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<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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articles/AMR.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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"> <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 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 page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was Markdown</a>. However, the methodology remains unchanged. This page was
generated on 08 February 2026.</p> generated on 09 February 2026.</p>
<div class="section level2"> <div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2> </h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2026-02-08</td> <td align="center">2026-02-09</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2026-02-08</td> <td align="center">2026-02-09</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2026-02-08</td> <td align="center">2026-02-09</td>
<td align="center">efgh</td> <td align="center">efgh</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">R</td>

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**Note:** values on this page will change with every website update **Note:** values on this page will change with every website update
since they are based on randomly created values and the page was written since they are based on randomly created values and the page was written
in [R Markdown](https://rmarkdown.rstudio.com/). However, the in [R Markdown](https://rmarkdown.rstudio.com/). However, the
methodology remains unchanged. This page was generated on 08 February methodology remains unchanged. This page was generated on 09 February
2026. 2026.
## Introduction ## Introduction
@@ -52,9 +52,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP | | date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:| |:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-02-08 | abcd | Escherichia coli | S | S | | 2026-02-09 | abcd | Escherichia coli | S | S |
| 2026-02-08 | abcd | Escherichia coli | S | R | | 2026-02-09 | abcd | Escherichia coli | S | R |
| 2026-02-08 | efgh | Escherichia coli | R | S | | 2026-02-09 | efgh | Escherichia coli | R | S |
### Needed R packages ### Needed R packages

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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articles/WHONET.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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articles/datasets.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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"> <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"> <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> <img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
<h4 data-toc-skip class="date">08 February 2026</h4> <h4 data-toc-skip class="date">09 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> <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> <div class="d-none name"><code>datasets.Rmd</code></div>
@@ -1294,7 +1294,7 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
<em>MUP</em>, and <em>RIF</em>.</p> <em>MUP</em>, and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>, <p>This data set is in R available as <code>example_isolates</code>,
after you load the <code>AMR</code> package.</p> after you load the <code>AMR</code> package.</p>
<p>It was last updated on 15 June 2024 13:33:49 UTC. Find more info <p>It was last updated on 9 February 2026 12:16:36 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/example_isolates.html">data set about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/example_isolates.html">data set
here</a>.</p> here</a>.</p>
<p><strong>Example content</strong></p> <p><strong>Example content</strong></p>

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@@ -414,8 +414,8 @@ column names:
This data set is in R available as `example_isolates`, after you load This data set is in R available as `example_isolates`, after you load
the `AMR` package. the `AMR` package.
It was last updated on 15 June 2024 13:33:49 UTC. Find more info about It was last updated on 9 February 2026 12:16:36 UTC. Find more info
the contents, (scientific) source, and structure of this [data set about the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/example_isolates.html). here](https://amr-for-r.org/reference/example_isolates.html).
**Example content** **Example content**

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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@@ -33,7 +33,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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"> <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>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9019" id="amr-3019019">AMR 3.0.1.9019<a class="anchor" aria-label="anchor" href="#amr-3019019"></a></h2> <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>
<div class="section level4"> <div class="section level4">
<h4 id="new-3-0-1-9019">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9019"></a></h4> <h4 id="new-3-0-1-9020">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9020"></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>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> <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> <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>
@@ -83,7 +83,7 @@
</ul></li> </ul></li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="fixes-3-0-1-9019">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9019"></a></h4> <h4 id="fixes-3-0-1-9020">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9020"></a></h4>
<ul><li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li> <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 some foreign translations of antimicrobial drugs</li>
@@ -92,7 +92,7 @@
<li>Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (<a href="https://github.com/msberends/AMR/issues/256" class="external-link">#256</a>)</li> <li>Fixed 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> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="updates-3-0-1-9019">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9019"></a></h4> <h4 id="updates-3-0-1-9020">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9020"></a></h4>
<ul><li> <ul><li>
<code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.mic.html">rescale_mic()</a></code> gained the argument <code>round_to_next_log2</code>, which can be set to <code>TRUE</code> to round all values up to the nearest next log2 level (<a href="https://github.com/msberends/AMR/issues/255" class="external-link">#255</a>)</li> <code><a href="../reference/as.mic.html">as.mic()</a></code> 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> <li>

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# Changelog # Changelog
## AMR 3.0.1.9019 ## AMR 3.0.1.9020
#### New #### New

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pkgdown.yml
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@@ -10,7 +10,7 @@ articles:
PCA: PCA.html PCA: PCA.html
WHONET: WHONET.html WHONET: WHONET.html
WISCA: WISCA.html WISCA: WISCA.html
last_built: 2026-02-08T22:24Z last_built: 2026-02-09T12:49Z
urls: urls:
reference: https://amr-for-r.org/reference reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles article: https://amr-for-r.org/articles

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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2
reference/AMR.html
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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/WHOCC.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/WHONET.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/ab_from_text.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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2
reference/ab_property.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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2
reference/add_custom_antimicrobials.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/add_custom_microorganisms.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

22
reference/age.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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@@ -112,16 +112,16 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</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> 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 45.94795 19</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 72.53973 46</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 76.43562 50</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 39.51781 13</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 93.22192 67</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 76.86301 50</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 29.63014 3</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 62.39726 36</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 73.73425 47</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 73.23562 47</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.23836 47</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

20
reference/age.md
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@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
df df
#> birth_date age age_exact age_at_y2k #> birth_date age age_exact age_at_y2k
#> 1 1980-02-27 45 45.94795 19 #> 1 1980-02-27 45 45.95068 19
#> 2 1953-07-26 72 72.53973 46 #> 2 1953-07-26 72 72.54247 46
#> 3 1949-09-02 76 76.43562 50 #> 3 1949-09-02 76 76.43836 50
#> 4 1986-08-03 39 39.51781 13 #> 4 1986-08-03 39 39.52055 13
#> 5 1932-11-19 93 93.22192 67 #> 5 1932-11-19 93 93.22466 67
#> 6 1949-03-30 76 76.86301 50 #> 6 1949-03-30 76 76.86575 50
#> 7 1996-06-23 29 29.63014 3 #> 7 1996-06-23 29 29.63288 3
#> 8 1963-09-16 62 62.39726 36 #> 8 1963-09-16 62 62.40000 36
#> 9 1952-05-16 73 73.73425 47 #> 9 1952-05-16 73 73.73699 47
#> 10 1952-11-14 73 73.23562 47 #> 10 1952-11-14 73 73.23836 47
``` ```

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reference/amr-tidymodels.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/antibiogram.html
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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/antimicrobial_selectors.html
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/antimicrobials.html
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/as.ab.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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2
reference/as.disk.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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2
reference/as.mic.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/as.mo.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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10
reference/as.sir.html
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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@@ -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> <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> 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: #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> 2026-02-08 <span style="color: #949494;">22:25:52</span> 1 MIC amoxicillin Escherich… human 8 </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> 2026-02-08 <span style="color: #949494;">22:25:53</span> 1 MIC cipro Escherich… human 0.256 </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> 2026-02-08 <span style="color: #949494;">22:25:53</span> 1 DISK tobra Escherich… human 16 </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> 2026-02-08 <span style="color: #949494;">22:25:54</span> 1 DISK genta Escherich… human 18 </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: #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;"># 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;"># 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> <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>

8
reference/as.sir.md
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@@ -660,10 +660,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18 #> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given #> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr> #> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2026-02-08 22:25:52 1 MIC amoxicillin Escherich… human 8 #> 1 2026-02-09 12:50:16 1 MIC amoxicillin Escherich… human 8
#> 2 2026-02-08 22:25:53 1 MIC cipro Escherich… human 0.256 #> 2 2026-02-09 12:50:17 1 MIC cipro Escherich… human 0.256
#> 3 2026-02-08 22:25:53 1 DISK tobra Escherich… human 16 #> 3 2026-02-09 12:50:17 1 DISK tobra Escherich… human 16
#> 4 2026-02-08 22:25:54 1 DISK genta Escherich… human 18 #> 4 2026-02-09 12:50:17 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>, #> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>, #> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr> #> # breakpoint_S_R <chr>, site <chr>

2
reference/atc_online.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <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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2
reference/av_from_text.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/av_property.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/availability.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/bug_drug_combinations.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/clinical_breakpoints.html
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@@ -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> <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="">3.0.1.9019</small> <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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2
reference/count.html
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@@ -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> <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="">3.0.1.9019</small> <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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2
reference/custom_eucast_rules.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/custom_mdro_guideline.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/dosage.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/esbl_isolates.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/example_isolates.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/example_isolates_unclean.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/export_ncbi_biosample.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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6803
reference/first_isolate.html
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6801
reference/first_isolate.md
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File diff suppressed because it is too large Load Diff

2
reference/g.test.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/get_episode.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
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> <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="">3.0.1.9019</small> <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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9
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> <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="">3.0.1.9019</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -257,13 +257,6 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">age_group</span>, <span class="va">CIP</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="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">age_group</span>, <span class="va">CIP</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="r-in"><span> <span class="fu">ggplot_sir</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"age_group"</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu">ggplot_sir</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"age_group"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 1131 warnings in `mutate()`.</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: `first_isolate = first_isolate()`.</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> in <span style="background-color: #444444;">`as.sir()`</span>: 7 results in column 'first_isolate' truncated (18%) that</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> were invalid antimicrobial interpretations: "."</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 1130 remaining warnings.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 6 rows containing missing values or values outside the scale range</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 6 rows containing missing values or values outside the scale range</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (`geom_col()`).</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> (`geom_col()`).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 6 rows containing missing values or values outside the scale range</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 6 rows containing missing values or values outside the scale range</span>

7
reference/ggplot_sir.md
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@@ -267,13 +267,6 @@ if (require("ggplot2") && require("dplyr")) {
select(age_group, CIP) %>% select(age_group, CIP) %>%
ggplot_sir(x = "age_group") ggplot_sir(x = "age_group")
} }
#> Warning: There were 1131 warnings in `mutate()`.
#> The first warning was:
#> ℹ In argument: `first_isolate = first_isolate()`.
#> Caused by warning:
#> ! in `as.sir()`: 7 results in column 'first_isolate' truncated (18%) that
#> were invalid antimicrobial interpretations: "."
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1130 remaining warnings.
#> Warning: Removed 6 rows containing missing values or values outside the scale range #> Warning: Removed 6 rows containing missing values or values outside the scale range
#> (`geom_col()`). #> (`geom_col()`).
#> Warning: Removed 6 rows containing missing values or values outside the scale range #> Warning: Removed 6 rows containing missing values or values outside the scale range

2
reference/guess_ab_col.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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2
reference/index.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">3.0.1.9019</small> <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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26
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> <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="">3.0.1.9019</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -64,19 +64,21 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
<div class="section level2"> <div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <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">interpretive_rules</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</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> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">interpretive_rules</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> <span class="st">"EUCAST"</span><span class="op">)</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_interpretive_rules"</span>, default <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"breakpoints"</span>,</span> <span> rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_interpretive_rules"</span>, default <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"breakpoints"</span>,</span>
<span> <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, version_breakpoints <span class="op">=</span> <span class="fl">15</span>,</span> <span> <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</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>
<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, version_breakpoints <span class="op">=</span> <span class="fl">15</span>,</span>
<span> version_expected_phenotypes <span class="op">=</span> <span class="fl">1.2</span>, version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,</span> <span> version_expected_phenotypes <span class="op">=</span> <span class="fl">1.2</span>, version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,</span>
<span> ampc_cephalosporin_resistance <span class="op">=</span> <span class="cn">NA</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span> <span> ampc_cephalosporin_resistance <span class="op">=</span> <span class="cn">NA</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
<span> custom_rules <span class="op">=</span> <span class="cn">NULL</span>, overwrite <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span> <span> custom_rules <span class="op">=</span> <span class="cn">NULL</span>, overwrite <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="fu">eucast_rules</span><span class="op">(</span><span class="va">x</span>, rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_interpretive_rules"</span>, default <span class="op">=</span></span> <span><span class="fu">eucast_rules</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"breakpoints"</span>, <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span> <span> rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_interpretive_rules"</span>, default <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"breakpoints"</span>,</span>
<span> <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="fu">clsi_rules</span><span class="op">(</span><span class="va">x</span>, rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_interpretive_rules"</span>, default <span class="op">=</span></span> <span><span class="fu">clsi_rules</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"breakpoints"</span>, <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span> <span> rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_interpretive_rules"</span>, default <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"breakpoints"</span>,</span>
<span> <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="va">ab</span>, administration <span class="op">=</span> <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">15</span><span class="op">)</span></span></code></pre></div> <span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="va">ab</span>, administration <span class="op">=</span> <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">15</span><span class="op">)</span></span></code></pre></div>
</div> </div>
@@ -106,10 +108,6 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dd><p>Column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd> <dd><p>Column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
<dd><p>A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option <code><a href="AMR-options.html">AMR_guideline</a></code>.</p></dd>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt> <dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.</p></dd> <dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.</p></dd>
@@ -118,6 +116,10 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expected_phenotypes"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expected_phenotypes")</code>. The default value can be set to another value using the package option <code><a href="AMR-options.html">AMR_interpretive_rules</a></code>: <code>options(AMR_interpretive_rules = "all")</code>. If using <code>"custom"</code>, be sure to fill in argument <code>custom_rules</code> too. Custom rules can be created with <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>.</p></dd> <dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expected_phenotypes"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expected_phenotypes")</code>. The default value can be set to another value using the package option <code><a href="AMR-options.html">AMR_interpretive_rules</a></code>: <code>options(AMR_interpretive_rules = "all")</code>. If using <code>"custom"</code>, be sure to fill in argument <code>custom_rules</code> too. Custom rules can be created with <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>.</p></dd>
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
<dd><p>A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option <code><a href="AMR-options.html">AMR_guideline</a></code>.</p></dd>
<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt> <dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.</p></dd> <dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.</p></dd>

28
reference/interpretive_rules.md
View File

@@ -22,19 +22,21 @@ at default, see *Details*.
## Usage ## Usage
``` r ``` r
interpretive_rules(x, col_mo = NULL, guideline = getOption("AMR_guideline", interpretive_rules(x, col_mo = NULL, info = interactive(),
"EUCAST"), info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints", rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), verbose = FALSE, version_breakpoints = 15, "expected_phenotypes")), guideline = getOption("AMR_guideline", "EUCAST"),
verbose = FALSE, version_breakpoints = 15,
version_expected_phenotypes = 1.2, version_expertrules = 3.3, version_expected_phenotypes = 1.2, version_expertrules = 3.3,
ampc_cephalosporin_resistance = NA, only_sir_columns = any(is.sir(x)), ampc_cephalosporin_resistance = NA, only_sir_columns = any(is.sir(x)),
custom_rules = NULL, overwrite = FALSE, ...) custom_rules = NULL, overwrite = FALSE, ...)
eucast_rules(x, rules = getOption("AMR_interpretive_rules", default = eucast_rules(x, col_mo = NULL, info = interactive(),
c("breakpoints", "expected_phenotypes")), ...) rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), ...)
clsi_rules(x, rules = getOption("AMR_interpretive_rules", default = clsi_rules(x, col_mo = NULL, info = interactive(),
c("breakpoints", "expected_phenotypes")), ...) rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), ...)
eucast_dosage(ab, administration = "iv", version_breakpoints = 15) eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
``` ```
@@ -87,12 +89,6 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
[`mo`](https://amr-for-r.org/reference/as.mo.md). Values will be [`mo`](https://amr-for-r.org/reference/as.mo.md). Values will be
coerced using [`as.mo()`](https://amr-for-r.org/reference/as.mo.md). coerced using [`as.mo()`](https://amr-for-r.org/reference/as.mo.md).
- guideline:
A guideline name, either "EUCAST" (default) or "CLSI". This can be set
with the package option
[`AMR_guideline`](https://amr-for-r.org/reference/AMR-options.md).
- info: - info:
A [logical](https://rdrr.io/r/base/logical.html) to indicate whether A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
@@ -113,6 +109,12 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
created with created with
[`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md). [`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md).
- guideline:
A guideline name, either "EUCAST" (default) or "CLSI". This can be set
with the package option
[`AMR_guideline`](https://amr-for-r.org/reference/AMR-options.md).
- verbose: - verbose:
A [logical](https://rdrr.io/r/base/logical.html) to turn Verbose mode A [logical](https://rdrr.io/r/base/logical.html) to turn Verbose mode

2
reference/intrinsic_resistant.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/italicise_taxonomy.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/join.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

14
reference/key_antimicrobials.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -168,14 +168,10 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># those strings can be compared with:</span></span></span> <span class="r-in"><span><span class="co"># those strings can be compared with:</span></span></span>
<span class="r-in"><span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #444444;">`as.sir()`</span>: 4 results truncated (33%) that were invalid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretations: "."</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
<span class="r-in"><span><span class="co"># TRUE, because I is ignored (as well as missing values)</span></span></span> <span class="r-in"><span><span class="co"># TRUE, because I is ignored (as well as missing values)</span></span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span>, ignore_I <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span>, ignore_I <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #444444;">`as.sir()`</span>: 4 results truncated (33%) that were invalid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretations: "."</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
<span class="r-in"><span><span class="co"># FALSE, because I is not ignored and so the 4th [character] differs</span></span></span> <span class="r-in"><span><span class="co"># FALSE, because I is not ignored and so the 4th [character] differs</span></span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
@@ -195,14 +191,6 @@
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_regular</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_regular</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_weighted</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_weighted</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 823 warnings in `mutate()`.</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: `first_weighted = first_isolate(col_keyantimicrobials =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "keyab")`.</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> in <span style="background-color: #444444;">`as.sir()`</span>: 1 result in column 'first_weighted' truncated (8%) that were</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> invalid antimicrobial interpretations: "."</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 822 remaining warnings.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1383</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1383</span>
<span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div> </code></pre></div>

12
reference/key_antimicrobials.md
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@@ -195,14 +195,10 @@ strainB <- "SSSIRSSSRSSS"
# those strings can be compared with: # those strings can be compared with:
antimicrobials_equal(strainA, strainB, type = "keyantimicrobials") antimicrobials_equal(strainA, strainB, type = "keyantimicrobials")
#> Warning: in `as.sir()`: 4 results truncated (33%) that were invalid antimicrobial
#> interpretations: "."
#> [1] TRUE #> [1] TRUE
# TRUE, because I is ignored (as well as missing values) # TRUE, because I is ignored (as well as missing values)
antimicrobials_equal(strainA, strainB, type = "keyantimicrobials", ignore_I = FALSE) antimicrobials_equal(strainA, strainB, type = "keyantimicrobials", ignore_I = FALSE)
#> Warning: in `as.sir()`: 4 results truncated (33%) that were invalid antimicrobial
#> interpretations: "."
#> [1] FALSE #> [1] FALSE
# FALSE, because I is not ignored and so the 4th [character] differs # FALSE, because I is not ignored and so the 4th [character] differs
@@ -222,14 +218,6 @@ if (require("dplyr")) {
sum(my_patients$first_regular, na.rm = TRUE) sum(my_patients$first_regular, na.rm = TRUE)
sum(my_patients$first_weighted, na.rm = TRUE) sum(my_patients$first_weighted, na.rm = TRUE)
} }
#> Warning: There were 823 warnings in `mutate()`.
#> The first warning was:
#> ℹ In argument: `first_weighted = first_isolate(col_keyantimicrobials =
#> "keyab")`.
#> Caused by warning:
#> ! in `as.sir()`: 1 result in column 'first_weighted' truncated (8%) that were
#> invalid antimicrobial interpretations: "."
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 822 remaining warnings.
#> [1] 1383 #> [1] 1383
# } # }
``` ```

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@@ -7,7 +7,7 @@
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reference/like.html
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@@ -7,7 +7,7 @@
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reference/mean_amr_distance.html
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@@ -7,7 +7,7 @@
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reference/microorganisms.codes.html
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reference/microorganisms.groups.html
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@@ -7,7 +7,7 @@
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reference/microorganisms.html
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
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reference/mo_matching_score.html
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@@ -7,7 +7,7 @@
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reference/mo_property.html
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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
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@@ -7,7 +7,7 @@
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reference/plot.html
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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reference/proportion.html
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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@@ -7,7 +7,7 @@
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@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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