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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">
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">
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>
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
```
articles/AMR_for_Python.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">
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>
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
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">
articles/PCA.html
+5 -1
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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>
articles/PCA.md
+4
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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
articles/WHONET.html
+6 -2
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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>
articles/WHONET.md
+4
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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**
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">
articles/datasets.html
+2 -2
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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>
articles/index.html
+1 -1
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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">
authors.html
+1 -1
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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">
index.html
+1 -1
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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">
news/index.html
+8 -6
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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>
news/index.md
+6 -2
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@@ -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
pkgdown.yml
+1 -1
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
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">
reference/AMR-options.html
+13 -5
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@@ -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>
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.
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">
reference/WHOCC.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">
reference/WHONET.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">
reference/ab_from_text.html
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@@ -7,7 +7,7 @@
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reference/age.html
+11 -11
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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>
reference/age.md
+10 -10
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@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
df
#> birth_date age age_exact age_at_y2k
#> 1 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
```
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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@@ -7,7 +7,7 @@
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+7 -7
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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>
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>
reference/atc_online.html
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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>
reference/availability.md
+4
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% |####################|
reference/bug_drug_combinations.html
+1 -1
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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">
reference/clinical_breakpoints.html
+1 -1
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">
reference/count.html
+24 -5
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>
reference/count.md
+33 -7
View File
@@ -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 -------------------------------------------------------------
reference/custom_eucast_rules.html
+1 -1
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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">
reference/custom_mdro_guideline.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">
reference/dosage.html
+1 -1
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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">
reference/esbl_isolates.html
+1 -1
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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">
reference/example_isolates.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">
reference/example_isolates_unclean.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">
reference/export_ncbi_biosample.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">
reference/first_isolate.html
+1 -1
View File
@@ -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">
reference/g.test.html
+1 -1
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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">
reference/get_episode.html
+1 -1
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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/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>
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 =
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>
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reference/guess_ab_col.html
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@@ -7,7 +7,7 @@
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reference/index.html
+1 -1
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@@ -7,7 +7,7 @@
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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
+1 -1
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@@ -7,7 +7,7 @@
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reference/italicise_taxonomy.html
+1 -1
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@@ -7,7 +7,7 @@
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reference/join.html
+1 -1
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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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@@ -7,7 +7,7 @@
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reference/like.html
+1 -1
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@@ -7,7 +7,7 @@
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+1 -1
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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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reference/microorganisms.codes.html
+1 -1
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@@ -7,7 +7,7 @@
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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
+1 -1
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@@ -7,7 +7,7 @@
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reference/mo_property.html
+1 -1
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@@ -7,7 +7,7 @@
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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
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reference/pca.html
+2 -2
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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>
reference/pca.md
+1 -1
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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 =
reference/plot.html
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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reference/proportion.html
+12 -4
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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>
reference/proportion.md
+20 -3
View File
@@ -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 =
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[{"path":"https://amr-for-r.org/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial drugs, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"Conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"Conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> <chr> <chr> <date> <chr> <chr> <chr> <chr> <chr> #> 1 J3 A 2012-11-21 E. coli R I S S #> 2 R7 A 2018-04-03 K. pneumoniae R I S S #> 3 P3 A 2014-09-19 E. coli R S S S #> 4 P10 A 2015-12-10 E. coli S I S S #> 5 B7 A 2015-03-02 E. coli S S S S #> 6 W3 A 2018-03-31 S. aureus R S R S #> 7 J8 A 2016-06-14 E. coli R S S S #> 8 M3 A 2015-10-25 E. coli R S S S #> 9 J3 A 2019-06-19 E. coli S S S S #> 10 G6 A 2015-04-27 S. aureus S S S S #> # ℹ 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://amr-for-r.org/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"Conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 24 Jun 2024. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLEPNE\") #> Class 'mo' #> [1] BLine truncated
[{"path":"https://amr-for-r.org/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial drugs, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"Conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"Conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> <chr> <chr> <date> <chr> <chr> <chr> <chr> <chr> #> 1 J3 A 2012-11-21 E. coli R I S S #> 2 R7 A 2018-04-03 K. pneumoniae R I S S #> 3 P3 A 2014-09-19 E. coli R S S S #> 4 P10 A 2015-12-10 E. coli S I S S #> 5 B7 A 2015-03-02 E. coli S S S S #> 6 W3 A 2018-03-31 S. aureus R S R S #> 7 J8 A 2016-06-14 E. coli R S S S #> 8 M3 A 2015-10-25 E. coli R S S S #> 9 J3 A 2019-06-19 E. coli S S S S #> 10 G6 A 2015-04-27 S. aureus S S S S #> # ℹ 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://amr-for-r.org/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"Conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 24 Jun 2024. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLEPNE\") #> Class 'mo' #> [1] BLine truncated