://github.com/msberends/AMR/issues/254))
- Faster parallel computing via the `future` package; **breaking
change**: a non-sequential plan
(e.g. `future::plan(future::multisession)`) must be active before
using `parallel = TRUE`;
[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) and
[`wisca()`](https://amr-for-r.org/reference/antibiogram.md) now also
support `parallel = TRUE`
([\#281](https://github.com/msberends/AMR/issues/281))
- 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)
to transform `<mic>` columns with log2, and
[`step_sir_numeric()`](https://amr-for-r.org/reference/amr-tidymodels.md)
to convert `<sir>` columns to numeric
- New `tidyselect` helpers:
- [`all_sir()`](https://amr-for-r.org/reference/amr-tidymodels.md),
[`all_sir_predictors()`](https://amr-for-r.org/reference/amr-tidymodels.md)
- [`all_mic()`](https://amr-for-r.org/reference/amr-tidymodels.md),
[`all_mic_predictors()`](https://amr-for-r.org/reference/amr-tidymodels.md)
- [`all_disk()`](https://amr-for-r.org/reference/amr-tidymodels.md),
[`all_disk_predictors()`](https://amr-for-r.org/reference/amr-tidymodels.md)
- Data set `esbl_isolates` to practise with AMR modelling
- AMR selectors
- *tidymodels* integration for using SIR, MIC and disk data in modelling
pipelines:
[`step_mic_log2()`](https://amr-for-r.org/reference/amr-tidymodels.md),
[`step_sir_numeric()`](https://amr-for-r.org/reference/amr-tidymodels.md),
and new column selectors
[`all_sir()`](https://amr-for-r.org/reference/amr-tidymodels.md),
[`all_mic()`](https://amr-for-r.org/reference/amr-tidymodels.md),
[`all_disk()`](https://amr-for-r.org/reference/amr-tidymodels.md)
- New `esbl_isolates` data set for practising AMR modelling
- New antimicrobial selectors:
[`ionophores()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
[`peptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
[`phosphonics()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
and
[`phosphonics()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
[`spiropyrimidinetriones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
- Support for Wildtype (WT) / Non-wildtype (NWT) in
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md), all plotting
functions, and all susceptibility/resistance functions.
- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) gained an
argument `as_wt_nwt`, which defaults to `TRUE` only when
`breakpoint_type = "ECOFF"`
([\#254](https://github.com/msberends/AMR/issues/254))
- This transforms the output from S/R to WT/NWT
- Functions such as
[`susceptibility()`](https://amr-for-r.org/reference/proportion.md)
count WT as S and NWT as R
- Function
- New
[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md),
which allows future implementation of CLSI interpretive rules
([\#235](https://github.com/msberends/AMR/issues/235))
- [`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
has become a wrapper around that function
- Gained argument `add_if_missing` (default: `TRUE`). When set to
`FALSE`, rules are only applied to cells that already contain an SIR
value; `NA` cells are left untouched. This is useful with
`overwrite = TRUE` to update reported results without imputing
values for drugs that were not tested
([\#259](https://github.com/msberends/AMR/issues/259))
- Function
[`amr_course()`](https://amr-for-r.org/reference/amr_course.md), which
allows for automated download and unpacking of a GitHub repository for
e.g. webinar use
- Two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R’s
`NA_character_` and `NA_integer_`, for use in pipelines that require
typed missing values
a unified function for EUCAST and CLSI interpretive rules;
[`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
is now a wrapper around it
([\#235](https://github.com/msberends/AMR/issues/235),
[\#259](https://github.com/msberends/AMR/issues/259))
- New [`amr_course()`](https://amr-for-r.org/reference/amr_course.md) to
download and unpack course or webinar materials from GitHub in one
call
- Typed missing value constants `NA_ab_` and `NA_mo_`, for use in
pipelines that need missing values of a specific class
#### Fixes
- Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
where values that were purely numeric (e.g., `"1"`) and matched the
broad SIR-matching regex would be incorrectly stripped of all content
by the Unicode letter filter
- Fixed a bug in [`as.mic()`](https://amr-for-r.org/reference/as.mic.md)
where MIC values in scientific notation (e.g., `"1e-3"`) were
incorrectly handled because the letter `e` was removed along with
other Unicode letters; scientific notation `e` is now preserved
- Fixed a bug in [`as.ab()`](https://amr-for-r.org/reference/as.ab.md)
where certain AB codes containing “PH” or “TH” (such as `ETH`, `MTH`,
`PHE`, `PHN`, `STH`, `THA`, `THI1`) would incorrectly return `NA` when
combined in a vector with any untranslatable value
- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) on data
frames: already-converted SIR columns no longer dropped on re-run
([\#278](https://github.com/msberends/AMR/issues/278)); metadata
columns (e.g. `patient`, `ward`) no longer misidentified as antibiotic
columns; `info = FALSE` now suppresses all messages, including for
columns without breakpoints
- [`as.mic()`](https://amr-for-r.org/reference/as.mic.md): values in
scientific notation (e.g. `1e-3`) now handled correctly
- [`as.ab()`](https://amr-for-r.org/reference/as.ab.md): codes
containing “PH” or “TH” (e.g. `ETH`, `PHE`) no longer return `NA` when
mixed with unrecognised input
([\#245](https://github.com/msberends/AMR/issues/245))
- Fixed a bug in
[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) for
when no antimicrobials are set
- Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
where for numeric input the arguments `S`, `I`, and `R` would not be
considered ([\#244](https://github.com/msberends/AMR/issues/244))
- Fixed a bug in plotting MIC values when `keep_operators = "all"`
- Fixed some foreign translations of antimicrobial drugs
- Fixed a bug for printing column names to the console when using
`mutate_at(vars(...), as.mic)`
([\#249](https://github.com/msberends/AMR/issues/249))
- Fixed a bug to disregard `NI` for susceptibility proportion functions
- Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo
and CoPS to Stafilococco coagulasi-positivo
([\#256](https://github.com/msberends/AMR/issues/256))
- Fixed SIR and MIC coercion of combined values,
e.g. `as.sir("<= 0.002; S")` or `as.mic("S; 0.002")`
- Combined MIC/SIR input values (e.g. `"<= 0.002; S"` or `"S; 0.002"`)
now parsed correctly
([\#252](https://github.com/msberends/AMR/issues/252))
- Fixed translation of foreign languages in
[`sir_df()`](https://amr-for-r.org/reference/proportion.md)
([\#272](https://github.com/msberends/AMR/issues/272))
- Fixed BRMO classification by including bacterial complexes
- BRMO classification now includes bacterial complexes
([\#275](https://github.com/msberends/AMR/issues/275))
- Fixed [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) for data
frames silently deleting columns whose AB class was already `<sir>`
when called a second time (re-running on already-converted data)
([\#278](https://github.com/msberends/AMR/issues/278))
- Fixed [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) for data
frames incorrectly treating metadata columns (e.g. `patient`, `ward`)
as antibiotic columns when their names coincidentally matched an
antibiotic code; column content is now validated against AMR data
patterns before inclusion
- Fixed [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) ignoring
`info = FALSE` for columns with no breakpoints (e.g. cefoxitin against
*E. coli*)
- Translation fixes for Italian CoNS/CoPS names
([\#256](https://github.com/msberends/AMR/issues/256)), Dutch
antimicrobials, and
[`sir_df()`](https://amr-for-r.org/reference/proportion.md)
foreign-language output
([\#272](https://github.com/msberends/AMR/issues/272))
#### Updates
- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) with
`reference_data`: custom guideline names now correctly classify values
as R using EUCAST convention (`> breakpoint_R` for MIC,
`< breakpoint_R` for disk); custom breakpoints with `host = NA` now
serve as a host-agnostic fallback when no host-specific row matches
([\#239](https://github.com/msberends/AMR/issues/239))
- Extensive `cli` integration for better message handling and clickable
links in messages and warnings
([\#191](https://github.com/msberends/AMR/issues/191),
[\#265](https://github.com/msberends/AMR/issues/265))
- [`mdro()`](https://amr-for-r.org/reference/mdro.md) now infers
resistance for a *missing* base drug column from an *available*
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
`infer_from_combinations`, which defaults to `TRUE`
([\#209](https://github.com/msberends/AMR/issues/209)). Note that this
can yield a higher MDRO detection (which is a good thing as it has
become more reliable).
- [`susceptibility()`](https://amr-for-r.org/reference/proportion.md)
and [`resistance()`](https://amr-for-r.org/reference/proportion.md)
gained the argument `guideline`, which defaults to EUCAST, for
interpreting the ‘I’ category correctly.
- Added to the `antimicrobials` data set: cefepime/taniborbactam
(`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`),
kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`),
thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`)
- [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) and
[`rescale_mic()`](https://amr-for-r.org/reference/as.mic.md) gained
the argument `round_to_next_log2`, which can be set to `TRUE` to round
all values up to the nearest next log2 level
([\#255](https://github.com/msberends/AMR/issues/255))
- `antimicrobials$group` is now a `list` instead of a `character`, to
contain any group the drug is in
([\#246](https://github.com/msberends/AMR/issues/246))
- [`ab_group()`](https://amr-for-r.org/reference/ab_property.md) gained
an argument `all_groups` to return all groups the antimicrobial drug
is in ([\#246](https://github.com/msberends/AMR/issues/246))
- Added explaining message to
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) when
interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R)
([\#244](https://github.com/msberends/AMR/issues/244))
- Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) in the
argument `capped_mic_handling`:
- [`custom_eucast_rules()`](https://amr-for-r.org/reference/AMR-deprecated.md)
renamed to
[`custom_interpretive_rules()`](https://amr-for-r.org/reference/custom_interpretive_rules.md);
old name deprecated but still works
([\#268](https://github.com/msberends/AMR/issues/268))
- [`mdro()`](https://amr-for-r.org/reference/mdro.md) can now infer
resistance from a drug+inhibitor combination when the base drug column
is absent (e.g. piperacillin inferred from piperacillin/tazobactam);
controlled via new `infer_from_combinations` argument (default `TRUE`)
([\#209](https://github.com/msberends/AMR/issues/209))
- [`susceptibility()`](https://amr-for-r.org/reference/proportion.md) /
[`resistance()`](https://amr-for-r.org/reference/proportion.md): new
`guideline` argument (default EUCAST) to ensure the ‘I’ category is
interpreted correctly per guideline
- Capped MIC handling in
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) reworked into
four clearly defined options: `"none"`, `"conservative"` (new
default), `"standard"`, `"lenient"`
([\#243](https://github.com/msberends/AMR/issues/243))
- Introduced four clearly defined options: `"none"`, `"conservative"`
(default), `"standard"`, and `"lenient"`
- Interpretation of capped MIC values now consistently returns `"NI"`
(non-interpretable) when the true MIC could be at either side of a
breakpoint, depending on the selected handling mode
- This results in more reliable behaviour compared to previous
versions for capped MIC values
- Removed the `"inverse"` option, which has now become redundant
- [`ab_group()`](https://amr-for-r.org/reference/ab_property.md) now
returns values consist with the AMR selectors
- [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) /
[`rescale_mic()`](https://amr-for-r.org/reference/as.mic.md): new
`round_to_next_log2` argument to round values up to the nearest log2
dilution level ([\#255](https://github.com/msberends/AMR/issues/255))
- `antimicrobials$group` now a `list`, so drugs belonging to multiple
groups are fully represented; use `ab_group(all_groups = TRUE)` to
retrieve all groups for a drug
([\#246](https://github.com/msberends/AMR/issues/246))
- New antimicrobials added: cefepime/taniborbactam (`FTA`),
ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin
(`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton
(`THS`), xeruborbactam (`XER`), zorbamycin (`ZOR`)
- Improved console messages with clickable links throughout, powered by
`cli` ([\#191](https://github.com/msberends/AMR/issues/191),
[\#265](https://github.com/msberends/AMR/issues/265))
## AMR 3.0.1
@@ -581,7 +496,7 @@ this change.
- Updated
[`italicise_taxonomy()`](https://amr-for-r.org/reference/italicise_taxonomy.md)
to support HTML output
- [`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md)
- [`custom_eucast_rules()`](https://amr-for-r.org/reference/AMR-deprecated.md)
now supports multiple antimicrobials and antimicrobial groups to be
affected by a single rule
- [`mo_info()`](https://amr-for-r.org/reference/mo_property.md) now

2
pkgdown.yml
View File

@@ -10,7 +10,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2026-04-30T17:47Z
last_built: 2026-05-02T13:01Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles

6
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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">
@@ -55,7 +55,9 @@
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ab_class</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">custom_eucast_rules</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">ab_class</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">ab_selector</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>

2
reference/AMR-deprecated.md
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@@ -9,6 +9,8 @@ warning with the name of the alternative object it has been replaced by
## Usage
``` r
custom_eucast_rules(...)
ab_class(...)
ab_selector(...)

2
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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/AMR.html
View File

@@ -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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/WHOCC.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/WHONET.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/ab_from_text.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/ab_property.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/add_custom_antimicrobials.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/add_custom_microorganisms.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">

22
reference/age.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">
@@ -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 26.83288 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.24932 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.40000 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.16438 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.49315 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.20548 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.19178 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.30137 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.67397 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.25753 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 26 26.83836 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.25479 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.40548 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.16986 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.49863 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.21096 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.19726 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.30685 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.67945 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.26301 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
View File

@@ -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 26.83288 0
#> 2 1968-01-29 58 58.24932 31
#> 3 1965-12-05 60 60.40000 34
#> 4 1980-03-01 46 46.16438 19
#> 5 1949-11-01 76 76.49315 50
#> 6 1947-02-14 79 79.20548 52
#> 7 1940-02-19 86 86.19178 59
#> 8 1988-01-10 38 38.30137 11
#> 9 1997-08-27 28 28.67397 2
#> 10 1978-01-26 48 48.25753 21
#> 1 1999-06-30 26 26.83836 0
#> 2 1968-01-29 58 58.25479 31
#> 3 1965-12-05 60 60.40548 34
#> 4 1980-03-01 46 46.16986 19
#> 5 1949-11-01 76 76.49863 50
#> 6 1947-02-14 79 79.21096 52
#> 7 1940-02-19 86 86.19726 59
#> 8 1988-01-10 38 38.30685 11
#> 9 1997-08-27 28 28.67945 2
#> 10 1978-01-26 48 48.26301 21
```

8
reference/age_groups.html
View File

@@ -1,5 +1,5 @@
<!DOCTYPE html>
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<!-- 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>Split Ages into Age Groups — age_groups • 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="Split Ages into Age Groups — age_groups"><meta name="description" content="Split ages into age groups defined by the `split` argument. This allows for easier demographic (antimicrobial resistance) analysis. The function returns an ordered [factor]."><meta property="og:description" content="Split ages into age groups defined by the `split` argument. This allows for easier demographic (antimicrobial resistance) analysis. The function returns an ordered [factor]."><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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@@ -7,7 +7,7 @@
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@@ -50,7 +50,7 @@
</div>
<div class="ref-description section level2">
<p>Split ages into age groups defined by the <code>split</code> argument. This allows for easier demographic (antimicrobial resistance) analysis. The function returns an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a>.</p>
<p>Split ages into age groups defined by the `split` argument. This allows for easier demographic (antimicrobial resistance) analysis. The function returns an ordered [factor].</p>
</div>
<div class="section level2">
@@ -81,7 +81,7 @@
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></p>
<p>Ordered [factor]</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>

8
reference/age_groups.md
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@@ -1,8 +1,8 @@
# Split Ages into Age Groups
Split ages into age groups defined by the `split` argument. This allows
for easier demographic (antimicrobial resistance) analysis. The function
returns an ordered [factor](https://rdrr.io/r/base/factor.html).
Split ages into age groups defined by the \`split\` argument. This
allows for easier demographic (antimicrobial resistance) analysis. The
function returns an ordered \[factor\].
## Usage
@@ -34,7 +34,7 @@ age_groups(x, split_at = c(0, 12, 25, 55, 75), names = NULL,
## Value
Ordered [factor](https://rdrr.io/r/base/factor.html)
Ordered \[factor\]
## Details

37
reference/amr-tidymodels.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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@@ -74,41 +74,6 @@
<span> skip <span class="op">=</span> <span class="cn">FALSE</span>, id <span class="op">=</span> <span class="fu">recipes</span><span class="fu">::</span><span class="fu"><a href="https://recipes.tidymodels.org/reference/rand_id.html" class="external-link">rand_id</a></span><span class="op">(</span><span class="st">"sir_numeric"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt id="arg-recipe">recipe<a class="anchor" aria-label="anchor" href="#arg-recipe"></a></dt>
<dd><p>A recipe object. The step will be added to the sequence of
operations for this recipe.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>One or more selector functions to choose variables for this step.
See <code><a href="https://recipes.tidymodels.org/reference/selections.html" class="external-link">selections()</a></code> for more details.</p></dd>
<dt id="arg-role">role<a class="anchor" aria-label="anchor" href="#arg-role"></a></dt>
<dd><p>Not used by this step since no new variables are created.</p></dd>
<dt id="arg-trained">trained<a class="anchor" aria-label="anchor" href="#arg-trained"></a></dt>
<dd><p>A logical to indicate if the quantities for preprocessing have
been estimated.</p></dd>
<dt id="arg-skip">skip<a class="anchor" aria-label="anchor" href="#arg-skip"></a></dt>
<dd><p>A logical. Should the step be skipped when the recipe is baked by
<code><a href="https://recipes.tidymodels.org/reference/bake.html" class="external-link">bake()</a></code>? While all operations are baked when <code><a href="https://recipes.tidymodels.org/reference/prep.html" class="external-link">prep()</a></code> is run, some
operations may not be able to be conducted on new data (e.g. processing the
outcome variable(s)). Care should be taken when using <code>skip = TRUE</code> as it
may affect the computations for subsequent operations.</p></dd>
<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a></dt>
<dd><p>A character string that is unique to this step to identify it.</p></dd>
</dl></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>You can read more in our online <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">AMR with tidymodels introduction</a>.</p>

37
reference/amr-tidymodels.md
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@@ -25,43 +25,6 @@ step_sir_numeric(recipe, ..., role = NA, trained = FALSE, columns = NULL,
skip = FALSE, id = recipes::rand_id("sir_numeric"))
```
## Arguments
- recipe:
A recipe object. The step will be added to the sequence of operations
for this recipe.
- ...:
One or more selector functions to choose variables for this step. See
[`selections()`](https://recipes.tidymodels.org/reference/selections.html)
for more details.
- role:
Not used by this step since no new variables are created.
- trained:
A logical to indicate if the quantities for preprocessing have been
estimated.
- skip:
A logical. Should the step be skipped when the recipe is baked by
[`bake()`](https://recipes.tidymodels.org/reference/bake.html)? While
all operations are baked when
[`prep()`](https://recipes.tidymodels.org/reference/prep.html) is run,
some operations may not be able to be conducted on new data (e.g.
processing the outcome variable(s)). Care should be taken when using
`skip = TRUE` as it may affect the computations for subsequent
operations.
- id:
A character string that is unique to this step to identify it.
## Details
You can read more in our online [AMR with tidymodels

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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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4
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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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@@ -132,7 +132,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<dt id="arg-syndromic-group">syndromic_group<a class="anchor" aria-label="anchor" href="#arg-syndromic-group"></a></dt>
<dd><p>A column name of <code>x</code>, or values calculated to split rows of <code>x</code>, e.g. by using <code><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse()</a></code> or <code><a href="https://dplyr.tidyverse.org/reference/case-and-replace-when.html" class="external-link">case_when()</a></code>. See <em>Examples</em>.</p></dd>
<dd><p>A column name of `x`, or values calculated to split rows of `x`, e.g. by using [ifelse()] or [`case_when()`][dplyr::case_when()]. See *Examples*.</p></dd>
<dt id="arg-add-total-n">add_total_n<a class="anchor" aria-label="anchor" href="#arg-add-total-n"></a></dt>

7
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@@ -154,10 +154,9 @@ knit_print(x, italicise = TRUE,
- syndromic_group:
A column name of `x`, or values calculated to split rows of `x`, e.g.
by using [`ifelse()`](https://rdrr.io/r/base/ifelse.html) or
[`case_when()`](https://dplyr.tidyverse.org/reference/case-and-replace-when.html).
See *Examples*.
A column name of \`x\`, or values calculated to split rows of \`x\`,
e.g. by using \[ifelse()\] or
\[\`case_when()\`\]\[dplyr::case_when()\]. See \*Examples\*.
- add_total_n:

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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<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="">3.0.1.9055</small>
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2
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<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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2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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76
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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="">3.0.1.9055</small>
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@@ -98,7 +98,7 @@
<dt id="arg-as-mic">as.mic<a class="anchor" aria-label="anchor" href="#arg-as-mic"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the <code>mic</code> class should be kept - the default is <code>TRUE</code> for <code>rescale_mic()</code> and <code>FALSE</code> for <code><a href="https://rdrr.io/pkg/data.table/man/fdroplevels.html" class="external-link">droplevels()</a></code>. When setting this to <code>FALSE</code> in <code>rescale_mic()</code>, the output will have factor levels that acknowledge <code>mic_range</code>.</p></dd>
<dd><p>A [logical] to indicate whether the `mic` class should be kept - the default is `TRUE` for [rescale_mic()] and `FALSE` for [droplevels()]. When setting this to `FALSE` in [rescale_mic()], the output will have factor levels that acknowledge `mic_range`.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
@@ -107,45 +107,45 @@
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>Ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> with additional class <code>mic</code>, that in mathematical operations acts as a <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector. Bear in mind that the outcome of any mathematical operation on MICs will return a <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> value.</p>
<p>Ordered [factor] with additional class [`mic`], that in mathematical operations acts as a [numeric] vector. Bear in mind that the outcome of any mathematical operation on MICs will return a [numeric] value.</p>
</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 (2011-2026) 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>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co">#&gt; Class &lt;mic&gt;</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="co">#&gt; [1] 16 1 8 8 64 &gt;=128 0.0625 32 32 16</span></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a></span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="fu">is.factor</span>(x)</span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a><span class="co">#&gt; [1] TRUE</span></span>
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a></span>
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a>x[<span class="dv">1</span>] <span class="sc">*</span> <span class="dv">2</span></span>
<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a><span class="co">#&gt; [1] 32</span></span>
<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a></span>
<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a><span class="fu">median</span>(x)</span>
<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a><span class="co">#&gt; [1] 26</span></span></code></pre><p></p></div>
<p>This makes it possible to maintain operators that often come with MIC values, such "&gt;=" and "&lt;=", even when filtering using <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> values in data analysis, e.g.:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a>x[x <span class="sc">&gt;</span> <span class="dv">4</span>]</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="co">#&gt; Class &lt;mic&gt;</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co">#&gt; [1] 16 8 8 64 &gt;=128 32 32 16</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a>df <span class="ot">&lt;-</span> <span class="fu">data.frame</span>(x, <span class="at">hospital =</span> <span class="st">"A"</span>)</span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="fu">subset</span>(df, x <span class="sc">&gt;</span> <span class="dv">4</span>) <span class="co"># or with dplyr: df %&gt;% filter(x &gt; 4)</span></span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a><span class="co">#&gt; x hospital</span></span>
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a><span class="co">#&gt; 1 16 A</span></span>
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a><span class="co">#&gt; 5 64 A</span></span>
<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a><span class="co">#&gt; 6 &gt;=128 A</span></span>
<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a><span class="co">#&gt; 8 32 A</span></span>
<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a><span class="co">#&gt; 9 32 A</span></span>
<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a><span class="co">#&gt; 10 16 A</span></span></code></pre><p></p></div>
<p>All so-called <a href="https://rdrr.io/r/base/groupGeneric.html" class="external-link">group generic functions</a> are implemented for the MIC class (such as <code>!</code>, <code>!=</code>, <code>&lt;</code>, <code>&gt;=</code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp()</a></code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2()</a></code>). Some mathematical functions are also implemented (such as <code><a href="https://rdrr.io/r/stats/quantile.html" class="external-link">quantile()</a></code>, <code><a href="https://rdrr.io/r/stats/median.html" class="external-link">median()</a></code>, <code><a href="https://rdrr.io/r/stats/fivenum.html" class="external-link">fivenum()</a></code>). Since <code><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd()</a></code> and <code><a href="https://rdrr.io/r/stats/cor.html" class="external-link">var()</a></code> are non-generic functions, these could not be extended. Use <code><a href="https://rdrr.io/r/stats/mad.html" class="external-link">mad()</a></code> as an alternative, or use e.g. <code>sd(as.numeric(x))</code> where <code>x</code> is your vector of MIC values.</p>
<p>Using <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> or <code><a href="https://rdrr.io/r/base/numeric.html" class="external-link">as.numeric()</a></code> on MIC values will remove the operators and return a numeric vector. Do <strong>not</strong> use <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on MIC values as by the <span style="R">R</span> convention on <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a>s, it will return the index of the factor levels (which is often useless for regular users).</p>
<p>The function <code>is.mic()</code> detects if the input contains class <code>mic</code>. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> or <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>, it iterates over all columns/items and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
<p>Use <code><a href="https://rdrr.io/pkg/data.table/man/fdroplevels.html" class="external-link">droplevels()</a></code> to drop unused levels. At default, it will return a plain factor. Use <code>droplevels(..., as.mic = TRUE)</code> to maintain the <code>mic</code> class.</p>
<p>With <code>rescale_mic()</code>, existing MIC ranges can be limited to a defined range of MIC values. This can be useful to better compare MIC distributions.</p>
<p>For <code>ggplot2</code>, use one of the <code><a href="plot.html">scale_*_mic()</a></code> functions to plot MIC values. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.</p>
<p>To interpret MIC values as SIR values, use [as.sir()] on MIC values. It supports guidelines from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline <!-- %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`). --></p>
<p>This class for MIC values is a quite a special data type: formally it is an ordered [factor] with valid MIC values as [factor] levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:</p>
<p>“`
x &lt;- random_mic(10)
x
#&gt; Class &lt;mic&gt;
#&gt; [1] 16 1 8 8 64 &gt;=128 0.0625 32 32 16</p>
<p>is.factor(x)
#&gt; [1] TRUE</p>
<p>x[1] * 2
#&gt; [1] 32</p>
<p>median(x)
#&gt; [1] 26
“`</p>
<p>This makes it possible to maintain operators that often come with MIC values, such "&gt;=" and "&lt;=", even when filtering using [numeric] values in data analysis, e.g.:</p>
<p>“`
x[x &gt; 4]
#&gt; Class &lt;mic&gt;
#&gt; [1] 16 8 8 64 &gt;=128 32 32 16</p>
<p>df &lt;- data.frame(x, hospital = "A")
subset(df, x &gt; 4) # or with dplyr: df <!-- %&gt;% filter(x &gt; 4) -->
#&gt; x hospital
#&gt; 1 16 A
#&gt; 5 64 A
#&gt; 6 &gt;=128 A
#&gt; 8 32 A
#&gt; 9 32 A
#&gt; 10 16 A
“`</p>
<p>All so-called [group generic functions][groupGeneric()] are implemented for the MIC class (such as `!`, `!=`, `&lt;`, `&gt;=`, [exp()], [log2()]). Some mathematical functions are also implemented (such as [quantile()], [median()], [fivenum()]). Since [sd()] and [var()] are non-generic functions, these could not be extended. Use [mad()] as an alternative, or use e.g. `sd(as.numeric(x))` where `x` is your vector of MIC values.</p>
<p>Using [as.double()] or [as.numeric()] on MIC values will remove the operators and return a numeric vector. Do **not** use [as.integer()] on MIC values as by the <span style="R">R</span> convention on [factor]s, it will return the index of the factor levels (which is often useless for regular users).</p>
<p>The function [is.mic()] detects if the input contains class `mic`. If the input is a [data.frame] or [list], it iterates over all columns/items and returns a [logical] vector.</p>
<p>Use [droplevels()] to drop unused levels. At default, it will return a plain factor. Use `droplevels(..., as.mic = TRUE)` to maintain the `mic` class.</p>
<p>With [rescale_mic()], existing MIC ranges can be limited to a defined range of MIC values. This can be useful to better compare MIC distributions.</p>
<p>For `ggplot2`, use one of the [`scale_*_mic()`][scale_x_mic()] functions to plot MIC values. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.</p>
<p><code>NA_mic_</code> is a missing value of the new <code>mic</code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
<p>Use <code>mic_p50()</code> and <code>mic_p90()</code> to get the 50th and 90th percentile of MIC values. They return 'normal' <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> values.</p>
</div>

124
reference/as.mic.md
View File

@@ -62,12 +62,10 @@ droplevels(x, as.mic = FALSE, ...)
- as.mic:
A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
the `mic` class should be kept - the default is `TRUE` for
`rescale_mic()` and `FALSE` for
[`droplevels()`](https://rdrr.io/pkg/data.table/man/fdroplevels.html).
When setting this to `FALSE` in `rescale_mic()`, the output will have
factor levels that acknowledge `mic_range`.
A \[logical\] to indicate whether the \`mic\` class should be kept -
the default is \`TRUE\` for \[rescale_mic()\] and \`FALSE\` for
\[droplevels()\]. When setting this to \`FALSE\` in \[rescale_mic()\],
the output will have factor levels that acknowledge \`mic_range\`.
- ...:
@@ -75,101 +73,71 @@ droplevels(x, as.mic = FALSE, ...)
## Value
Ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with
additional class `mic`, that in mathematical operations acts as a
[numeric](https://rdrr.io/r/base/numeric.html) vector. Bear in mind that
Ordered \[factor\] with additional class \[\`mic\`\], that in
mathematical operations acts as a \[numeric\] vector. Bear in mind that
the outcome of any mathematical operation on MICs will return a
[numeric](https://rdrr.io/r/base/numeric.html) value.
\[numeric\] value.
## Details
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 (2011-2026) and CLSI (2011-2026).
To interpret MIC values as SIR values, use \[as.sir()\] on MIC values.
It supports guidelines from EUCAST (\`r min(as.integer(gsub("\[^0-9\]",
"", subset(clinical_breakpoints, guideline
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
valid MIC values as
[factor](https://rdrr.io/pkg/data.table/man/fctr.html) levels (to make
sure only valid MIC values are retained), but for any mathematical
an ordered \[factor\] with valid MIC values as \[factor\] levels (to
make sure only valid MIC values are retained), but for any mathematical
operation it acts as decimal numbers:
x <- random_mic(10)
x
#> Class <mic>
#> [1] 16 1 8 8 64 >=128 0.0625 32 32 16
“\` x \<- random_mic(10) x \#\> Class \<mic\> \#\> \[1\] 16 1 8 8 64
\>=128 0.0625 32 32 16
is.factor(x)
#> [1] TRUE
is.factor(x) \#\> \[1\] TRUE
x[1] * 2
#> [1] 32
x\[1\] \* 2 \#\> \[1\] 32
median(x)
#> [1] 26
median(x) \#\> \[1\] 26 “\`
This makes it possible to maintain operators that often come with MIC
values, such "\>=" and "\<=", even when filtering using
[numeric](https://rdrr.io/r/base/numeric.html) values in data analysis,
e.g.:
values, such "\>=" and "\<=", even when filtering using \[numeric\]
values in data analysis, e.g.:
x[x > 4]
#> Class <mic>
#> [1] 16 8 8 64 >=128 32 32 16
“\` x\[x \> 4\] \#\> Class \<mic\> \#\> \[1\] 16 8 8 64 \>=128 32 32 16
df <- data.frame(x, hospital = "A")
subset(df, x > 4) # or with dplyr: df %>% filter(x > 4)
#> x hospital
#> 1 16 A
#> 5 64 A
#> 6 >=128 A
#> 8 32 A
#> 9 32 A
#> 10 16 A
df \<- data.frame(x, hospital = "A") subset(df, x \> 4) \# or with
dplyr: df \#\> x hospital \#\> 1 16 A \#\> 5 64 A \#\> 6 \>=128 A \#\> 8
32 A \#\> 9 32 A \#\> 10 16 A “\`
All so-called [group generic
functions](https://rdrr.io/r/base/groupGeneric.html) are implemented for
the MIC class (such as `!`, `!=`, `<`, `>=`,
[`exp()`](https://rdrr.io/r/base/Log.html),
[`log2()`](https://rdrr.io/r/base/Log.html)). Some mathematical
functions are also implemented (such as
[`quantile()`](https://rdrr.io/r/stats/quantile.html),
[`median()`](https://rdrr.io/r/stats/median.html),
[`fivenum()`](https://rdrr.io/r/stats/fivenum.html)). Since
[`sd()`](https://rdrr.io/r/stats/sd.html) and
[`var()`](https://rdrr.io/r/stats/cor.html) are non-generic functions,
these could not be extended. Use
[`mad()`](https://rdrr.io/r/stats/mad.html) as an alternative, or use
e.g. `sd(as.numeric(x))` where `x` is your vector of MIC values.
All so-called \[group generic functions\]\[groupGeneric()\] are
implemented for the MIC class (such as \`!\`, \`!=\`, \`\<\`, \`\>=\`,
\[exp()\], \[log2()\]). Some mathematical functions are also implemented
(such as \[quantile()\], \[median()\], \[fivenum()\]). Since \[sd()\]
and \[var()\] are non-generic functions, these could not be extended.
Use \[mad()\] as an alternative, or use e.g. \`sd(as.numeric(x))\` where
\`x\` is your vector of MIC values.
Using [`as.double()`](https://rdrr.io/r/base/double.html) or
[`as.numeric()`](https://rdrr.io/r/base/numeric.html) on MIC values will
remove the operators and return a numeric vector. Do **not** use
[`as.integer()`](https://rdrr.io/r/base/integer.html) on MIC values as
by the R convention on
[factor](https://rdrr.io/pkg/data.table/man/fctr.html)s, it will return
the index of the factor levels (which is often useless for regular
users).
Using \[as.double()\] or \[as.numeric()\] on MIC values will remove the
operators and return a numeric vector. Do \*\*not\*\* use
\[as.integer()\] on MIC values as by the R convention on \[factor\]s, it
will return the index of the factor levels (which is often useless for
regular users).
The function `is.mic()` detects if the input contains class `mic`. If
the input is a [data.frame](https://rdrr.io/r/base/data.frame.html) or
[list](https://rdrr.io/r/base/list.html), it iterates over all
columns/items and returns a
[logical](https://rdrr.io/r/base/logical.html) vector.
The function \[is.mic()\] detects if the input contains class \`mic\`.
If the input is a \[data.frame\] or \[list\], it iterates over all
columns/items and returns a \[logical\] vector.
Use
[`droplevels()`](https://rdrr.io/pkg/data.table/man/fdroplevels.html) to
drop unused levels. At default, it will return a plain factor. Use
`droplevels(..., as.mic = TRUE)` to maintain the `mic` class.
Use \[droplevels()\] to drop unused levels. At default, it will return a
plain factor. Use \`droplevels(..., as.mic = TRUE)\` to maintain the
\`mic\` class.
With `rescale_mic()`, existing MIC ranges can be limited to a defined
With \[rescale_mic()\], existing MIC ranges can be limited to a defined
range of MIC values. This can be useful to better compare MIC
distributions.
For `ggplot2`, use one of the
[`scale_*_mic()`](https://amr-for-r.org/reference/plot.md) functions to
plot MIC values. They allows custom MIC ranges and to plot intermediate
log2 levels for missing MIC values.
For \`ggplot2\`, use one of the
\[\`scale\_\*\_mic()\`\]\[scale_x_mic()\] functions to plot MIC values.
They allows custom MIC ranges and to plot intermediate log2 levels for
missing MIC values.
`NA_mic_` is a missing value of the new `mic` class, analogous to e.g.
base R's [`NA_character_`](https://rdrr.io/r/base/NA.html).

2
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View File

@@ -7,7 +7,7 @@
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reference/as.sir.html
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@@ -52,8 +52,8 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
</div>
<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 2011-2026 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>
<p>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`.</p>
<p>Breakpoints are currently implemented from EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline <!-- %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`, see *Details*. All breakpoints used for interpretation are available in our [clinical_breakpoints] data set. --></p>
</div>
<div class="section level2">
@@ -236,7 +236,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>Ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> with new class <code>sir</code></p>
<p>Ordered [factor] with new class `sir`</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -420,10 +420,10 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<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> 2026-04-30 <span style="color: #949494;">17:47:55</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> 2026-04-30 <span style="color: #949494;">17:47:55</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> 2026-04-30 <span style="color: #949494;">17:47:55</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> 2026-04-30 <span style="color: #949494;">17:47:55</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> 2026-05-02 <span style="color: #949494;">13:02:42</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> 2026-05-02 <span style="color: #949494;">13:02:42</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> 2026-05-02 <span style="color: #949494;">13:02:42</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> 2026-05-02 <span style="color: #949494;">13:02:43</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>

26
reference/as.sir.md
View File

@@ -2,16 +2,13 @@
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](https://rdrr.io/pkg/data.table/man/fctr.html) containing the
levels `S`, `SDD`, `I`, `R`, `NI`.
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](https://amr-for-r.org/reference/clinical_breakpoints.md)
data set.
Breakpoints are currently implemented from EUCAST \`r
min(as.integer(gsub("\[^0-9\]", "", subset(AMR::clinical_breakpoints,
guideline
## Usage
@@ -367,8 +364,7 @@ disk diffusion diameters:
## Value
Ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with new
class `sir`
Ordered \[factor\] with new class \`sir\`
## Details
@@ -667,10 +663,10 @@ 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 2026-04-30 17:47:55 1 MIC amoxicillin Escherich… human 8
#> 2 2026-04-30 17:47:55 1 MIC cipro Escherich… human 0.256
#> 3 2026-04-30 17:47:55 1 DISK tobra Escherich… human 16
#> 4 2026-04-30 17:47:55 1 DISK genta Escherich… human 18
#> 1 2026-05-02 13:02:42 1 MIC amoxicillin Escherich… human 8
#> 2 2026-05-02 13:02:42 1 MIC cipro Escherich… human 0.256
#> 3 2026-05-02 13:02:42 1 DISK tobra Escherich… human 16
#> 4 2026-05-02 13:02:43 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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@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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<img src="../logo.svg" class="logo" alt=""><h1>Define Custom EUCAST Rules</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/custom_eucast_rules.R" class="external-link"><code>R/custom_eucast_rules.R</code></a></small>
<div class="d-none name"><code>custom_eucast_rules.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in <code><a href="interpretive_rules.html">eucast_rules()</a></code>.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">custom_eucast_rules</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Rules in <a href="https://rdrr.io/r/base/tilde.html" class="external-link">formula</a> notation, see below for instructions, and in <em>Examples</em>.</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>A <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a> containing the custom rules</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the <code><a href="interpretive_rules.html">eucast_rules()</a></code> function.</p><div class="section">
<h3 id="basics">Basics<a class="anchor" aria-label="anchor" href="#basics"></a></h3>
<p>If you are familiar with the <code><a href="https://dplyr.tidyverse.org/reference/case-and-replace-when.html" class="external-link">case_when()</a></code> function of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation'. The rule itself is written <em>before</em> the tilde (<code>~</code>) and the consequence of the rule is written <em>after</em> the tilde:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"S"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"S"</span>,</span>
<span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span></code></pre><p></p></div>
<p>These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span></span>
<span><span class="co">#&gt; A set of custom EUCAST rules:</span></span>
<span><span class="co">#&gt;</span></span>
<span><span class="co">#&gt; 1. If TZP is "S" then set to S :</span></span>
<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP)</span></span>
<span><span class="co">#&gt;</span></span>
<span><span class="co">#&gt; 2. If TZP is "R" then set to R :</span></span>
<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP)</span></span></code></pre><p></p></div>
<p>The rules (the part <em>before</em> the tilde, in above example <code>TZP == "S"</code> and <code>TZP == "R"</code>) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column <code>TZP</code> must exist. We will create a sample data set and test the rules set:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span>,</span>
<span> TZP <span class="op">=</span> <span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="st">"R"</span><span class="op">)</span>,</span>
<span> ampi <span class="op">=</span> <span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span>,</span>
<span> cipro <span class="op">=</span> <span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="va">df</span></span>
<span><span class="co">#&gt; mo TZP ampi cipro</span></span>
<span><span class="co">#&gt; 1 Escherichia coli R S S</span></span>
<span><span class="co">#&gt; 2 Klebsiella pneumoniae R S S</span></span>
<span></span>
<span><span class="fu"><a href="../reference/interpretive_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">df</span>,</span>
<span> rules <span class="op">=</span> <span class="st">"custom"</span>,</span>
<span> custom_rules <span class="op">=</span> <span class="va">x</span>,</span>
<span> info <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="co">#&gt; mo TZP ampi cipro</span></span>
<span><span class="co">#&gt; 1 Escherichia coli R R S</span></span>
<span><span class="co">#&gt; 2 Klebsiella pneumoniae R R S</span></span></code></pre><p></p></div>
</div>
<div class="section">
<h3 id="using-taxonomic-properties-in-rules">Using taxonomic properties in rules<a class="anchor" aria-label="anchor" href="#using-taxonomic-properties-in-rules"></a></h3>
<p>There is one exception in columns used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: <code>"mo"</code>, <code>"fullname"</code>, <code>"status"</code>, <code>"kingdom"</code>, <code>"phylum"</code>, <code>"class"</code>, <code>"order"</code>, <code>"family"</code>, <code>"genus"</code>, <code>"species"</code>, <code>"subspecies"</code>, <code>"rank"</code>, <code>"ref"</code>, <code>"oxygen_tolerance"</code>, <code>"source"</code>, <code>"lpsn"</code>, <code>"lpsn_parent"</code>, <code>"lpsn_renamed_to"</code>, <code>"mycobank"</code>, <code>"mycobank_parent"</code>, <code>"mycobank_renamed_to"</code>, <code>"gbif"</code>, <code>"gbif_parent"</code>, <code>"gbif_renamed_to"</code>, <code>"prevalence"</code>, and <code>"snomed"</code>. Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span></span>
<span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"S"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"S"</span>,</span>
<span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="../reference/interpretive_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">df</span>,</span>
<span> rules <span class="op">=</span> <span class="st">"custom"</span>,</span>
<span> custom_rules <span class="op">=</span> <span class="va">y</span>,</span>
<span> info <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="co">#&gt; mo TZP ampi cipro</span></span>
<span><span class="co">#&gt; 1 Escherichia coli R S S</span></span>
<span><span class="co">#&gt; 2 Klebsiella pneumoniae R R S</span></span></code></pre><p></p></div>
</div>
<div class="section">
<h3 id="sharing-rules-among-multiple-users">Sharing rules among multiple users<a class="anchor" aria-label="anchor" href="#sharing-rules-among-multiple-users"></a></h3>
<p>The rules set (the <code>y</code> object in this case) could be exported to a shared file location using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS()</a></code>.</p>
</div>
<div class="section">
<h3 id="usage-of-multiple-antimicrobials-and-antimicrobial-group-names">Usage of multiple antimicrobials and antimicrobial group names<a class="anchor" aria-label="anchor" href="#usage-of-multiple-antimicrobials-and-antimicrobial-group-names"></a></h3>
<p>You can define antimicrobial groups instead of single antimicrobials for the rule consequence, which is the part <em>after</em> the tilde (~). In the examples above, the antimicrobial group <code>aminopenicillins</code> includes both ampicillin and amoxicillin.</p>
<p>Rules can also be applied to multiple antimicrobials and antimicrobial groups simultaneously. Use the <code><a href="https://rdrr.io/r/base/c.html" class="external-link">c()</a></code> function to combine multiple antimicrobials. For instance, the following example sets all aminopenicillins and ureidopenicillins to "R" if column TZP (piperacillin/tazobactam) is "R":</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</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="va">aminopenicillins</span>, <span class="va">ureidopenicillins</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span>
<span><span class="va">x</span></span>
<span><span class="co">#&gt; A set of custom EUCAST rules:</span></span>
<span><span class="co">#&gt;</span></span>
<span><span class="co">#&gt; 1. If TZP is "R" then set to "R":</span></span>
<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)</span></span></code></pre><p></p></div>
<p>These 43 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminocoumarins<br>(clorobiocin, novobiocin, and penicillin/novobiocin)</p></li>
<li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
<li><p>aminopenicillins<br>(amoxicillin, amoxicillin/clavulanic acid, and ampicillin)</p></li>
<li><p>antifungals<br>(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
<li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>
<li><p>betalactamase_inhibitors<br>(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, avibactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/sulbactam, ceftaroline/avibactam, ceftazidime/avibactam, ceftibuten/avibactam, ceftolozane/tazobactam, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, nacubactam, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, sulbactam, sultamicillin, taniborbactam, tazobactam, ticarcillin/clavulanic acid, xeruborbactam, and zidebactam)</p></li>
<li><p>betalactams<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, taniborbactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)</p></li>
<li><p>betalactams_with_inhibitor<br>(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftibuten/avibactam, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)</p></li>
<li><p>carbapenems<br>(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, taniborbactam, and tebipenem)</p></li>
<li><p>cephalosporins<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>cephalosporins_1st<br>(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine)</p></li>
<li><p>cephalosporins_2nd<br>(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening test, cefprozil, cefuroxime, cefuroxime axetil, and loracarbef)</p></li>
<li><p>cephalosporins_3rd<br>(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef)</p></li>
<li><p>cephalosporins_4th<br>(cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)</p></li>
<li><p>cephalosporins_5th<br>(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam)</p></li>
<li><p>cephalosporins_except_caz<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>fluoroquinolones<br>(besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>fusidanes<br>(fusidic acid)</p></li>
<li><p>glycopeptides<br>(avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod, and zorbamycin)</p></li>
<li><p>glycopeptides_except_lipo<br>(avoparcin, bleomycin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, vancomycin-macromethod, and zorbamycin)</p></li>
<li><p>ionophores<br>(lasalocid, monensin sodium, narasin, nystatin, and salinomycin)</p></li>
<li><p>isoxazolylpenicillins<br>(cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test)</p></li>
<li><p>lincosamides<br>(clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin)</p></li>
<li><p>lipoglycopeptides<br>(dalbavancin, oritavancin, and telavancin)</p></li>
<li><p>macrolides<br>(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, clindamycin inducible screening test, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin)</p></li>
<li><p>monobactams<br>(aztreonam, aztreonam/avibactam, aztreonam/nacubactam, carumonam, and tigemonam)</p></li>
<li><p>nitrofurans<br>(furazidin, furazolidone, nifurtoinol, nitrofurantoin, and nitrofurazone)</p></li>
<li><p>oxazolidinones<br>(cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone)</p></li>
<li><p>penicillins<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic acid)</p></li>
<li><p>peptides<br>(avoparcin, bacitracin, bleomycin, dalbavancin, daptomycin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, thiostrepton, vancomycin, vancomycin-macromethod, and zorbamycin)</p></li>
<li><p>phenicols<br>(chloramphenicol, florfenicol, and thiamphenicol)</p></li>
<li><p>phosphonics<br>(amikacin/fosfomycin and fosfomycin)</p></li>
<li><p>pleuromutilins<br>(retapamulin and tiamulin)</p></li>
<li><p>polymyxins<br>(colistin, polymyxin B, and polymyxin B/polysorbate 80)</p></li>
<li><p>quinolones<br>(besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, ozenoxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>rifamycins<br>(rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine)</p></li>
<li><p>spiropyrimidinetriones<br>(zoliflodacin)</p></li>
<li><p>streptogramins<br>(ostreogrycin, pristinamycin, quinupristin/dalfopristin, and virginiamycine)</p></li>
<li><p>sulfonamides<br>(isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea, sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole)</p></li>
<li><p>tetracyclines<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, tetracycline/oleandomycin, and tigecycline)</p></li>
<li><p>tetracyclines_except_tgc<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tetracycline/oleandomycin)</p></li>
<li><p>trimethoprims<br>(brodimoprim, iclaprim, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole)</p></li>
<li><p>ureidopenicillins<br>(azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam)</p></li>
</ul></div>
</div>
<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">x</span> <span class="op">&lt;-</span> <span class="fu">custom_eucast_rules</span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="va">AMC</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span>,</span></span>
<span class="r-in"><span> <span class="va">AMC</span> <span class="op">==</span> <span class="st">"I"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"I"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> A set of custom EUCAST rules:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #BBBBBB;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FF5F5F;"> R </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">amoxicillin/clavulanic acid</span> (AMC), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FFD787;"> I </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #BBBBBB;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FFD787;"> I </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">amoxicillin/clavulanic acid</span> (AMC), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># run the custom rule set (verbose = TRUE will return a logbook instead of the data set):</span></span></span>
<span class="r-in"><span><span class="fu"><a href="interpretive_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> rules <span class="op">=</span> <span class="st">"custom"</span>,</span></span>
<span class="r-in"><span> custom_rules <span class="op">=</span> <span class="va">x</span>,</span></span>
<span class="r-in"><span> info <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
<span class="r-in"><span> overwrite <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
<span class="r-in"><span> verbose <span class="op">=</span> <span class="cn">TRUE</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 8 × 9</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> row col mo_fullname old new rule rule_group rule_name rule_source</span>
<span class="r-out co"><span class="r-pr">#&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;ord&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> 33 AMP Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 33 AMX Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 34 AMP Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 34 AMX Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> 531 AMP Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> 531 AMX Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">7</span> <span style="text-decoration: underline;">1</span>485 AMP Klebsiella oxy… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">8</span> <span style="text-decoration: underline;">1</span>485 AMX Klebsiella oxy… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># combine rule sets</span></span></span>
<span class="r-in"><span><span class="va">x2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="va">x</span>,</span></span>
<span class="r-in"><span> <span class="fu">custom_eucast_rules</span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="va">carbapenems</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x2</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> A set of custom EUCAST rules:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #BBBBBB;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FF5F5F;"> R </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">amoxicillin/clavulanic acid</span> (AMC), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FFD787;"> I </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #BBBBBB;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FFD787;"> I </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">amoxicillin/clavulanic acid</span> (AMC), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">TZP</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FF5F5F;"> R </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">biapenem</span> (BIA), <span style="color: #0000BB;">doripenem</span> (DOR), <span style="color: #0000BB;">ertapenem</span> (ETP), <span style="color: #0000BB;">imipenem</span> (IPM), <span style="color: #0000BB;">imipenem/EDTA</span> (IPE), <span style="color: #0000BB;">imipenem/relebactam</span> (IMR), <span style="color: #0000BB;">meropenem</span> (MEM), <span style="color: #0000BB;">meropenem/nacubactam</span> (MNC), <span style="color: #0000BB;">meropenem/vaborbactam</span> (MEV), <span style="color: #0000BB;">panipenem</span> (PAN), <span style="color: #0000BB;">razupenem</span> (RZM), <span style="color: #0000BB;">ritipenem</span> (RIT), <span style="color: #0000BB;">ritipenem acoxil</span> (RIA), <span style="color: #0000BB;">taniborbactam</span> (TAN), <span style="color: #0000BB;">tebipenem</span> (TBP)</span>
</code></pre></div>
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<img src="../logo.svg" class="logo" alt=""><h1>Define Custom Interpretive Rules</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/custom_interpretive_rules.R" class="external-link"><code>R/custom_interpretive_rules.R</code></a></small>
<div class="d-none name"><code>custom_interpretive_rules.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Define custom interpretive rules for your organisation or specific analysis and use the output of this function in <code><a href="interpretive_rules.html">interpretive_rules()</a></code>.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">custom_interpretive_rules</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Rules in <a href="https://rdrr.io/r/base/tilde.html" class="external-link">formula</a> notation, see below for instructions, and in <em>Examples</em>.</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>A <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a> containing the custom rules</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>Some organisations have their own adoption of interpretive rules. This function can be used to define custom rules to be used in the <code><a href="interpretive_rules.html">interpretive_rules()</a></code> function.</p><div class="section">
<h3 id="basics">Basics<a class="anchor" aria-label="anchor" href="#basics"></a></h3>
<p>If you are familiar with the <code><a href="https://dplyr.tidyverse.org/reference/case-and-replace-when.html" class="external-link">case_when()</a></code> function of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation'. The rule itself is written <em>before</em> the tilde (<code>~</code>) and the consequence of the rule is written <em>after</em> the tilde:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_interpretive_rules.html">custom_interpretive_rules</a></span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"S"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"S"</span>,</span>
<span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span></code></pre><p></p></div>
<p>These are two custom interpretive rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span></span>
<span><span class="co">#&gt; A set of custom interpretive rules:</span></span>
<span><span class="co">#&gt;</span></span>
<span><span class="co">#&gt; 1. If TZP is "S" then set to S :</span></span>
<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP)</span></span>
<span><span class="co">#&gt;</span></span>
<span><span class="co">#&gt; 2. If TZP is "R" then set to R :</span></span>
<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP)</span></span></code></pre><p></p></div>
<p>The rules (the part <em>before</em> the tilde, in above example <code>TZP == "S"</code> and <code>TZP == "R"</code>) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column <code>TZP</code> must exist. We will create a sample data set and test the rules set:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span>,</span>
<span> TZP <span class="op">=</span> <span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="st">"R"</span><span class="op">)</span>,</span>
<span> ampi <span class="op">=</span> <span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span>,</span>
<span> cipro <span class="op">=</span> <span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="va">df</span></span>
<span><span class="co">#&gt; mo TZP ampi cipro</span></span>
<span><span class="co">#&gt; 1 Escherichia coli R S S</span></span>
<span><span class="co">#&gt; 2 Klebsiella pneumoniae R S S</span></span>
<span></span>
<span><span class="fu"><a href="../reference/interpretive_rules.html">interpretive_rules</a></span><span class="op">(</span><span class="va">df</span>,</span>
<span> rules <span class="op">=</span> <span class="st">"custom"</span>,</span>
<span> custom_rules <span class="op">=</span> <span class="va">x</span>,</span>
<span> info <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="co">#&gt; mo TZP ampi cipro</span></span>
<span><span class="co">#&gt; 1 Escherichia coli R R S</span></span>
<span><span class="co">#&gt; 2 Klebsiella pneumoniae R R S</span></span></code></pre><p></p></div>
</div>
<div class="section">
<h3 id="using-taxonomic-properties-in-rules">Using taxonomic properties in rules<a class="anchor" aria-label="anchor" href="#using-taxonomic-properties-in-rules"></a></h3>
<p>There is one exception in columns used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: <code>"mo"</code>, <code>"fullname"</code>, <code>"status"</code>, <code>"kingdom"</code>, <code>"phylum"</code>, <code>"class"</code>, <code>"order"</code>, <code>"family"</code>, <code>"genus"</code>, <code>"species"</code>, <code>"subspecies"</code>, <code>"rank"</code>, <code>"ref"</code>, <code>"oxygen_tolerance"</code>, <code>"source"</code>, <code>"lpsn"</code>, <code>"lpsn_parent"</code>, <code>"lpsn_renamed_to"</code>, <code>"mycobank"</code>, <code>"mycobank_parent"</code>, <code>"mycobank_renamed_to"</code>, <code>"gbif"</code>, <code>"gbif_parent"</code>, <code>"gbif_renamed_to"</code>, <code>"prevalence"</code>, and <code>"snomed"</code>. Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_interpretive_rules.html">custom_interpretive_rules</a></span><span class="op">(</span></span>
<span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"S"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"S"</span>,</span>
<span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="../reference/interpretive_rules.html">interpretive_rules</a></span><span class="op">(</span><span class="va">df</span>,</span>
<span> rules <span class="op">=</span> <span class="st">"custom"</span>,</span>
<span> custom_rules <span class="op">=</span> <span class="va">y</span>,</span>
<span> info <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="co">#&gt; mo TZP ampi cipro</span></span>
<span><span class="co">#&gt; 1 Escherichia coli R S S</span></span>
<span><span class="co">#&gt; 2 Klebsiella pneumoniae R R S</span></span></code></pre><p></p></div>
</div>
<div class="section">
<h3 id="sharing-rules-among-multiple-users">Sharing rules among multiple users<a class="anchor" aria-label="anchor" href="#sharing-rules-among-multiple-users"></a></h3>
<p>The rules set (the <code>y</code> object in this case) could be exported to a shared file location using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS()</a></code>.</p>
</div>
<div class="section">
<h3 id="usage-of-multiple-antimicrobials-and-antimicrobial-group-names">Usage of multiple antimicrobials and antimicrobial group names<a class="anchor" aria-label="anchor" href="#usage-of-multiple-antimicrobials-and-antimicrobial-group-names"></a></h3>
<p>You can define antimicrobial groups instead of single antimicrobials for the rule consequence, which is the part <em>after</em> the tilde (~). In the examples above, the antimicrobial group <code>aminopenicillins</code> includes both ampicillin and amoxicillin.</p>
<p>Rules can also be applied to multiple antimicrobials and antimicrobial groups simultaneously. Use the <code><a href="https://rdrr.io/r/base/c.html" class="external-link">c()</a></code> function to combine multiple antimicrobials. For instance, the following example sets all aminopenicillins and ureidopenicillins to "R" if column TZP (piperacillin/tazobactam) is "R":</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_interpretive_rules.html">custom_interpretive_rules</a></span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</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="va">aminopenicillins</span>, <span class="va">ureidopenicillins</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span>
<span><span class="va">x</span></span>
<span><span class="co">#&gt; A set of custom interpretive rules:</span></span>
<span><span class="co">#&gt;</span></span>
<span><span class="co">#&gt; 1. If TZP is "R" then set to "R":</span></span>
<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)</span></span></code></pre><p></p></div>
<p>These 43 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminocoumarins<br>(clorobiocin, novobiocin, and penicillin/novobiocin)</p></li>
<li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
<li><p>aminopenicillins<br>(amoxicillin, amoxicillin/clavulanic acid, and ampicillin)</p></li>
<li><p>antifungals<br>(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
<li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>
<li><p>betalactamase_inhibitors<br>(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, avibactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/sulbactam, ceftaroline/avibactam, ceftazidime/avibactam, ceftibuten/avibactam, ceftolozane/tazobactam, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, nacubactam, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, sulbactam, sultamicillin, taniborbactam, tazobactam, ticarcillin/clavulanic acid, xeruborbactam, and zidebactam)</p></li>
<li><p>betalactams<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, taniborbactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)</p></li>
<li><p>betalactams_with_inhibitor<br>(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftibuten/avibactam, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)</p></li>
<li><p>carbapenems<br>(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, taniborbactam, and tebipenem)</p></li>
<li><p>cephalosporins<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>cephalosporins_1st<br>(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine)</p></li>
<li><p>cephalosporins_2nd<br>(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening test, cefprozil, cefuroxime, cefuroxime axetil, and loracarbef)</p></li>
<li><p>cephalosporins_3rd<br>(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef)</p></li>
<li><p>cephalosporins_4th<br>(cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)</p></li>
<li><p>cephalosporins_5th<br>(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam)</p></li>
<li><p>cephalosporins_except_caz<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>fluoroquinolones<br>(besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>fusidanes<br>(fusidic acid)</p></li>
<li><p>glycopeptides<br>(avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod, and zorbamycin)</p></li>
<li><p>glycopeptides_except_lipo<br>(avoparcin, bleomycin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, vancomycin-macromethod, and zorbamycin)</p></li>
<li><p>ionophores<br>(lasalocid, monensin sodium, narasin, nystatin, and salinomycin)</p></li>
<li><p>isoxazolylpenicillins<br>(cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test)</p></li>
<li><p>lincosamides<br>(clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin)</p></li>
<li><p>lipoglycopeptides<br>(dalbavancin, oritavancin, and telavancin)</p></li>
<li><p>macrolides<br>(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, clindamycin inducible screening test, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin)</p></li>
<li><p>monobactams<br>(aztreonam, aztreonam/avibactam, aztreonam/nacubactam, carumonam, and tigemonam)</p></li>
<li><p>nitrofurans<br>(furazidin, furazolidone, nifurtoinol, nitrofurantoin, and nitrofurazone)</p></li>
<li><p>oxazolidinones<br>(cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone)</p></li>
<li><p>penicillins<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic acid)</p></li>
<li><p>peptides<br>(avoparcin, bacitracin, bleomycin, dalbavancin, daptomycin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, thiostrepton, vancomycin, vancomycin-macromethod, and zorbamycin)</p></li>
<li><p>phenicols<br>(chloramphenicol, florfenicol, and thiamphenicol)</p></li>
<li><p>phosphonics<br>(amikacin/fosfomycin and fosfomycin)</p></li>
<li><p>pleuromutilins<br>(retapamulin and tiamulin)</p></li>
<li><p>polymyxins<br>(colistin, polymyxin B, and polymyxin B/polysorbate 80)</p></li>
<li><p>quinolones<br>(besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, ozenoxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>rifamycins<br>(rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine)</p></li>
<li><p>spiropyrimidinetriones<br>(zoliflodacin)</p></li>
<li><p>streptogramins<br>(ostreogrycin, pristinamycin, quinupristin/dalfopristin, and virginiamycine)</p></li>
<li><p>sulfonamides<br>(isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea, sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole)</p></li>
<li><p>tetracyclines<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, tetracycline/oleandomycin, and tigecycline)</p></li>
<li><p>tetracyclines_except_tgc<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tetracycline/oleandomycin)</p></li>
<li><p>trimethoprims<br>(brodimoprim, iclaprim, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole)</p></li>
<li><p>ureidopenicillins<br>(azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam)</p></li>
</ul></div>
</div>
<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">x</span> <span class="op">&lt;-</span> <span class="fu">custom_interpretive_rules</span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="va">AMC</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span>,</span></span>
<span class="r-in"><span> <span class="va">AMC</span> <span class="op">==</span> <span class="st">"I"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"I"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> A set of custom interpretive rules:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #BBBBBB;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FF5F5F;"> R </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">amoxicillin/clavulanic acid</span> (AMC), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FFD787;"> I </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #BBBBBB;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FFD787;"> I </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">amoxicillin/clavulanic acid</span> (AMC), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># run the custom rule set (verbose = TRUE will return a logbook instead of the data set):</span></span></span>
<span class="r-in"><span><span class="fu"><a href="interpretive_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> rules <span class="op">=</span> <span class="st">"custom"</span>,</span></span>
<span class="r-in"><span> custom_rules <span class="op">=</span> <span class="va">x</span>,</span></span>
<span class="r-in"><span> info <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
<span class="r-in"><span> overwrite <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
<span class="r-in"><span> verbose <span class="op">=</span> <span class="cn">TRUE</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 8 × 9</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> row col mo_fullname old new rule rule_group rule_name rule_source</span>
<span class="r-out co"><span class="r-pr">#&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;ord&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> 33 AMP Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom in… Custom i… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 33 AMX Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom in… Custom i… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 34 AMP Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom in… Custom i… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 34 AMX Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom in… Custom i… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> 531 AMP Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom in… Custom i… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> 531 AMX Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom in… Custom i… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">7</span> <span style="text-decoration: underline;">1</span>485 AMP Klebsiella oxy… R I <span style="color: #949494;">"</span>rep… Custom in… Custom i… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">8</span> <span style="text-decoration: underline;">1</span>485 AMX Klebsiella oxy… R I <span style="color: #949494;">"</span>rep… Custom in… Custom i… Object 'x'…</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># combine rule sets</span></span></span>
<span class="r-in"><span><span class="va">x2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="va">x</span>,</span></span>
<span class="r-in"><span> <span class="fu">custom_interpretive_rules</span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="va">carbapenems</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x2</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> A set of custom interpretive rules:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #BBBBBB;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FF5F5F;"> R </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">amoxicillin/clavulanic acid</span> (AMC), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FFD787;"> I </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #BBBBBB;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FFD787;"> I </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">amoxicillin/clavulanic acid</span> (AMC), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">TZP</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FF5F5F;"> R </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">biapenem</span> (BIA), <span style="color: #0000BB;">doripenem</span> (DOR), <span style="color: #0000BB;">ertapenem</span> (ETP), <span style="color: #0000BB;">imipenem</span> (IPM), <span style="color: #0000BB;">imipenem/EDTA</span> (IPE), <span style="color: #0000BB;">imipenem/relebactam</span> (IMR), <span style="color: #0000BB;">meropenem</span> (MEM), <span style="color: #0000BB;">meropenem/nacubactam</span> (MNC), <span style="color: #0000BB;">meropenem/vaborbactam</span> (MEV), <span style="color: #0000BB;">panipenem</span> (PAN), <span style="color: #0000BB;">razupenem</span> (RZM), <span style="color: #0000BB;">ritipenem</span> (RIT), <span style="color: #0000BB;">ritipenem acoxil</span> (RIA), <span style="color: #0000BB;">taniborbactam</span> (TAN), <span style="color: #0000BB;">tebipenem</span> (TBP)</span>
</code></pre></div>
</div>
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64
reference/custom_eucast_rules.md → reference/custom_interpretive_rules.md
View File

@@ -1,13 +1,13 @@
# Define Custom EUCAST Rules
# Define Custom Interpretive Rules
Define custom EUCAST rules for your organisation or specific analysis
and use the output of this function in
[`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md).
Define custom interpretive rules for your organisation or specific
analysis and use the output of this function in
[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md).
## Usage
``` r
custom_eucast_rules(...)
custom_interpretive_rules(...)
```
## Arguments
@@ -23,9 +23,9 @@ A [list](https://rdrr.io/r/base/list.html) containing the custom rules
## Details
Some organisations have their own adoption of EUCAST rules. This
function can be used to define custom EUCAST rules to be used in the
[`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
Some organisations have their own adoption of interpretive rules. This
function can be used to define custom rules to be used in the
[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
function.
### Basics
@@ -37,17 +37,17 @@ set your own rules. Rules must be set using what R considers to be the
'formula notation'. The rule itself is written *before* the tilde (`~`)
and the consequence of the rule is written *after* the tilde:
x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S",
x <- custom_interpretive_rules(TZP == "S" ~ aminopenicillins == "S",
TZP == "R" ~ aminopenicillins == "R")
These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is
"S", all aminopenicillins (ampicillin and amoxicillin) must be made "S",
and if TZP is "R", aminopenicillins must be made "R". These rules can
also be printed to the console, so it is immediately clear how they
work:
These are two custom interpretive rules: if TZP
(piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and
amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must
be made "R". These rules can also be printed to the console, so it is
immediately clear how they work:
x
#> A set of custom EUCAST rules:
#> A set of custom interpretive rules:
#>
#> 1. If TZP is "S" then set to S :
#> amoxicillin (AMX), ampicillin (AMP)
@@ -70,7 +70,7 @@ data set and test the rules set:
#> 1 Escherichia coli R S S
#> 2 Klebsiella pneumoniae R S S
eucast_rules(df,
interpretive_rules(df,
rules = "custom",
custom_rules = x,
info = FALSE,
@@ -94,12 +94,12 @@ column names are: `"mo"`, `"fullname"`, `"status"`, `"kingdom"`,
example will work as well, despite the fact that the `df` data set does
not contain a column `genus`:
y <- custom_eucast_rules(
y <- custom_interpretive_rules(
TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R"
)
eucast_rules(df,
interpretive_rules(df,
rules = "custom",
custom_rules = y,
info = FALSE,
@@ -129,9 +129,9 @@ function to combine multiple antimicrobials. For instance, the following
example sets all aminopenicillins and ureidopenicillins to "R" if column
TZP (piperacillin/tazobactam) is "R":
x <- custom_eucast_rules(TZP == "R" ~ c(aminopenicillins, ureidopenicillins) == "R")
x <- custom_interpretive_rules(TZP == "R" ~ c(aminopenicillins, ureidopenicillins) == "R")
x
#> A set of custom EUCAST rules:
#> A set of custom interpretive rules:
#>
#> 1. If TZP is "R" then set to "R":
#> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
@@ -499,12 +499,12 @@ These 43 antimicrobial groups are allowed in the rules
## Examples
``` r
x <- custom_eucast_rules(
x <- custom_interpretive_rules(
AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I"
)
x
#> A set of custom EUCAST rules:
#> A set of custom interpretive rules:
#>
#> 1. If AMC is R and genus is "Klebsiella" then set to R :
#> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), ampicillin (AMP)
@@ -523,22 +523,22 @@ eucast_rules(example_isolates,
#> # A tibble: 8 × 9
#> row col mo_fullname old new rule rule_group rule_name rule_source
#> <int> <chr> <chr> <ord> <chr> <chr> <chr> <chr> <chr>
#> 1 33 AMP Klebsiella pne… R I "rep… Custom EU… Custom E… Object 'x'…
#> 2 33 AMX Klebsiella pne… R I "rep… Custom EU… Custom E… Object 'x'…
#> 3 34 AMP Klebsiella pne… R I "rep… Custom EU… Custom E… Object 'x'…
#> 4 34 AMX Klebsiella pne… R I "rep… Custom EU… Custom E… Object 'x'…
#> 5 531 AMP Klebsiella pne… R I "rep… Custom EU… Custom E… Object 'x'…
#> 6 531 AMX Klebsiella pne… R I "rep… Custom EU… Custom E… Object 'x'…
#> 7 1485 AMP Klebsiella oxy… R I "rep… Custom EU… Custom E… Object 'x'…
#> 8 1485 AMX Klebsiella oxy… R I "rep… Custom EU… Custom E… Object 'x'…
#> 1 33 AMP Klebsiella pne… R I "rep… Custom in… Custom i… Object 'x'…
#> 2 33 AMX Klebsiella pne… R I "rep… Custom in… Custom i… Object 'x'…
#> 3 34 AMP Klebsiella pne… R I "rep… Custom in… Custom i… Object 'x'…
#> 4 34 AMX Klebsiella pne… R I "rep… Custom in… Custom i… Object 'x'…
#> 5 531 AMP Klebsiella pne… R I "rep… Custom in… Custom i… Object 'x'…
#> 6 531 AMX Klebsiella pne… R I "rep… Custom in… Custom i… Object 'x'…
#> 7 1485 AMP Klebsiella oxy… R I "rep… Custom in… Custom i… Object 'x'…
#> 8 1485 AMX Klebsiella oxy… R I "rep… Custom in… Custom i… Object 'x'…
# combine rule sets
x2 <- c(
x,
custom_eucast_rules(TZP == "R" ~ carbapenems == "R")
custom_interpretive_rules(TZP == "R" ~ carbapenems == "R")
)
x2
#> A set of custom EUCAST rules:
#> A set of custom interpretive rules:
#>
#> 1. If AMC is R and genus is "Klebsiella" then set to R :
#> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), ampicillin (AMP)

4
reference/custom_mdro_guideline.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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 @@
<dt id="arg-as-factor">as_factor<a class="anchor" aria-label="anchor" href="#arg-as-factor"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the returned value should be an ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> (<code>TRUE</code>, default), or otherwise a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector. For combining rules sets (using <code><a href="https://rdrr.io/r/base/c.html" class="external-link">c()</a></code>) this value will be inherited from the first set at default.</p></dd>
<dd><p>A [logical] to indicate whether the returned value should be an ordered [factor] (`TRUE`, default), or otherwise a [character] vector. For combining rules sets (using [c()]) this value will be inherited from the first set at default.</p></dd>
<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>

11
reference/custom_mdro_guideline.md
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@@ -22,13 +22,10 @@ c(x, ..., as_factor = NULL)
- as_factor:
A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
the returned value should be an ordered
[factor](https://rdrr.io/pkg/data.table/man/fctr.html) (`TRUE`,
default), or otherwise a
[character](https://rdrr.io/r/base/character.html) vector. For
combining rules sets (using [`c()`](https://rdrr.io/r/base/c.html))
this value will be inherited from the first set at default.
A \[logical\] to indicate whether the returned value should be an
ordered \[factor\] (\`TRUE\`, default), or otherwise a \[character\]
vector. For combining rules sets (using \[c()\]) this value will be
inherited from the first set at default.
- x:

2
reference/dosage.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/esbl_isolates.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/example_isolates.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/example_isolates_unclean.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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2
reference/export_ncbi_biosample.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/first_isolate.html
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@@ -9,7 +9,7 @@
<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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">

7
reference/g.test.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">
@@ -124,8 +124,9 @@
<dt>stdres</dt>
<dd><p>standardized residuals,
<code>(observed - expected) / sqrt(V)</code>, where <code>V</code> is the residual cell variance (Agresti, 2007,
section 2.4.5 for the case where <code>x</code> is a matrix, <code>n * p * (1 - p)</code> otherwise).</p></dd>
<code>(observed - expected) / sqrt(V)</code>, where <code>V</code> is the
residual cell variance (<a href="#reference+chisq.test.Rd+R+3AAgresti+3A2007" class="citation">Agresti 2007</a>, section 2.4.5)
for the case where <code>x</code> is a matrix, <code>n * p * (1 - p)</code> otherwise).</p></dd>
</dl></div>
<div class="section level2">

5
reference/g.test.md
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@@ -93,8 +93,9 @@ A list with class `"htest"` containing the following components:
- stdres:
standardized residuals, `(observed - expected) / sqrt(V)`, where `V`
is the residual cell variance (Agresti, 2007, section 2.4.5 for the
case where `x` is a matrix, `n * p * (1 - p)` otherwise).
is the residual cell variance ([Agresti
2007](#reference+chisq.test.Rd+R+3AAgresti+3A2007), section 2.4.5) for
the case where `x` is a matrix, `n * p * (1 - p)` otherwise).
## Details

2
reference/get_episode.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">

7
reference/ggplot_pca.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">
@@ -96,8 +96,9 @@
<dt id="arg-pc-biplot">pc.biplot<a class="anchor" aria-label="anchor" href="#arg-pc-biplot"></a></dt>
<dd><p>If true, use what Gabriel (1971) refers to as a "principal component
biplot", with <code>lambda = 1</code> and observations scaled up by sqrt(n) and
<dd><p>If true, use what <cite></cite><a href="#reference+biplot.princomp.Rd+R+3AGabriel+3A1971" class="citation">Gabriel (1971)</a> refers to as a
“principal component biplot”,
with <code>lambda = 1</code> and observations scaled up by sqrt(n) and
variables scaled down by sqrt(n). Then inner products between
variables approximate covariances and distances between observations
approximate Mahalanobis distance.</p></dd>

11
reference/ggplot_pca.md
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@@ -68,11 +68,12 @@ the changes made based on the source code were:
- pc.biplot:
If true, use what Gabriel (1971) refers to as a "principal component
biplot", with `lambda = 1` and observations scaled up by sqrt(n) and
variables scaled down by sqrt(n). Then inner products between
variables approximate covariances and distances between observations
approximate Mahalanobis distance.
If true, use what [Gabriel
(1971)](#reference+biplot.princomp.Rd+R+3AGabriel+3A1971) refers to as
a “principal component biplot”, with `lambda = 1` and observations
scaled up by sqrt(n) and variables scaled down by sqrt(n). Then inner
products between variables approximate covariances and distances
between observations approximate Mahalanobis distance.
- labels:

2
reference/ggplot_sir.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/guess_ab_col.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/index.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">
@@ -145,9 +145,9 @@
</dt>
<dd>Add Custom Antimicrobials</dd>
</dl></div><div class="section level2">
<h2 id="preparing-data-antimicrobial-results">Preparing data: antimicrobial results<a class="anchor" aria-label="anchor" href="#preparing-data-antimicrobial-results"></a></h2>
<h2 id="interpreting-data-antimicrobial-results">Interpreting data: antimicrobial results<a class="anchor" aria-label="anchor" href="#interpreting-data-antimicrobial-results"></a></h2>
<div class="section-desc"><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.sir.html">as.sir()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as SIR based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/interpretive_rules.html">eucast_rules()</a></code>.</p></div>
<div class="section-desc"><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.sir.html">as.sir()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as SIR based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying interpretive rules, for example <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">from EUCAST</a> with <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>.</p></div>
<dl></dl></div><div class="section level2">
@@ -184,10 +184,10 @@
<dt>
<code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>
<code><a href="custom_interpretive_rules.html">custom_interpretive_rules()</a></code>
</dt>
<dd>Define Custom EUCAST Rules</dd>
<dd>Define Custom Interpretive Rules</dd>
</dl></div><div class="section level2">
<h2 id="analysing-data">Analysing data<a class="anchor" aria-label="anchor" href="#analysing-data"></a></h2>
@@ -560,7 +560,7 @@
</dl></div><div class="section level2">
<h2 id="other-statistical-tests">Other: statistical tests<a class="anchor" aria-label="anchor" href="#other-statistical-tests"></a></h2>
<div class="section-desc"><p>Some statistical tests or methods are not part of base R and were added to this package for convenience.</p></div>
<div class="section-desc"><p>Some statistical tests or methods usable for AMR analyses are not part of base R and were added to this package for convenience.</p></div>
<dl></dl></div><div class="section level2">
@@ -599,7 +599,7 @@
<dl><dt>
<code><a href="AMR-deprecated.html">ab_class()</a></code> <code><a href="AMR-deprecated.html">ab_selector()</a></code>
<code><a href="AMR-deprecated.html">custom_eucast_rules()</a></code> <code><a href="AMR-deprecated.html">ab_class()</a></code> <code><a href="AMR-deprecated.html">ab_selector()</a></code>
</dt>
<dd>Deprecated Functions, Arguments, or Datasets</dd>

19
reference/index.md
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@@ -116,7 +116,7 @@ from clinical text records, using
[`clear_custom_antimicrobials()`](https://amr-for-r.org/reference/add_custom_antimicrobials.md)
: Add Custom Antimicrobials
## Preparing data: antimicrobial results
## Interpreting data: antimicrobial results
With [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) and
[`as.disk()`](https://amr-for-r.org/reference/as.disk.md) you can
@@ -125,10 +125,10 @@ transform your raw input to valid MIC or disk diffusion values. Use
data to let it only contain “R”, “I” and “S”, or to interpret MIC or
disk diffusion values as SIR based on the lastest EUCAST and CLSI
guidelines. Afterwards, you can extend antibiotic interpretations by
applying [EUCAST
rules](https://www.eucast.org/expert_rules_and_intrinsic_resistance/)
applying interpretive rules, for example [from
EUCAST](https://www.eucast.org/expert_rules_and_intrinsic_resistance/)
with
[`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md).
[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md).
- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
[`NA_sir_`](https://amr-for-r.org/reference/as.sir.md)
@@ -153,8 +153,8 @@ with
[`clsi_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
[`eucast_dosage()`](https://amr-for-r.org/reference/interpretive_rules.md)
: Apply Interpretive Rules
- [`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md)
: Define Custom EUCAST Rules
- [`custom_interpretive_rules()`](https://amr-for-r.org/reference/custom_interpretive_rules.md)
: Define Custom Interpretive Rules
## Analysing data
@@ -465,8 +465,8 @@ and other utilities. Especially the ‘like’ function can be useful:
## Other: statistical tests
Some statistical tests or methods are not part of base R and were added
to this package for convenience.
Some statistical tests or methods usable for AMR analyses are not part
of base R and were added to this package for convenience.
- [`g.test()`](https://amr-for-r.org/reference/g.test.md) :
@@ -483,6 +483,7 @@ to this package for convenience.
These objects are deprecated, meaning that they will still work but show
a warning that they will be removed in a future version.
- [`ab_class()`](https://amr-for-r.org/reference/AMR-deprecated.md)
- [`custom_eucast_rules()`](https://amr-for-r.org/reference/AMR-deprecated.md)
[`ab_class()`](https://amr-for-r.org/reference/AMR-deprecated.md)
[`ab_selector()`](https://amr-for-r.org/reference/AMR-deprecated.md) :
Deprecated Functions, Arguments, or Datasets

24
reference/interpretive_rules.html
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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
<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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">
@@ -107,7 +107,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt id="arg-rules">rules<a class="anchor" aria-label="anchor" href="#arg-rules"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expected_phenotypes"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expected_phenotypes")</code>. The default value can be set to another value using the package option <code><a href="AMR-options.html">AMR_interpretive_rules</a></code>: <code>options(AMR_interpretive_rules = "all")</code>. If using <code>"custom"</code>, be sure to fill in argument <code>custom_rules</code> too. Custom rules can be created with <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>.</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expected_phenotypes"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expected_phenotypes")</code>. The default value can be set to another value using the package option <code><a href="AMR-options.html">AMR_interpretive_rules</a></code>: <code>options(AMR_interpretive_rules = "all")</code>. If using <code>"custom"</code>, be sure to fill in argument <code>custom_rules</code> too. Custom rules can be created with <code><a href="custom_interpretive_rules.html">custom_interpretive_rules()</a></code>.</p></dd>
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
@@ -139,7 +139,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt id="arg-custom-rules">custom_rules<a class="anchor" aria-label="anchor" href="#arg-custom-rules"></a></dt>
<dd><p>Custom rules to apply, created with <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>.</p></dd>
<dd><p>Custom rules to apply, created with <code><a href="custom_interpretive_rules.html">custom_interpretive_rules()</a></code>.</p></dd>
<dt id="arg-overwrite">overwrite<a class="anchor" aria-label="anchor" href="#arg-overwrite"></a></dt>
@@ -169,15 +169,15 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p><strong>Note:</strong> This function does not translate MIC or disk values to SIR values. Use <code><a href="as.sir.html">as.sir()</a></code> for that. <br><strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br></p>
<p>The file containing all EUCAST rules is located here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The <code>AMR</code> package contains the full microbial taxonomy updated until June 24th, 2024, see <a href="microorganisms.html">microorganisms</a>.</p><div class="section">
<p>The file containing all interpretive rules is located here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The <code>AMR</code> package contains the full microbial taxonomy updated until June 24th, 2024, see <a href="microorganisms.html">microorganisms</a>.</p><div class="section">
<h3 id="custom-rules">Custom Rules<a class="anchor" aria-label="anchor" href="#custom-rules"></a></h3>
<p>Custom rules can be created using <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>, e.g.:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">AMC</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span>,</span>
<p>Custom rules can be created using <code><a href="custom_interpretive_rules.html">custom_interpretive_rules()</a></code>, e.g.:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_interpretive_rules.html">custom_interpretive_rules</a></span><span class="op">(</span><span class="va">AMC</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span>,</span>
<span> <span class="va">AMC</span> <span class="op">==</span> <span class="st">"I"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"I"</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="../reference/interpretive_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">example_isolates</span>, rules <span class="op">=</span> <span class="st">"custom"</span>, custom_rules <span class="op">=</span> <span class="va">x</span><span class="op">)</span></span></code></pre><p></p></div>
<span><span class="fu"><a href="../reference/interpretive_rules.html">interpretive_rules</a></span><span class="op">(</span><span class="va">example_isolates</span>, rules <span class="op">=</span> <span class="st">"custom"</span>, custom_rules <span class="op">=</span> <span class="va">x</span><span class="op">)</span></span></code></pre><p></p></div>
</div>
<div class="section">
@@ -187,7 +187,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol><li><p>A drug <strong>with</strong> enzyme inhibitor will be set to S if the same drug <strong>without</strong> enzyme inhibitor is S</p></li>
<li><p>A drug <strong>without</strong> enzyme inhibitor will be set to R if the same drug <strong>with</strong> enzyme inhibitor is R</p></li>
</ol><p>Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.</p>
<p>Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include <code>"other"</code> to the <code>rules</code> argument, or use <code>eucast_rules(..., rules = "all")</code>. You can also set the package option <code><a href="AMR-options.html">AMR_interpretive_rules</a></code>, i.e. run <code>options(AMR_interpretive_rules = "all")</code>.</p>
<p>Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include <code>"other"</code> to the <code>rules</code> argument, or use <code>interpretive_rules(..., rules = "all")</code>. You can also set the package option <code><a href="AMR-options.html">AMR_interpretive_rules</a></code>, i.e. run <code>options(AMR_interpretive_rules = "all")</code>.</p>
</div>
</div>
@@ -232,8 +232,8 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># apply EUCAST rules: some results wil be changed</span></span></span>
<span class="r-in"><span><span class="va">b</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of class</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `interpretive_rules()`: not all columns with antimicrobial results are of</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> class <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> </span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> • x <span style="color: #D7AF00;">|&gt;</span> <span style="font-weight: bold;">as.sir</span><span style="color: #D7AF00;">(</span>CXM<span style="color: #D7AF00;">:</span>AMX<span style="color: #D7AF00;">)</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> </span>
@@ -253,8 +253,8 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span><span class="co"># do not apply EUCAST rules, but rather get a data.frame</span></span></span>
<span class="r-in"><span><span class="co"># containing all details about the transformations:</span></span></span>
<span class="r-in"><span><span class="va">c</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of class</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `interpretive_rules()`: not all columns with antimicrobial results are of</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> class <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> </span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> • x <span style="color: #D7AF00;">|&gt;</span> <span style="font-weight: bold;">as.sir</span><span style="color: #D7AF00;">(</span>CXM<span style="color: #D7AF00;">:</span>AMX<span style="color: #D7AF00;">)</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> </span>

26
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@@ -100,7 +100,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
`options(AMR_interpretive_rules = "all")`. If using `"custom"`, be
sure to fill in argument `custom_rules` too. Custom rules can be
created with
[`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md).
[`custom_interpretive_rules()`](https://amr-for-r.org/reference/custom_interpretive_rules.md).
- guideline:
@@ -166,7 +166,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
- custom_rules:
Custom rules to apply, created with
[`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md).
[`custom_interpretive_rules()`](https://amr-for-r.org/reference/custom_interpretive_rules.md).
- overwrite:
@@ -226,8 +226,8 @@ where there is a dependency on ampicillin. These drugs are
interchangeable when it comes to expression of antimicrobial
resistance.
The file containing all EUCAST rules is located here:
<https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv>.
The file containing all interpretive rules is located here:
<https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv>.
**Note:** Old taxonomic names are replaced with the current taxonomy
where applicable. For example, *Ochrobactrum anthropi* was renamed to
*Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did
@@ -238,13 +238,13 @@ full microbial taxonomy updated until June 24th, 2024, see
### Custom Rules
Custom rules can be created using
[`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md),
[`custom_interpretive_rules()`](https://amr-for-r.org/reference/custom_interpretive_rules.md),
e.g.:
x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
x <- custom_interpretive_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
eucast_rules(example_isolates, rules = "custom", custom_rules = x)
interpretive_rules(example_isolates, rules = "custom", custom_rules = x)
### 'Other' Rules
@@ -264,8 +264,8 @@ these rules to work, both drugs must be available in the data set.
Since these rules are not officially approved by EUCAST, they are not
applied at default. To use these rules, include `"other"` to the `rules`
argument, or use `eucast_rules(..., rules = "all")`. You can also set
the package option
argument, or use `interpretive_rules(..., rules = "all")`. You can also
set the package option
[`AMR_interpretive_rules`](https://amr-for-r.org/reference/AMR-options.md),
i.e. run `options(AMR_interpretive_rules = "all")`.
@@ -318,8 +318,8 @@ head(a)
# apply EUCAST rules: some results wil be changed
b <- eucast_rules(a, overwrite = TRUE)
#> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of class
#> <sir>. Transform them on beforehand, e.g.:
#> Warning: in `interpretive_rules()`: not all columns with antimicrobial results are of
#> class <sir>. Transform them on beforehand, e.g.:
#>
#> • x |> as.sir(CXM:AMX)
#>
@@ -339,8 +339,8 @@ head(b)
# do not apply EUCAST rules, but rather get a data.frame
# containing all details about the transformations:
c <- eucast_rules(a, overwrite = TRUE, verbose = TRUE)
#> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of class
#> <sir>. Transform them on beforehand, e.g.:
#> Warning: in `interpretive_rules()`: not all columns with antimicrobial results are of
#> class <sir>. Transform them on beforehand, e.g.:
#>
#> • x |> as.sir(CXM:AMX)
#>

2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">

6
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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">
@@ -94,8 +94,8 @@
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p><strong>Note:</strong> As opposed to the <code>join()</code> functions of <code>dplyr</code>, <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vectors are supported and at default existing columns will get a suffix <code>"2"</code> and the newly joined columns will not get a suffix.</p>
<p>If the <code>dplyr</code> package is installed, their join functions will be used. Otherwise, the much slower <code><a href="https://rdrr.io/pkg/data.table/man/merge.html" class="external-link">merge()</a></code> and <code><a href="https://rdrr.io/r/base/interaction.html" class="external-link">interaction()</a></code> functions from base <span style="R">R</span> will be used.</p>
<p>**Note:** As opposed to the `join()` functions of `dplyr`, [character] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix.</p>
<p>If the `dplyr` package is installed, their join functions will be used. Otherwise, the much slower [merge()] and [interaction()] functions from base <span style="R">R</span> will be used.</p>
</div>
<div class="section level2">

15
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@@ -59,16 +59,13 @@ a [data.frame](https://rdrr.io/r/base/data.frame.html)
## Details
**Note:** As opposed to the `join()` functions of `dplyr`,
[character](https://rdrr.io/r/base/character.html) vectors are supported
and at default existing columns will get a suffix `"2"` and the newly
joined columns will not get a suffix.
\*\*Note:\*\* As opposed to the \`join()\` functions of \`dplyr\`,
\[character\] vectors are supported and at default existing columns will
get a suffix \`"2"\` and the newly joined columns will not get a suffix.
If the `dplyr` package is installed, their join functions will be used.
Otherwise, the much slower
[`merge()`](https://rdrr.io/pkg/data.table/man/merge.html) and
[`interaction()`](https://rdrr.io/r/base/interaction.html) functions
from base R will be used.
If the \`dplyr\` package is installed, their join functions will be
used. Otherwise, the much slower \[merge()\] and \[interaction()\]
functions from base R will be used.
## Examples

2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/kurtosis.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/like.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">

25
reference/mdro.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">
@@ -144,18 +144,17 @@
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<ul><li><p>If <code>verbose</code> is set to <code>TRUE</code>:<br>
A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns <code>row_number</code>, <code>microorganism</code>, <code>MDRO</code>, <code>reason</code>, <code>all_nonsusceptible_columns</code>, <code>guideline</code></p></li>
<li><p>CMI 2012 paper - function <code>mdr_cmi2012()</code> or <code>mdro()</code>:<br>
Ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> with levels <code>Negative</code> &lt; <code>Multi-drug-resistant (MDR)</code> &lt; <code>Extensively drug-resistant (XDR)</code> &lt; <code>Pandrug-resistant (PDR)</code></p></li>
<li><p>TB guideline - function <code>mdr_tb()</code> or <code>mdro(..., guideline = "TB")</code>:<br>
Ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> with levels <code>Negative</code> &lt; <code>Mono-resistant</code> &lt; <code>Poly-resistant</code> &lt; <code>Multi-drug-resistant</code> &lt; <code>Extensively drug-resistant</code></p></li>
<li><p>German guideline - function <code>mrgn()</code> or <code>mdro(..., guideline = "MRGN")</code>:<br>
Ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> with levels <code>Negative</code> &lt; <code>3MRGN</code> &lt; <code>4MRGN</code></p></li>
<li><p>Everything else, except for custom guidelines:<br>
Ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> with levels <code>Negative</code> &lt; <code>Positive, unconfirmed</code> &lt; <code>Positive</code>. The value <code>"Positive, unconfirmed"</code> means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. genotypic) tests</p></li>
</ul></div>
<p>- If `verbose` is set to `TRUE`:<br>
A [data.frame] containing columns `row_number`, `microorganism`, `MDRO`, `reason`, `all_nonsusceptible_columns`, `guideline`
- CMI 2012 paper - function [mdr_cmi2012()] or [mdro()]:<br>
Ordered [factor] with levels `Negative` &lt; `Multi-drug-resistant (MDR)` &lt; `Extensively drug-resistant (XDR)` &lt; `Pandrug-resistant (PDR)`
- TB guideline - function [mdr_tb()] or [`mdro(..., guideline = "TB")`][mdro()]:<br>
Ordered [factor] with levels `Negative` &lt; `Mono-resistant` &lt; `Poly-resistant` &lt; `Multi-drug-resistant` &lt; `Extensively drug-resistant`
- German guideline - function [mrgn()] or [`mdro(..., guideline = "MRGN")`][mdro()]:<br>
Ordered [factor] with levels `Negative` &lt; `3MRGN` &lt; `4MRGN`
- Everything else, except for custom guidelines:<br>
Ordered [factor] with levels `Negative` &lt; `Positive, unconfirmed` &lt; `Positive`. The value `"Positive, unconfirmed"` means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. genotypic) tests</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>These functions are context-aware. This means that the <code>x</code> argument can be left blank if used inside a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> call, see <em>Examples</em>.</p>

45
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@@ -152,32 +152,25 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
## Value
- If `verbose` is set to `TRUE`:
A [data.frame](https://rdrr.io/r/base/data.frame.html) containing
columns `row_number`, `microorganism`, `MDRO`, `reason`,
`all_nonsusceptible_columns`, `guideline`
- CMI 2012 paper - function `mdr_cmi2012()` or `mdro()`:
Ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with
levels `Negative` \< `Multi-drug-resistant (MDR)` \<
`Extensively drug-resistant (XDR)` \< `Pandrug-resistant (PDR)`
- TB guideline - function `mdr_tb()` or `mdro(..., guideline = "TB")`:
Ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with
levels `Negative` \< `Mono-resistant` \< `Poly-resistant` \<
`Multi-drug-resistant` \< `Extensively drug-resistant`
- German guideline - function `mrgn()` or
`mdro(..., guideline = "MRGN")`:
Ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with
levels `Negative` \< `3MRGN` \< `4MRGN`
- Everything else, except for custom guidelines:
Ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with
levels `Negative` \< `Positive, unconfirmed` \< `Positive`. The value
`"Positive, unconfirmed"` means that, according to the guideline, it
is not entirely sure if the isolate is multi-drug resistant and this
should be confirmed with additional (e.g. genotypic) tests
\- If \`verbose\` is set to \`TRUE\`:
A \[data.frame\] containing columns \`row_number\`, \`microorganism\`,
\`MDRO\`, \`reason\`, \`all_nonsusceptible_columns\`, \`guideline\` -
CMI 2012 paper - function \[mdr_cmi2012()\] or \[mdro()\]:
Ordered \[factor\] with levels \`Negative\` \< \`Multi-drug-resistant
(MDR)\` \< \`Extensively drug-resistant (XDR)\` \< \`Pandrug-resistant
(PDR)\` - TB guideline - function \[mdr_tb()\] or \[\`mdro(...,
guideline = "TB")\`\]\[mdro()\]:
Ordered \[factor\] with levels \`Negative\` \< \`Mono-resistant\` \<
\`Poly-resistant\` \< \`Multi-drug-resistant\` \< \`Extensively
drug-resistant\` - German guideline - function \[mrgn()\] or
\[\`mdro(..., guideline = "MRGN")\`\]\[mdro()\]:
Ordered \[factor\] with levels \`Negative\` \< \`3MRGN\` \< \`4MRGN\` -
Everything else, except for custom guidelines:
Ordered \[factor\] with levels \`Negative\` \< \`Positive, unconfirmed\`
\< \`Positive\`. The value \`"Positive, unconfirmed"\` means that,
according to the guideline, it is not entirely sure if the isolate is
multi-drug resistant and this should be confirmed with additional (e.g.
genotypic) tests
## Details

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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">

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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">

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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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">
@@ -201,32 +201,32 @@
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<ul><li><p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> in case of <code>mo_year()</code></p></li>
<li><p>An <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">ordered factor</a> in case of <code>mo_pathogenicity()</code></p></li>
<li><p>A <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a> in case of <code>mo_taxonomy()</code>, <code>mo_synonyms()</code>, <code>mo_snomed()</code>, and <code>mo_info()</code></p></li>
<li><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> in case of <code>mo_is_anaerobic()</code>, <code>mo_is_gram_negative()</code>, <code>mo_is_gram_positive()</code>, <code>mo_is_intrinsic_resistant()</code>, and <code>mo_is_yeast()</code></p></li>
<li><p>A named <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> in case of <code>mo_synonyms()</code> and <code>mo_url()</code></p></li>
<li><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> in all other cases</p></li>
</ul></div>
<p>- An [integer] in case of [mo_year()]
- An [ordered factor][factor] in case of [mo_pathogenicity()]
- A [list] in case of [mo_taxonomy()], [mo_synonyms()], [mo_snomed()], and [mo_info()]
- A [logical] in case of [mo_is_anaerobic()], [mo_is_gram_negative()], [mo_is_gram_positive()], [mo_is_intrinsic_resistant()], and [mo_is_yeast()]
- A named [character] in case of [mo_synonyms()] and [mo_url()]
- A [character] in all other cases</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>All functions will, at default, <strong>not</strong> keep old taxonomic properties, as synonyms are automatically replaced with the current taxonomy. Take for example <em>Enterobacter aerogenes</em>, which was initially named in 1960 but renamed to <em>Klebsiella aerogenes</em> in 2017:</p><ul><li><p><code>mo_genus("Enterobacter aerogenes")</code> will return <code>"Klebsiella"</code> (with a note about the renaming)</p></li>
<li><p><code>mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)</code> will return <code>"Enterobacter"</code> (with a once-per-session warning that the name is outdated)</p></li>
<li><p><code>mo_ref("Enterobacter aerogenes")</code> will return <code>"Tindall et al., 2017"</code> (with a note about the renaming)</p></li>
<li><p><code>mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)</code> will return <code>"Hormaeche et al., 1960"</code> (with a once-per-session warning that the name is outdated)</p></li>
</ul><p>The short name (<code>mo_shortname()</code>) returns the first character of the genus and the full species, such as <code>"E. coli"</code>, for species and subspecies. Exceptions are abbreviations of staphylococci (such as <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as <em>"GBS"</em>, Group B Streptococci). Please bear in mind that e.g. <em>E. coli</em> could mean <em>Escherichia coli</em> (kingdom of Bacteria) as well as <em>Entamoeba coli</em> (kingdom of Protozoa). Returning to the full name will be done using <code><a href="as.mo.html">as.mo()</a></code> internally, giving priority to bacteria and human pathogens, i.e. <code>"E. coli"</code> will be considered <em>Escherichia coli</em>. As a result, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
<p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions <code>mo_kingdom()</code> and <code>mo_domain()</code> return the exact same results.</p>
<p>Determination of human pathogenicity (<code>mo_pathogenicity()</code>) is strongly based on Bartlett <em>et al.</em> (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
). This function returns a <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> with the levels <em>Pathogenic</em>, <em>Potentially pathogenic</em>, <em>Non-pathogenic</em>, and <em>Unknown</em>.</p>
<p>Determination of the Gram stain (<code>mo_gramstain()</code>) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318/" class="external-link">PMID 11837318</a>), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, <a href="https://pubmed.ncbi.nlm.nih.gov/34694987/" class="external-link">PMID 34694987</a>). Bacteria in these phyla are considered Gram-positive in this <code>AMR</code> package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
<p>Determination of yeasts (<code>mo_is_yeast()</code>) will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. <em>True yeasts</em> quite specifically refers to yeasts in the underlying order Saccharomycetales (such as <em>Saccharomyces cerevisiae</em>). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
<p>Determination of intrinsic resistance (<code>mo_is_intrinsic_resistant()</code>) will be based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023). The <code>mo_is_intrinsic_resistant()</code> function can be vectorised over both argument <code>x</code> (input for microorganisms) and <code>ab</code> (input for antimicrobials).</p>
<p>Determination of bacterial oxygen tolerance (<code>mo_oxygen_tolerance()</code>) will be based on BacDive, see <em>Source</em>. The function <code>mo_is_anaerobic()</code> only returns <code>TRUE</code> if the oxygen tolerance is <code>"anaerobe"</code>, indicting an obligate anaerobic species or genus. It always returns <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. <a href="https://www.mycobank.org" class="external-link">This MycoBank URL</a> will be used for fungi wherever available , <a href="https://www.mycobank.org" class="external-link">this LPSN URL</a> for bacteria wherever available, and <a href="https://www.gbif.org" class="external-link">this GBIF link</a> otherwise.</p>
<p>SNOMED codes (<code>mo_snomed()</code>) was last updated on July 16th, 2024. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
<p>Old taxonomic names (so-called 'synonyms') can be retrieved with <code>mo_synonyms()</code> (which will have the scientific reference as <a href="https://rdrr.io/r/base/names.html" class="external-link">name</a>), the current taxonomic name can be retrieved with <code>mo_current()</code>. Both functions return full names.</p>
<p>All output <a href="translate.html">will be translated</a> where possible.</p>
<p>All functions will, at default, **not** keep old taxonomic properties, as synonyms are automatically replaced with the current taxonomy. Take for example *Enterobacter aerogenes*, which was initially named in 1960 but renamed to *Klebsiella aerogenes* in 2017:
- `mo_genus("Enterobacter aerogenes")` will return `"Klebsiella"` (with a note about the renaming)
- `mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)` will return `"Enterobacter"` (with a once-per-session warning that the name is outdated)
- `mo_ref("Enterobacter aerogenes")` will return `"Tindall et al., 2017"` (with a note about the renaming)
- `mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)` will return `"Hormaeche et al., 1960"` (with a once-per-session warning that the name is outdated)</p>
<p>The short name ([mo_shortname()]) returns the first character of the genus and the full species, such as `"E. coli"`, for species and subspecies. Exceptions are abbreviations of staphylococci (such as *"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as *"GBS"*, Group B Streptococci). Please bear in mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning to the full name will be done using [as.mo()] internally, giving priority to bacteria and human pathogens, i.e. `"E. coli"` will be considered *Escherichia coli*. As a result, `mo_fullname(mo_shortname("Entamoeba coli"))` returns `"Escherichia coli"`.</p>
<p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions [mo_kingdom()] and [mo_domain()] return the exact same results.</p>
<p>Determination of human pathogenicity ([mo_pathogenicity()]) is strongly based on Bartlett *et al.* (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
). This function returns a [factor] with the levels *Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and *Unknown*.</p>
<p>Determination of the Gram stain ([mo_gramstain()]) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, [PMID 34694987](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria in these phyla are considered Gram-positive in this `AMR` package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (or `NA` when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.</p>
<p>Determination of yeasts ([mo_is_yeast()]) will be based on the taxonomic kingdom and class. *Budding yeasts* are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. *True yeasts* quite specifically refers to yeasts in the underlying order Saccharomycetales (such as *Saccharomyces cerevisiae*). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is `NA` or the MO code is `UNKNOWN`).</p>
<p>Determination of intrinsic resistance ([mo_is_intrinsic_resistant()]) will be based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(names(EUCAST_VERSION_EXPECTED_PHENOTYPES[1]))`. The [mo_is_intrinsic_resistant()] function can be vectorised over both argument `x` (input for microorganisms) and `ab` (input for antimicrobials).</p>
<p>Determination of bacterial oxygen tolerance ([mo_oxygen_tolerance()]) will be based on BacDive, see *Source*. The function [mo_is_anaerobic()] only returns `TRUE` if the oxygen tolerance is `"anaerobe"`, indicting an obligate anaerobic species or genus. It always returns `FALSE` for species outside the taxonomic kingdom of Bacteria.</p>
<p>The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. [This MycoBank URL](`r TAXONOMY_VERSION$MycoBank$url`) will be used for fungi wherever available , [this LPSN URL](`r TAXONOMY_VERSION$MycoBank$url`) for bacteria wherever available, and [this GBIF link](`r TAXONOMY_VERSION$GBIF$url`) otherwise.</p>
<p>SNOMED codes ([mo_snomed()]) was last updated on `r documentation_date(TAXONOMY_VERSION$SNOMED$accessed_date)`. See *Source* and the [microorganisms] data set for more info.</p>
<p>Old taxonomic names (so-called 'synonyms') can be retrieved with [mo_synonyms()] (which will have the scientific reference as [name][base::names()]), the current taxonomic name can be retrieved with [mo_current()]. Both functions return full names.</p>
<p>All output [will be translated][translate] where possible.</p>
</div>
<div class="section level2">
<h2 id="matching-score-for-microorganisms">Matching Score for Microorganisms<a class="anchor" aria-label="anchor" href="#matching-score-for-microorganisms"></a></h2>

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@@ -184,135 +184,116 @@ mo_property(x, property = "fullname", language = get_AMR_locale(),
## Value
- An [integer](https://rdrr.io/r/base/integer.html) in case of
`mo_year()`
- An [ordered factor](https://rdrr.io/pkg/data.table/man/fctr.html) in
case of `mo_pathogenicity()`
- A [list](https://rdrr.io/r/base/list.html) in case of `mo_taxonomy()`,
`mo_synonyms()`, `mo_snomed()`, and `mo_info()`
- A [logical](https://rdrr.io/r/base/logical.html) in case of
`mo_is_anaerobic()`, `mo_is_gram_negative()`, `mo_is_gram_positive()`,
`mo_is_intrinsic_resistant()`, and `mo_is_yeast()`
- A named [character](https://rdrr.io/r/base/character.html) in case of
`mo_synonyms()` and `mo_url()`
- A [character](https://rdrr.io/r/base/character.html) in all other
cases
\- An \[integer\] in case of \[mo_year()\] - An \[ordered
factor\]\[factor\] in case of \[mo_pathogenicity()\] - A \[list\] in
case of \[mo_taxonomy()\], \[mo_synonyms()\], \[mo_snomed()\], and
\[mo_info()\] - A \[logical\] in case of \[mo_is_anaerobic()\],
\[mo_is_gram_negative()\], \[mo_is_gram_positive()\],
\[mo_is_intrinsic_resistant()\], and \[mo_is_yeast()\] - A named
\[character\] in case of \[mo_synonyms()\] and \[mo_url()\] - A
\[character\] in all other cases
## Details
All functions will, at default, **not** keep old taxonomic properties,
as synonyms are automatically replaced with the current taxonomy. Take
for example *Enterobacter aerogenes*, which was initially named in 1960
but renamed to *Klebsiella aerogenes* in 2017:
All functions will, at default, \*\*not\*\* keep old taxonomic
properties, as synonyms are automatically replaced with the current
taxonomy. Take for example \*Enterobacter aerogenes\*, which was
initially named in 1960 but renamed to \*Klebsiella aerogenes\* in
2017: - \`mo_genus("Enterobacter aerogenes")\` will return
\`"Klebsiella"\` (with a note about the renaming) -
\`mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)\` will return
\`"Enterobacter"\` (with a once-per-session warning that the name is
outdated) - \`mo_ref("Enterobacter aerogenes")\` will return \`"Tindall
et al., 2017"\` (with a note about the renaming) -
\`mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)\` will return
\`"Hormaeche et al., 1960"\` (with a once-per-session warning that the
name is outdated)
- `mo_genus("Enterobacter aerogenes")` will return `"Klebsiella"` (with
a note about the renaming)
- `mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)` will return
`"Enterobacter"` (with a once-per-session warning that the name is
outdated)
- `mo_ref("Enterobacter aerogenes")` will return
`"Tindall et al., 2017"` (with a note about the renaming)
- `mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)` will return
`"Hormaeche et al., 1960"` (with a once-per-session warning that the
name is outdated)
The short name (`mo_shortname()`) returns the first character of the
genus and the full species, such as `"E. coli"`, for species and
The short name (\[mo_shortname()\]) returns the first character of the
genus and the full species, such as \`"E. coli"\`, for species and
subspecies. Exceptions are abbreviations of staphylococci (such as
*"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic
streptococci (such as *"GBS"*, Group B Streptococci). Please bear in
mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of
Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning
to the full name will be done using
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) internally, giving
priority to bacteria and human pathogens, i.e. `"E. coli"` will be
considered *Escherichia coli*. As a result,
`mo_fullname(mo_shortname("Entamoeba coli"))` returns
`"Escherichia coli"`.
\*"CoNS"\*, Coagulase-Negative Staphylococci) and beta-haemolytic
streptococci (such as \*"GBS"\*, Group B Streptococci). Please bear in
mind that e.g. \*E. coli\* could mean \*Escherichia coli\* (kingdom of
Bacteria) as well as \*Entamoeba coli\* (kingdom of Protozoa). Returning
to the full name will be done using \[as.mo()\] internally, giving
priority to bacteria and human pathogens, i.e. \`"E. coli"\` will be
considered \*Escherichia coli\*. As a result,
\`mo_fullname(mo_shortname("Entamoeba coli"))\` returns \`"Escherichia
coli"\`.
Since the top-level of the taxonomy is sometimes referred to as
'kingdom' and sometimes as 'domain', the functions `mo_kingdom()` and
`mo_domain()` return the exact same results.
'kingdom' and sometimes as 'domain', the functions \[mo_kingdom()\] and
\[mo_domain()\] return the exact same results.
Determination of human pathogenicity (`mo_pathogenicity()`) is strongly
based on Bartlett *et al.* (2022,
Determination of human pathogenicity (\[mo_pathogenicity()\]) is
strongly based on Bartlett \*et al.\* (2022,
[doi:10.1099/mic.0.001269](https://doi.org/10.1099/mic.0.001269) ). This
function returns a
[factor](https://rdrr.io/pkg/data.table/man/fctr.html) with the levels
*Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and *Unknown*.
function returns a \[factor\] with the levels \*Pathogenic\*,
\*Potentially pathogenic\*, \*Non-pathogenic\*, and \*Unknown\*.
Determination of the Gram stain (`mo_gramstain()`) will be based on the
taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the
so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID
11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only
Determination of the Gram stain (\[mo_gramstain()\]) will be based on
the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the
so-called subkingdoms Negibacteria and Posibacteria (2002, \[PMID
11837318\](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only
considered these phyla as Posibacteria: Actinobacteria, Chloroflexi,
Firmicutes, and Tenericutes. These phyla were later renamed to
Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021,
[PMID 34694987](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria in
these phyla are considered Gram-positive in this `AMR` package, except
for members of the class Negativicutes (within phylum Bacillota) which
are Gram-negative. All other bacteria are considered Gram-negative.
Species outside the kingdom of Bacteria will return a value `NA`.
Functions `mo_is_gram_negative()` and `mo_is_gram_positive()` always
return `TRUE` or `FALSE` (or `NA` when the input is `NA` or the MO code
is `UNKNOWN`), thus always return `FALSE` for species outside the
taxonomic kingdom of Bacteria.
\[PMID 34694987\](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria
in these phyla are considered Gram-positive in this \`AMR\` package,
except for members of the class Negativicutes (within phylum Bacillota)
which are Gram-negative. All other bacteria are considered
Gram-negative. Species outside the kingdom of Bacteria will return a
value \`NA\`. Functions \[mo_is_gram_negative()\] and
\[mo_is_gram_positive()\] always return \`TRUE\` or \`FALSE\` (or \`NA\`
when the input is \`NA\` or the MO code is \`UNKNOWN\`), thus always
return \`FALSE\` for species outside the taxonomic kingdom of Bacteria.
Determination of yeasts (`mo_is_yeast()`) will be based on the taxonomic
kingdom and class. *Budding yeasts* are yeasts that reproduce asexually
through a process called budding, where a new cell develops from a small
protrusion on the parent cell. Taxonomically, these are members of the
phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes)
or Pichiomycetes. *True yeasts* quite specifically refers to yeasts in
the underlying order Saccharomycetales (such as *Saccharomyces
cerevisiae*). Thus, for all microorganisms that are member of the
taxonomic class Saccharomycetes or Pichiomycetes, the function will
return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is
`NA` or the MO code is `UNKNOWN`).
Determination of yeasts (\[mo_is_yeast()\]) will be based on the
taxonomic kingdom and class. \*Budding yeasts\* are yeasts that
reproduce asexually through a process called budding, where a new cell
develops from a small protrusion on the parent cell. Taxonomically,
these are members of the phylum Ascomycota, class Saccharomycetes (also
called Hemiascomycetes) or Pichiomycetes. \*True yeasts\* quite
specifically refers to yeasts in the underlying order Saccharomycetales
(such as \*Saccharomyces cerevisiae\*). Thus, for all microorganisms
that are member of the taxonomic class Saccharomycetes or Pichiomycetes,
the function will return \`TRUE\`. It returns \`FALSE\` otherwise (or
\`NA\` when the input is \`NA\` or the MO code is \`UNKNOWN\`).
Determination of intrinsic resistance (`mo_is_intrinsic_resistant()`)
will be based on the
[intrinsic_resistant](https://amr-for-r.org/reference/intrinsic_resistant.md)
data set, which is based on ['EUCAST Expected Resistant Phenotypes'
v1.2](https://www.eucast.org/bacteria/important-additional-information/expert-rules/)
(2023). The `mo_is_intrinsic_resistant()` function can be vectorised
over both argument `x` (input for microorganisms) and `ab` (input for
Determination of intrinsic resistance (\[mo_is_intrinsic_resistant()\])
will be based on the \[intrinsic_resistant\] data set, which is based on
\`r
format_eucast_version_nr(names(EUCAST_VERSION_EXPECTED_PHENOTYPES\[1\]))\`.
The \[mo_is_intrinsic_resistant()\] function can be vectorised over both
argument \`x\` (input for microorganisms) and \`ab\` (input for
antimicrobials).
Determination of bacterial oxygen tolerance (`mo_oxygen_tolerance()`)
will be based on BacDive, see *Source*. The function `mo_is_anaerobic()`
only returns `TRUE` if the oxygen tolerance is `"anaerobe"`, indicting
an obligate anaerobic species or genus. It always returns `FALSE` for
species outside the taxonomic kingdom of Bacteria.
Determination of bacterial oxygen tolerance (\[mo_oxygen_tolerance()\])
will be based on BacDive, see \*Source\*. The function
\[mo_is_anaerobic()\] only returns \`TRUE\` if the oxygen tolerance is
\`"anaerobe"\`, indicting an obligate anaerobic species or genus. It
always returns \`FALSE\` for species outside the taxonomic kingdom of
Bacteria.
The function `mo_url()` will return the direct URL to the online
The function \[mo_url()\] will return the direct URL to the online
database entry, which also shows the scientific reference of the
concerned species. [This MycoBank URL](https://www.mycobank.org) will be
used for fungi wherever available , [this LPSN
URL](https://www.mycobank.org) for bacteria wherever available, and
[this GBIF link](https://www.gbif.org) otherwise.
concerned species. \[This MycoBank URL\](\`r
TAXONOMY_VERSION\$MycoBank\$url\`) will be used for fungi wherever
available , \[this LPSN URL\](\`r TAXONOMY_VERSION\$MycoBank\$url\`) for
bacteria wherever available, and \[this GBIF link\](\`r
TAXONOMY_VERSION\$GBIF\$url\`) otherwise.
SNOMED codes (`mo_snomed()`) was last updated on July 16th, 2024. See
*Source* and the
[microorganisms](https://amr-for-r.org/reference/microorganisms.md) data
set for more info.
SNOMED codes (\[mo_snomed()\]) was last updated on \`r
documentation_date(TAXONOMY_VERSION\$SNOMED\$accessed_date)\`. See
\*Source\* and the \[microorganisms\] data set for more info.
Old taxonomic names (so-called 'synonyms') can be retrieved with
`mo_synonyms()` (which will have the scientific reference as
[name](https://rdrr.io/r/base/names.html)), the current taxonomic name
can be retrieved with `mo_current()`. Both functions return full names.
\[mo_synonyms()\] (which will have the scientific reference as
\[name\]\[base::names()\]), the current taxonomic name can be retrieved
with \[mo_current()\]. Both functions return full names.
All output [will be
translated](https://amr-for-r.org/reference/translate.md) where
possible.
All output \[will be translated\]\[translate\] where possible.
## Matching Score for Microorganisms

2
reference/mo_source.html
View File

@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/pca.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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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">
@@ -98,7 +98,7 @@
standard deviations are less than or equal to <code>tol</code> times the
standard deviation of the first component.) With the default null
setting, no components are omitted (unless <code>rank.</code> is specified
less than <code>min(dim(x))</code>.). Other settings for tol could be
less than <code>min(dim(x))</code>.). Other settings for <code>tol</code> could be
<code>tol = 0</code> or <code>tol = sqrt(.Machine$double.eps)</code>, which
would omit essentially constant components.</p></dd>

4
reference/pca.md
View File

@@ -51,8 +51,8 @@ pca(x, ..., retx = TRUE, center = TRUE, scale. = TRUE, tol = NULL,
than or equal to `tol` times the standard deviation of the first
component.) With the default null setting, no components are omitted
(unless `rank.` is specified less than `min(dim(x))`.). Other settings
for tol could be `tol = 0` or `tol = sqrt(.Machine$double.eps)`, which
would omit essentially constant components.
for `tol` could be `tol = 0` or `tol = sqrt(.Machine$double.eps)`,
which would omit essentially constant components.
- rank.:

2
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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</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
reference/proportion.html
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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="">3.0.1.9055</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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