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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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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
LICENSE-text.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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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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articles/AMR.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -91,7 +91,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 09 February 2026.</p>
generated on 12 February 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">2026-02-09</td>
<td align="center">2026-02-12</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">2026-02-09</td>
<td align="center">2026-02-12</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">2026-02-09</td>
<td align="center">2026-02-12</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -1285,6 +1285,10 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ </span><span style="color: #0000BB; background-color: #444444;">`resistance()`</span><span style="color: #0000BB;"> assumes the EUCAST guideline and thus considers the 'I'</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; category susceptible. Set the </span><span style="color: #0000BB; background-color: #444444;">`guideline`</span><span style="color: #0000BB;"> argument or the </span><span style="color: #0000BB; background-color: #444444;">`AMR_guideline`</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; option to either "CLSI" or "EUCAST", see </span><span style="color: #0000BB; background-color: #444444;">`?AMR-options`</span><span style="color: #0000BB;">.</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span>
<span><span class="co">#&gt; [1] 0.4294272</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>

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articles/AMR.md
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@@ -3,7 +3,7 @@
**Note:** values on this page will change with every website update
since they are based on randomly created values and the page was written
in [R Markdown](https://rmarkdown.rstudio.com/). However, the
methodology remains unchanged. This page was generated on 09 February
methodology remains unchanged. This page was generated on 12 February
2026.
## Introduction
@@ -52,9 +52,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-02-09 | abcd | Escherichia coli | S | S |
| 2026-02-09 | abcd | Escherichia coli | S | R |
| 2026-02-09 | efgh | Escherichia coli | R | S |
| 2026-02-12 | abcd | Escherichia coli | S | S |
| 2026-02-12 | abcd | Escherichia coli | S | R |
| 2026-02-12 | efgh | Escherichia coli | R | S |
### Needed R packages
@@ -845,6 +845,10 @@ These functions can be used on their own:
``` r
our_data_1st %>% resistance(AMX)
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
#> [1] 0.4294272
```

2
articles/AMR_for_Python.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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
articles/AMR_with_tidymodels.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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">
@@ -738,6 +738,10 @@ into a structured time-series format.</p>
<span> .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMX</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMC</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_CIP</span><span class="op">)</span><span class="op">)</span> <span class="co"># Drop missing values</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #444444;">`col_mo`</span><span style="color: #0000BB;">.</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ </span><span style="color: #0000BB; background-color: #444444;">`resistance()`</span><span style="color: #0000BB;"> assumes the EUCAST guideline and thus considers the 'I'</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; category susceptible. Set the </span><span style="color: #0000BB; background-color: #444444;">`guideline`</span><span style="color: #0000BB;"> argument or the </span><span style="color: #0000BB; background-color: #444444;">`AMR_guideline`</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; option to either "CLSI" or "EUCAST", see </span><span style="color: #0000BB; background-color: #444444;">`?AMR-options`</span><span style="color: #0000BB;">.</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span>
<span></span>
<span><span class="va">data_time</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 32 × 5</span></span></span>

4
articles/AMR_with_tidymodels.md
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@@ -636,6 +636,10 @@ data_time <- example_isolates %>%
.groups = "drop") %>%
filter(!is.na(res_AMX) & !is.na(res_AMC) & !is.na(res_CIP)) # Drop missing values
#> ℹ Using column 'mo' as input for `col_mo`.
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
data_time
#> # A tibble: 32 × 5

2
articles/EUCAST.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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
articles/PCA.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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">
@@ -163,6 +163,10 @@ per taxonomic order and genus:</p>
<span> <span class="va">order</span>, <span class="va">genus</span>, <span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>,</span>
<span> <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span></span>
<span> <span class="op">)</span> <span class="co"># and select only relevant columns</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ </span><span style="color: #0000BB; background-color: #444444;">`resistance()`</span><span style="color: #0000BB;"> assumes the EUCAST guideline and thus considers the 'I'</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; category susceptible. Set the </span><span style="color: #0000BB; background-color: #444444;">`guideline`</span><span style="color: #0000BB;"> argument or the </span><span style="color: #0000BB; background-color: #444444;">`AMR_guideline`</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; option to either "CLSI" or "EUCAST", see </span><span style="color: #0000BB; background-color: #444444;">`?AMR-options`</span><span style="color: #0000BB;">.</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 6 × 10</span></span></span>

4
articles/PCA.md
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@@ -78,6 +78,10 @@ resistance_data <- example_isolates %>%
order, genus, AMC, CXM, CTX,
CAZ, GEN, TOB, TMP, SXT
) # and select only relevant columns
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
head(resistance_data)
#> # A tibble: 6 × 10

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articles/WHONET.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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">
@@ -254,7 +254,11 @@ Longest: 40</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># our transformed antibiotic columns</span></span>
<span><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></span>
<span><span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">AMC_ND2</span><span class="op">)</span></span></code></pre></div>
<span><span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">AMC_ND2</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ </span><span style="color: #0000BB; background-color: #444444;">`susceptibility()`</span><span style="color: #0000BB;"> assumes the EUCAST guideline and thus considers the</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; 'I' category susceptible. Set the </span><span style="color: #0000BB; background-color: #444444;">`guideline`</span><span style="color: #0000BB;"> argument or the</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; </span><span style="color: #0000BB; background-color: #444444;">`AMR_guideline`</span><span style="color: #0000BB;"> option to either "CLSI" or "EUCAST", see </span><span style="color: #0000BB; background-color: #444444;">`?AMR-options`</span><span style="color: #0000BB;">.</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered &gt; sir (numeric)<br>
Length: 500<br>

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articles/WHONET.md
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@@ -101,6 +101,10 @@ Longest: 40
# our transformed antibiotic columns
# amoxicillin/clavulanic acid (J01CR02) as an example
data %>% freq(AMC_ND2)
#> ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the
#> 'I' category susceptible. Set the `guideline` argument or the
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
```
**Frequency table**

2
articles/WISCA.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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
articles/datasets.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -80,7 +80,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
<h4 data-toc-skip class="date">09 February 2026</h4>
<h4 data-toc-skip class="date">12 February 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>

2
articles/index.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
authors.html
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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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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
index.html
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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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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
news/index.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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">
@@ -49,9 +49,9 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9020" id="amr-3019020">AMR 3.0.1.9020<a class="anchor" aria-label="anchor" href="#amr-3019020"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9021" id="amr-3019021">AMR 3.0.1.9021<a class="anchor" aria-label="anchor" href="#amr-3019021"></a></h2>
<div class="section level4">
<h4 id="new-3-0-1-9020">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9020"></a></h4>
<h4 id="new-3-0-1-9021">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9021"></a></h4>
<ul><li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
<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>
@@ -83,17 +83,19 @@
</ul></li>
</ul></div>
<div class="section level4">
<h4 id="fixes-3-0-1-9020">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9020"></a></h4>
<h4 id="fixes-3-0-1-9021">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9021"></a></h4>
<ul><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 <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 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>
</ul></div>
<div class="section level4">
<h4 id="updates-3-0-1-9020">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9020"></a></h4>
<h4 id="updates-3-0-1-9021">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9021"></a></h4>
<ul><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>
<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>
<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>

8
news/index.md
View File

@@ -1,6 +1,6 @@
# Changelog
## AMR 3.0.1.9020
## AMR 3.0.1.9021
#### New
@@ -45,7 +45,7 @@
[`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
where for numeric input the arguments `S`, `I`, and `R` would not be
considered ([\#244](https://github.com/msberends/AMR/issues/244))
- Fixed some foreign translations of antimicrobial drugs
- Fixed a bug for printing column names to the console when using
@@ -58,6 +58,10 @@
#### Updates
- [`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.
- [`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

2
pkgdown.yml
View File

@@ -10,7 +10,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2026-02-09T12:49Z
last_built: 2026-02-12T19:40Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles

2
reference/AMR-deprecated.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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">

18
reference/AMR-options.html
View File

@@ -1,5 +1,7 @@
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Options for the AMR package — AMR-options • 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="Options for the AMR package — AMR-options"><meta name="description" content="This is an overview of all the package-specific options() you can set in the AMR package."><meta property="og:description" content="This is an overview of all the package-specific options() you can set in the AMR package."><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>
<!-- 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>Options for the AMR package — AMR-options • 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="Options for the AMR package — AMR-options"><meta name="description" content='This is an overview of all the package-specific options you can set in the AMR package. Set them using the options() function, e.g.:
options(AMR_guideline = "CLSI")'><meta property="og:description" content='This is an overview of all the package-specific options you can set in the AMR package. Set them using the options() function, e.g.:
options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -7,7 +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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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">
@@ -50,12 +52,13 @@
</div>
<div class="ref-description section level2">
<p>This is an overview of all the package-specific <code><a href="https://rdrr.io/r/base/options.html" class="external-link">options()</a></code> you can set in the <code>AMR</code> package.</p>
<p>This is an overview of all the package-specific options you can set in the <code>AMR</code> package. Set them using the <code><a href="https://rdrr.io/r/base/options.html" class="external-link">options()</a></code> function, e.g.:</p>
<p><code>options(AMR_guideline = "CLSI")</code></p>
</div>
<div class="section level2">
<h2 id="options">Options<a class="anchor" aria-label="anchor" href="#options"></a></h2>
<h2 id="options-alphabetical-order-">Options (alphabetical order)<a class="anchor" aria-label="anchor" href="#options-alphabetical-order-"></a></h2>
<ul><li><p><code>AMR_antibiogram_formatting_type</code> <br> A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> (1-22) to use in <code><a href="antibiogram.html">antibiogram()</a></code>, to indicate which formatting type to use.</p></li>
@@ -65,6 +68,11 @@
<li><p><code>AMR_custom_ab</code> <br> A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li>
<li><p><code>AMR_custom_mo</code> <br> A file location to an RDS file, to use custom microorganisms with this package. This is explained in <code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code>.</p></li>
<li><p><code>AMR_eucastrules</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default types of rules for <code><a href="interpretive_rules.html">eucast_rules()</a></code> function, must be one or more of: <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expert")</code>.</p></li>
<li><p><code>AMR_guideline</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default guideline used throughout the <code>AMR</code> package wherever a <code>guideline</code> argument is available. This option is used as the default in e.g. <code><a href="as.sir.html">as.sir()</a></code>, <code><a href="proportion.html">resistance()</a></code>, <code><a href="proportion.html">susceptibility()</a></code>, <code><a href="interpretive_rules.html">interpretive_rules()</a></code> and many plotting functions. <strong>While unset</strong>, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2025).</p><ul><li><p>For <code><a href="as.sir.html">as.sir()</a></code>, this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., <code>"CLSI"</code> or <code>"EUCAST"</code>) or the name including a year (e.g., <code>"CLSI 2019"</code>). Supported guidelines are EUCAST 2011 to 2025, and CLSI 2011 to 2025.</p></li>
<li><p>For <code><a href="proportion.html">resistance()</a></code> and <code><a href="proportion.html">susceptibility()</a></code>, this setting determines how the <code>"I"</code> (Intermediate / Increased exposure) category is handled in calculations. Under CLSI, <code>"I"</code> is considered <em>resistant</em> in susceptibility calculations; under EUCAST, <code>"I"</code> is considered <em>susceptible</em> in susceptibility calculations. Explicitly setting this option ensures reproducible AMR proportion estimates.</p></li>
<li><p>For <code><a href="interpretive_rules.html">interpretive_rules()</a></code>, this determines which guideline-specific interpretive (expert) rules are applied to antimicrobial test results, either EUCAST or CLSI.</p></li>
<li><p>For many plotting functions (e.g., for MIC or disk diffusion values), supplying <code>mo</code> and <code>ab</code> enables automatic SIR-based interpretative colouring. These colours are derived from <code><a href="as.sir.html">as.sir()</a></code> in the background and therefore depend on the active <code>guideline</code> setting, which again uses EUCAST 2025 if not set explicitly.</p></li>
</ul></li>
<li><p><code>AMR_guideline</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default guideline for interpreting MIC values and disk diffusion diameters with <code><a href="as.sir.html">as.sir()</a></code>. Can be only the guideline name (e.g., <code>"CLSI"</code>) or the name with a year (e.g. <code>"CLSI 2019"</code>). The default to the latest implemented EUCAST guideline, currently <code>"EUCAST 2025"</code>. Supported guideline are currently EUCAST (2011-2025) and CLSI (2011-2025).</p></li>
<li><p><code>AMR_ignore_pattern</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to ignore (i.e., make <code>NA</code>) any match given in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions.</p></li>
<li><p><code>AMR_include_PKPD</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>.</p></li>
@@ -87,7 +95,7 @@
<h3 id="share-options-within-team">Share Options Within Team<a class="anchor" aria-label="anchor" href="#share-options-within-team"></a></h3>
<p>For a more global approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:</p><ol><li><p>Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.</p></li>
<p>For a more collaborative approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:</p><ol><li><p>Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.</p></li>
<li><p>For each user, open the <code>.Rprofile</code> file using <code>utils::file.edit("~/.Rprofile")</code> and put in there:</p>
<p></p><div class="sourceCode r"><pre><code><span> <span class="kw"><a href="https://rdrr.io/r/base/source.html" class="external-link">source</a></span><span class="op">(</span><span class="st">"X:/team_folder/R_options.R"</span><span class="op">)</span></span></code></pre><p></p></div></li>
<li><p>Reload R/RStudio and check the settings with <code><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption()</a></code>, e.g. <code>getOption("AMR_locale")</code> if you have set that value.</p></li>

58
reference/AMR-options.md
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@@ -1,10 +1,12 @@
# Options for the AMR package
This is an overview of all the package-specific
[`options()`](https://rdrr.io/r/base/options.html) you can set in the
`AMR` package.
This is an overview of all the package-specific options you can set in
the `AMR` package. Set them using the
[`options()`](https://rdrr.io/r/base/options.html) function, e.g.:
## Options
`options(AMR_guideline = "CLSI")`
## Options (alphabetical order)
- `AMR_antibiogram_formatting_type`
A [numeric](https://rdrr.io/r/base/numeric.html) (1-22) to use in
@@ -52,6 +54,46 @@ This is an overview of all the package-specific
`"other"`, `"custom"`, `"all"`, and defaults to
`c("breakpoints", "expert")`.
- `AMR_guideline`
A [character](https://rdrr.io/r/base/character.html) to set the
default guideline used throughout the `AMR` package wherever a
`guideline` argument is available. This option is used as the default
in e.g. [`as.sir()`](https://amr-for-r.org/reference/as.sir.md),
[`resistance()`](https://amr-for-r.org/reference/proportion.md),
[`susceptibility()`](https://amr-for-r.org/reference/proportion.md),
[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
and many plotting functions. **While unset**, the AMR package uses the
latest implemented EUCAST guideline (currently EUCAST 2025).
- For [`as.sir()`](https://amr-for-r.org/reference/as.sir.md), this
determines which clinical breakpoint guideline is used to interpret
MIC values and disk diffusion diameters. It can be either the
guideline name (e.g., `"CLSI"` or `"EUCAST"`) or the name including
a year (e.g., `"CLSI 2019"`). Supported guidelines are EUCAST 2011
to 2025, and CLSI 2011 to 2025.
- For [`resistance()`](https://amr-for-r.org/reference/proportion.md)
and
[`susceptibility()`](https://amr-for-r.org/reference/proportion.md),
this setting determines how the `"I"` (Intermediate / Increased
exposure) category is handled in calculations. Under CLSI, `"I"` is
considered *resistant* in susceptibility calculations; under EUCAST,
`"I"` is considered *susceptible* in susceptibility calculations.
Explicitly setting this option ensures reproducible AMR proportion
estimates.
- For
[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md),
this determines which guideline-specific interpretive (expert) rules
are applied to antimicrobial test results, either EUCAST or CLSI.
- For many plotting functions (e.g., for MIC or disk diffusion
values), supplying `mo` and `ab` enables automatic SIR-based
interpretative colouring. These colours are derived from
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) in the
background and therefore depend on the active `guideline` setting,
which again uses EUCAST 2025 if not set explicitly.
- `AMR_guideline`
A [character](https://rdrr.io/r/base/character.html) to set the
default guideline for interpreting MIC values and disk diffusion
@@ -132,10 +174,10 @@ rules when interpreting MIC values with
### Share Options Within Team
For a more global approach, e.g. within a (data) team, save an options
file to a remote file location, such as a shared network drive, and have
each user read in this file automatically at start-up. This would work
in this way:
For a more collaborative approach, e.g. within a (data) team, save an
options file to a remote file location, such as a shared network drive,
and have each user read in this file automatically at start-up. This
would work in this way:
1. Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill
it with preferred settings.

2
reference/AMR.html
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@@ -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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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 @@
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reference/ab_property.html
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reference/add_custom_antimicrobials.html
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@@ -7,7 +7,7 @@
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reference/add_custom_microorganisms.html
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@@ -7,7 +7,7 @@
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22
reference/age.html
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@@ -7,7 +7,7 @@
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@@ -112,16 +112,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 45 45.95068 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.54247 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.43836 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.52055 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.22466 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.86575 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.63288 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.40000 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.73699 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.23836 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 45 45.95890 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.55068 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.44658 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.52877 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.23288 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.87397 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.64110 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.40822 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.74521 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.24658 47</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 1980-02-27 45 45.95068 19
#> 2 1953-07-26 72 72.54247 46
#> 3 1949-09-02 76 76.43836 50
#> 4 1986-08-03 39 39.52055 13
#> 5 1932-11-19 93 93.22466 67
#> 6 1949-03-30 76 76.86575 50
#> 7 1996-06-23 29 29.63288 3
#> 8 1963-09-16 62 62.40000 36
#> 9 1952-05-16 73 73.73699 47
#> 10 1952-11-14 73 73.23836 47
#> 1 1980-02-27 45 45.95890 19
#> 2 1953-07-26 72 72.55068 46
#> 3 1949-09-02 76 76.44658 50
#> 4 1986-08-03 39 39.52877 13
#> 5 1932-11-19 93 93.23288 67
#> 6 1949-03-30 76 76.87397 50
#> 7 1996-06-23 29 29.64110 3
#> 8 1963-09-16 62 62.40822 36
#> 9 1952-05-16 73 73.74521 47
#> 10 1952-11-14 73 73.24658 47
```

2
reference/age_groups.html
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@@ -7,7 +7,7 @@
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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
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reference/as.sir.html
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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@@ -310,8 +310,8 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<h3 id="after-interpretation">After Interpretation<a class="anchor" aria-label="anchor" href="#after-interpretation"></a></h3>
<p>After using <code>as.sir()</code>, you can use the <code><a href="interpretive_rules.html">eucast_rules()</a></code> defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<p>To determine which isolates are multi-drug resistant, be sure to run <code><a href="mdro.html">mdro()</a></code> (which applies the MDR/PDR/XDR guideline from 2012 at default) on a data set that contains S/I/R values. Read more about <a href="mdro.html">interpreting multidrug-resistant organisms here</a>.</p>
<p>After using <code>as.sir()</code>, you can use the <code><a href="interpretive_rules.html">interpretive_rules()</a></code> to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<p>To determine which isolates are multi-drug resistant, be sure to run <code><a href="mdro.html">mdro()</a></code> (which applies the MDR/PDR/XDR guideline from 2012 at default) on a data set that contains S/I/R values. Read more about <a href="mdro.html">detecting multidrug-resistant organisms here</a>.</p>
</div>
<div class="section">
@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-02-09 <span style="color: #949494;">12:50:16</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> 2026-02-09 <span style="color: #949494;">12:50:17</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-02-09 <span style="color: #949494;">12:50:17</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> 2026-02-09 <span style="color: #949494;">12:50:17</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> 2026-02-12 <span style="color: #949494;">19:41:27</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> 2026-02-12 <span style="color: #949494;">19:41:27</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> 2026-02-12 <span style="color: #949494;">19:41:28</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> 2026-02-12 <span style="color: #949494;">19:41:28</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>

20
reference/as.sir.md
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@@ -504,16 +504,16 @@ options to set before analysis:
### After Interpretation
After using `as.sir()`, you can use the
[`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
defined by EUCAST to (1) apply inferred susceptibility and resistance
based on results of other antimicrobials and (2) apply intrinsic
resistance based on taxonomic properties of a microorganism.
[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
to (1) apply inferred susceptibility and resistance based on results of
other antimicrobials and (2) apply intrinsic resistance based on
taxonomic properties of a microorganism.
To determine which isolates are multi-drug resistant, be sure to run
[`mdro()`](https://amr-for-r.org/reference/mdro.md) (which applies the
MDR/PDR/XDR guideline from 2012 at default) on a data set that contains
S/I/R values. Read more about [interpreting multidrug-resistant
organisms here](https://amr-for-r.org/reference/mdro.md).
S/I/R values. Read more about [detecting multidrug-resistant organisms
here](https://amr-for-r.org/reference/mdro.md).
### Other
@@ -660,10 +660,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2026-02-09 12:50:16 1 MIC amoxicillin Escherich… human 8
#> 2 2026-02-09 12:50:17 1 MIC cipro Escherich… human 0.256
#> 3 2026-02-09 12:50:17 1 DISK tobra Escherich… human 16
#> 4 2026-02-09 12:50:17 1 DISK genta Escherich… human 18
#> 1 2026-02-12 19:41:27 1 MIC amoxicillin Escherich… human 8
#> 2 2026-02-12 19:41:27 1 MIC cipro Escherich… human 0.256
#> 3 2026-02-12 19:41:28 1 DISK tobra Escherich… human 16
#> 4 2026-02-12 19:41:28 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>

2
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@@ -7,7 +7,7 @@
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6
reference/availability.html
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@@ -7,7 +7,7 @@
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@@ -82,6 +82,10 @@
<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="fu">availability</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ </span><span style="color: #0000BB; background-color: #444444;">`resistance()`</span><span style="color: #0000BB;"> assumes the EUCAST guideline and thus considers the 'I'</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> category susceptible. Set the </span><span style="color: #0000BB; background-color: #444444;">`guideline`</span><span style="color: #0000BB;"> argument or the </span><span style="color: #0000BB; background-color: #444444;">`AMR_guideline`</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> option to either "CLSI" or "EUCAST", see </span><span style="color: #0000BB; background-color: #444444;">`?AMR-options`</span><span style="color: #0000BB;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> count available visual_availabilty resistant visual_resistance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date 2000 100.0% |####################| </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient 2000 100.0% |####################| </span>

4
reference/availability.md
View File

@@ -41,6 +41,10 @@ calculated with
``` r
availability(example_isolates)
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
#> count available visual_availabilty resistant visual_resistance
#> date 2000 100.0% |####################|
#> patient 2000 100.0% |####################|

2
reference/bug_drug_combinations.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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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/clinical_breakpoints.html
View File

@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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">

29
reference/count.html
View File

@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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">
@@ -58,9 +58,11 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<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">count_resistant</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">count_resistant</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">count_S</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span></span>
@@ -92,6 +94,12 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antimicrobials, see section <em>Combination Therapy</em> below.</p></dd>
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
<dd><p>Either <code>"EUCAST"</code> (default) or <code>"CLSI"</code>. With EUCAST, the 'I' category will be considered as susceptible (see <a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/" class="external-link">EUCAST website</a>), but with with CLSI, it will be considered resistant. Therefore:</p><ul><li><p>EUCAST: <code>count_susceptible()</code> \(= N_{S} + N_{I}\), <code>count_resistant()</code> \(= N_{R}\)</p></li>
<li><p>CLSI: <code>count_susceptible()</code> \(= N_{S} + N_{SDD}\), <code>count_resistant()</code> \(= N_{I} + N_{R}\)</p></li>
</ul><p>You can also use e.g. <code>count_R()</code> or <code>count_S()</code> instead, to be explicit.</p></dd>
<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns with class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>).</p></dd>
@@ -115,8 +123,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>These functions are meant to count isolates. Use the <code><a href="proportion.html">resistance()</a></code>/<code><a href="proportion.html">susceptibility()</a></code> functions to calculate microbial resistance/susceptibility.</p>
<p>The function <code>count_resistant()</code> is equal to the function <code>count_R()</code>. The function <code>count_susceptible()</code> is equal to the function <code>count_SI()</code>.</p>
<p>The function <code>n_sir()</code> is an alias of <code>count_all()</code>. They can be used to count all available isolates, i.e. where all input antimicrobials have an available result (S, I or R). Their use is equal to <code><a href="https://dplyr.tidyverse.org/reference/n_distinct.html" class="external-link">n_distinct()</a></code>. Their function is equal to <code>count_susceptible(...) + count_resistant(...)</code>.</p>
<p>The function <code>n_sir()</code> is an alias of <code>count_all()</code>. They can be used to count all available isolates, i.e. where all input antimicrobials have an available result (S, I or R). Their use is equal to <code>dplyr</code>'s <code><a href="https://dplyr.tidyverse.org/reference/n_distinct.html" class="external-link">n_distinct()</a></code>. Their function is equal to <code>count_susceptible(...) + count_resistant(...)</code>.</p>
<p>The function <code>count_df()</code> takes any variable from <code>data</code> that has an <code><a href="as.sir.html">sir</a></code> class (created with <code><a href="as.sir.html">as.sir()</a></code>) and counts the number of S's, I's and R's. It also supports grouped variables. The function <code><a href="proportion.html">sir_df()</a></code> works exactly like <code>count_df()</code>, but adds the percentage of S, I and R.</p>
</div>
<div class="section level2">
@@ -167,8 +174,16 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># base R ------------------------------------------------------------</span></span></span>
<span class="r-in"><span><span class="fu">count_resistant</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "R"</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ </span><span style="color: #0000BB; background-color: #444444;">`count_resistant()`</span><span style="color: #0000BB;"> assumes the EUCAST guideline and thus considers the</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> 'I' category susceptible. Set the </span><span style="color: #0000BB; background-color: #444444;">`guideline`</span><span style="color: #0000BB;"> argument or the</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> </span><span style="color: #0000BB; background-color: #444444;">`AMR_guideline`</span><span style="color: #0000BB;"> option to either "CLSI" or "EUCAST", see </span><span style="color: #0000BB; background-color: #444444;">`?AMR-options`</span><span style="color: #0000BB;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 804</span>
<span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S" and "I"</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ </span><span style="color: #0000BB; background-color: #444444;">`count_susceptible()`</span><span style="color: #0000BB;"> assumes the EUCAST guideline and thus considers the</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> 'I' category susceptible. Set the </span><span style="color: #0000BB; background-color: #444444;">`guideline`</span><span style="color: #0000BB;"> argument or the</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> </span><span style="color: #0000BB; background-color: #444444;">`AMR_guideline`</span><span style="color: #0000BB;"> option to either "CLSI" or "EUCAST", see </span><span style="color: #0000BB; background-color: #444444;">`?AMR-options`</span><span style="color: #0000BB;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span>
<span class="r-in"><span><span class="fu">count_all</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S", "I" and "R"</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1350</span>
@@ -198,6 +213,10 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span>
<span class="r-in"><span><span class="fu"><a href="proportion.html">susceptibility</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="op">*</span> <span class="fu">n_sir</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ </span><span style="color: #0000BB; background-color: #444444;">`susceptibility()`</span><span style="color: #0000BB;"> assumes the EUCAST guideline and thus considers the</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> 'I' category susceptible. Set the </span><span style="color: #0000BB; background-color: #444444;">`guideline`</span><span style="color: #0000BB;"> argument or the</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> </span><span style="color: #0000BB; background-color: #444444;">`AMR_guideline`</span><span style="color: #0000BB;"> option to either "CLSI" or "EUCAST", see </span><span style="color: #0000BB; background-color: #444444;">`?AMR-options`</span><span style="color: #0000BB;">.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------</span></span></span>

40
reference/count.md
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@@ -12,9 +12,11 @@ from the `dplyr` package and also support grouped variables, see
## Usage
``` r
count_resistant(..., only_all_tested = FALSE)
count_resistant(..., only_all_tested = FALSE,
guideline = getOption("AMR_guideline", "EUCAST"))
count_susceptible(..., only_all_tested = FALSE)
count_susceptible(..., only_all_tested = FALSE,
guideline = getOption("AMR_guideline", "EUCAST"))
count_S(..., only_all_tested = FALSE)
@@ -49,6 +51,22 @@ count_df(data, translate_ab = "name", language = get_AMR_locale(),
that isolates must be tested for all antimicrobials, see section
*Combination Therapy* below.
- guideline:
Either `"EUCAST"` (default) or `"CLSI"`. With EUCAST, the 'I' category
will be considered as susceptible (see [EUCAST
website](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/)),
but with with CLSI, it will be considered resistant. Therefore:
- EUCAST: `count_susceptible()` \\= N\_{S} + N\_{I}\\,
`count_resistant()` \\= N\_{R}\\
- CLSI: `count_susceptible()` \\= N\_{S} + N\_{SDD}\\,
`count_resistant()` \\= N\_{I} + N\_{R}\\
You can also use e.g. `count_R()` or `count_S()` instead, to be
explicit.
- data:
A [data.frame](https://rdrr.io/r/base/data.frame.html) containing
@@ -88,13 +106,9 @@ These functions are meant to count isolates. Use the
[`resistance()`](https://amr-for-r.org/reference/proportion.md)/[`susceptibility()`](https://amr-for-r.org/reference/proportion.md)
functions to calculate microbial resistance/susceptibility.
The function `count_resistant()` is equal to the function `count_R()`.
The function `count_susceptible()` is equal to the function
`count_SI()`.
The function `n_sir()` is an alias of `count_all()`. They can be used to
count all available isolates, i.e. where all input antimicrobials have
an available result (S, I or R). Their use is equal to
an available result (S, I or R). Their use is equal to `dplyr`'s
[`n_distinct()`](https://dplyr.tidyverse.org/reference/n_distinct.html).
Their function is equal to
`count_susceptible(...) + count_resistant(...)`.
@@ -174,8 +188,16 @@ calculate microbial resistance and susceptibility.
# base R ------------------------------------------------------------
count_resistant(example_isolates$AMX) # counts "R"
#> ℹ `count_resistant()` assumes the EUCAST guideline and thus considers the
#> 'I' category susceptible. Set the `guideline` argument or the
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
#> [1] 804
count_susceptible(example_isolates$AMX) # counts "S" and "I"
#> ℹ `count_susceptible()` assumes the EUCAST guideline and thus considers the
#> 'I' category susceptible. Set the `guideline` argument or the
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
#> [1] 546
count_all(example_isolates$AMX) # counts "S", "I" and "R"
#> [1] 1350
@@ -205,6 +227,10 @@ n_sir(example_isolates$AMX)
count_susceptible(example_isolates$AMX)
#> [1] 546
susceptibility(example_isolates$AMX) * n_sir(example_isolates$AMX)
#> ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the
#> 'I' category susceptible. Set the `guideline` argument or the
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
#> [1] 546
# dplyr -------------------------------------------------------------

2
reference/custom_eucast_rules.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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/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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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/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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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/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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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/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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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/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="">3.0.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</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/ggplot_pca.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -220,7 +220,7 @@
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 73 warnings in `summarise()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `PEN = (function (..., minimum = 30, as_percent = FALSE,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> only_all_tested = FALSE) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> only_all_tested = FALSE, ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 5: `order = "Lactobacillales"`, `genus = "Enterococcus"`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: only 14 results available for PEN in group: order =</span>

2
reference/ggplot_pca.md
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@@ -211,7 +211,7 @@ if (require("dplyr")) {
#> Warning: There were 73 warnings in `summarise()`.
#> The first warning was:
#> ℹ In argument: `PEN = (function (..., minimum = 30, as_percent = FALSE,
#> only_all_tested = FALSE) ...`.
#> only_all_tested = FALSE, ...`.
#> ℹ In group 5: `order = "Lactobacillales"`, `genus = "Enterococcus"`.
#> Caused by warning:
#> ! Introducing NA: only 14 results available for PEN in group: order =

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="">3.0.1.9020</small>
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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>
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2
reference/index.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/interpretive_rules.html
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@@ -13,7 +13,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/intrinsic_resistant.html
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@@ -7,7 +7,7 @@
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reference/italicise_taxonomy.html
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@@ -7,7 +7,7 @@
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reference/join.html
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@@ -7,7 +7,7 @@
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reference/key_antimicrobials.html
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@@ -7,7 +7,7 @@
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reference/kurtosis.html
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@@ -7,7 +7,7 @@
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reference/like.html
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@@ -7,7 +7,7 @@
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reference/mdro.html
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@@ -7,7 +7,7 @@
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reference/mean_amr_distance.html
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@@ -7,7 +7,7 @@
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2
reference/microorganisms.codes.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/microorganisms.groups.html
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@@ -7,7 +7,7 @@
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reference/microorganisms.html
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
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reference/mo_matching_score.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/mo_property.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/mo_source.html
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@@ -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>
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4
reference/pca.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -148,7 +148,7 @@
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 73 warnings in `summarise()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `PEN = (function (..., minimum = 30, as_percent = FALSE,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> only_all_tested = FALSE) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> only_all_tested = FALSE, ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 5: `order = "Lactobacillales"`, `genus = "Enterococcus"`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: only 14 results available for PEN in group: order =</span>

2
reference/pca.md
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@@ -110,7 +110,7 @@ if (require("dplyr")) {
#> Warning: There were 73 warnings in `summarise()`.
#> The first warning was:
#> ℹ In argument: `PEN = (function (..., minimum = 30, as_percent = FALSE,
#> only_all_tested = FALSE) ...`.
#> only_all_tested = FALSE, ...`.
#> ℹ In group 5: `order = "Lactobacillales"`, `genus = "Enterococcus"`.
#> Caused by warning:
#> ! Introducing NA: only 14 results available for PEN in group: order =

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>
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16
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>
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@@ -59,10 +59,12 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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">resistance</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span> only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>,</span>
<span> <span class="st">"EUCAST"</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">susceptibility</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span> only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>,</span>
<span> <span class="st">"EUCAST"</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">sir_confidence_interval</span><span class="op">(</span><span class="va">...</span>, ab_result <span class="op">=</span> <span class="st">"R"</span>, minimum <span class="op">=</span> <span class="fl">30</span>,</span>
<span> as_percent <span class="op">=</span> <span class="cn">FALSE</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, confidence_level <span class="op">=</span> <span class="fl">0.95</span>,</span>
@@ -116,6 +118,12 @@ resistance() should be used to calculate resistance, susceptibility() should be
<dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antimicrobials, see section <em>Combination Therapy</em> below.</p></dd>
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
<dd><p>Either <code>"EUCAST"</code> (default) or <code>"CLSI"</code>. With EUCAST, the 'I' category will be considered as susceptible (see <a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/" class="external-link">EUCAST website</a>), but with with CLSI, it will be considered resistant. Therefore:</p><ul><li><p>EUCAST: <code>susceptibility()</code> \(= \%S + \%I\), <code>resistance()</code> \(= \%R\)</p></li>
<li><p>CLSI: <code>susceptibility()</code> \(= \%S + \%SDD\), <code>resistance()</code> \(= \%I + \%R\)</p></li>
</ul><p>You can also use e.g. <code>proportion_R()</code> or <code>proportion_S()</code> instead, to be explicit.</p></dd>
<dt id="arg-ab-result">ab_result<a class="anchor" aria-label="anchor" href="#arg-ab-result"></a></dt>
<dd><p>Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R".</p></dd>
@@ -311,7 +319,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`carbapenems()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `summarise()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `KAN = (function (..., minimum = 30, as_percent = FALSE,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> only_all_tested = FALSE) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> only_all_tested = FALSE, ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 3: `ward = "Outpatient"`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: only 23 results available for KAN in group: ward =</span>

23
reference/proportion.md
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@@ -14,10 +14,12 @@ from the `dplyr` package and also support grouped variables, see
``` r
resistance(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
only_all_tested = FALSE, guideline = getOption("AMR_guideline",
"EUCAST"))
susceptibility(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
only_all_tested = FALSE, guideline = getOption("AMR_guideline",
"EUCAST"))
sir_confidence_interval(..., ab_result = "R", minimum = 30,
as_percent = FALSE, only_all_tested = FALSE, confidence_level = 0.95,
@@ -85,6 +87,21 @@ Standards Institute (CLSI)*.
that isolates must be tested for all antimicrobials, see section
*Combination Therapy* below.
- guideline:
Either `"EUCAST"` (default) or `"CLSI"`. With EUCAST, the 'I' category
will be considered as susceptible (see [EUCAST
website](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/)),
but with with CLSI, it will be considered resistant. Therefore:
- EUCAST: `susceptibility()` \\= \\S + \\I\\, `resistance()` \\= \\R\\
- CLSI: `susceptibility()` \\= \\S + \\SDD\\, `resistance()` \\= \\I +
\\R\\
You can also use e.g. `proportion_R()` or `proportion_S()` instead, to
be explicit.
- ab_result:
Antibiotic results to test against, must be one or more values of "S",
@@ -360,7 +377,7 @@ if (require("dplyr")) {
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> Warning: There was 1 warning in `summarise()`.
#> ℹ In argument: `KAN = (function (..., minimum = 30, as_percent = FALSE,
#> only_all_tested = FALSE) ...`.
#> only_all_tested = FALSE, ...`.
#> ℹ In group 3: `ward = "Outpatient"`.
#> Caused by warning:
#> ! Introducing NA: only 23 results available for KAN in group: ward =

2
reference/random.html
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@@ -7,7 +7,7 @@
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reference/resistance_predict.html
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@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
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reference/skewness.html
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@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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reference/top_n_microorganisms.html
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@@ -7,7 +7,7 @@
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reference/translate.html
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@@ -7,7 +7,7 @@
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search.json
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