P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-07-12 15:50:55 +02:00
Code Releases Activity

Built site for AMR@3.0.1.9084: 9237bfb

Browse Source
This commit is contained in:
github-actions
2026-07-09 15:31:07 +00:00
parent 2fc13ce76c
commit 91acb769c9
96 changed files with 239 additions and 278 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
404.html
View File

@@ -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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
CLAUDE.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
LICENSE-text.html
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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">

10
articles/AMR.html
View File

@@ -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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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 03 July 2026.</p>
generated on 09 July 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">2026-07-03</td>
<td align="center">2026-07-09</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">2026-07-03</td>
<td align="center">2026-07-09</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">2026-07-03</td>
<td align="center">2026-07-09</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

8
articles/AMR.md
View File

@@ -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 03 July 2026.
methodology remains unchanged. This page was generated on 09 July 2026.
## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-07-03 | abcd | Escherichia coli | S | S |
| 2026-07-03 | abcd | Escherichia coli | S | R |
| 2026-07-03 | efgh | Escherichia coli | R | S |
| 2026-07-09 | abcd | Escherichia coli | S | S |
| 2026-07-09 | abcd | Escherichia coli | S | R |
| 2026-07-09 | efgh | Escherichia coli | R | S |
### Needed R packages

2
articles/AMR_for_Python.html
View File

@@ -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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/AMR_with_tidymodels.html
View File

@@ -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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/EUCAST.html
View File

@@ -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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
articles/PCA.html
View File

@@ -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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">
@@ -196,7 +196,7 @@ function:</p>
<span><span class="co">#&gt; [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co">#&gt; Importance of components:</span></span>
<span><span class="co">#&gt; PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
<span><span class="co">#&gt; Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co">#&gt; Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>

2
articles/PCA.md
View File

@@ -119,7 +119,7 @@ summary(pca_result)
#> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"
#> Importance of components:
#> PC1 PC2 PC3 PC4 PC5 PC6 PC7
#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16
#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17
#> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00
#> Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00
```

2
articles/WHONET.html
View File

@@ -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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/WISCA.html
View File

@@ -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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

18
articles/datasets.html
View File

@@ -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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">03 July 2026</h4>
<h4 data-toc-skip class="date">09 July 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>
@@ -441,8 +441,8 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antimicrobials</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 June 2026 12:31:58 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
<p>It was last updated on 9 July 2026 15:14:59 UTC. Find more info about
the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@@ -612,20 +612,20 @@ inhibitors</td>
<code>clinical_breakpoints</code>: Interpretation from MIC values
&amp; disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
</h2>
<p>A data set with 45 555 rows and 14 columns, containing the following
<p>A data set with 45 735 rows and 14 columns, containing the following
column names:<br><em>guideline</em>, <em>type</em>, <em>host</em>, <em>method</em>,
<em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>,
<em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>,
<em>breakpoint_R</em>, <em>uti</em>, and <em>is_SDD</em>.</p>
<p>This data set is in R available as <code>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 22 June 2026 23:38:13 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/clinical_breakpoints.html">data
<p>It was last updated on 9 July 2026 15:14:59 UTC. Find more info about
the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/clinical_breakpoints.html">data
set here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.rds" class="external-link">original
R Data Structure (RDS) file</a> (92 kB)<br>
R Data Structure (RDS) file</a> (93 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.txt" class="external-link">tab-separated
text file</a> (4.2 MB)<br>
@@ -637,7 +637,7 @@ Excel workbook</a> (2.7 MB)<br>
Feather file</a> (2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.parquet" class="external-link">Apache
Parquet file</a> (0.1 MB)<br>
Parquet file</a> (0.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.sav" class="external-link">IBM
SPSS Statistics data file</a> (7.5 MB)<br>

10
articles/datasets.md
View File

@@ -100,7 +100,7 @@ names:
This data set is in R available as `antimicrobials`, after you load the
`AMR` package.
It was last updated on 27 June 2026 12:31:58 UTC. Find more info about
It was last updated on 9 July 2026 15:14:59 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/antimicrobials.html).
@@ -147,7 +147,7 @@ as comma separated values.
## `clinical_breakpoints`: Interpretation from MIC values & disk diameters to SIR
A data set with 45 555 rows and 14 columns, containing the following
A data set with 45 735 rows and 14 columns, containing the following
column names:
*guideline*, *type*, *host*, *method*, *site*, *mo*, *rank_index*, *ab*,
*ref_tbl*, *disk_dose*, *breakpoint_S*, *breakpoint_R*, *uti*, and
@@ -156,7 +156,7 @@ column names:
This data set is in R available as `clinical_breakpoints`, after you
load the `AMR` package.
It was last updated on 22 June 2026 23:38:13 UTC. Find more info about
It was last updated on 9 July 2026 15:14:59 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/clinical_breakpoints.html).
@@ -164,7 +164,7 @@ here](https://amr-for-r.org/reference/clinical_breakpoints.html).
- Download as [original R Data Structure (RDS)
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.rds)
(92 kB)
(93 kB)
- Download as [tab-separated text
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.txt)
(4.2 MB)
@@ -176,7 +176,7 @@ here](https://amr-for-r.org/reference/clinical_breakpoints.html).
(2 MB)
- Download as [Apache Parquet
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.parquet)
(0.1 MB)
(0.2 MB)
- Download as [IBM SPSS Statistics data
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.sav)
(7.5 MB)

2
articles/index.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
authors.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">

86
index.html
View File

@@ -33,7 +33,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -112,7 +112,7 @@
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
<p>The <code>AMR</code> package is a peer-reviewed, <a href="#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of <a href="./authors.html">many different researchers</a> from around the globe to make this a successful and durable project! The <code>AMR</code> package was already cited <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC" class="external-link">over 100 times</a> in scientific research.</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated mei 2026) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated May 2026) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<div class="section level3">
<h3 id="used-in-over-175-countries-available-in-28-languages">Used in over 175 countries, available in 28 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-available-in-28-languages"></a>
</h3>
@@ -145,13 +145,11 @@
<span><span class="co">#&gt; ℹ Using column mo as input for `mo_fullname()`</span></span>
<span><span class="co">#&gt; ℹ Using column mo as input for `mo_is_gram_negative()`</span></span>
<span><span class="co">#&gt; ℹ Using column mo as input for `mo_is_intrinsic_resistant()`</span></span>
<span><span class="co">#&gt; ℹ Determining intrinsic resistance based on 'EUCAST Expected</span></span>
<span><span class="co">#&gt; Resistant Phenotypes' v1.2 (2023). This note will be shown</span></span>
<span><span class="co">#&gt; once per session.</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB</span></span>
<span><span class="co">#&gt; (tobramycin), AMK (amikacin), and KAN (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM</span></span>
<span><span class="co">#&gt; (meropenem)</span></span>
<span><span class="co">#&gt; ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023).</span></span>
<span><span class="co">#&gt; This note will be shown once per session.</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN</span></span>
<span><span class="co">#&gt; (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span>
<span><span class="co">#&gt; # A tibble: 35 × 7</span></span>
<span><span class="co">#&gt; bacteria GEN TOB AMK KAN IPM MEM </span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span></span>
@@ -180,9 +178,9 @@
<span><span class="co">#&gt; Warning: invalid microorganism code, NA generated</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="24%">
<col width="37%">
<col width="37%">
<col width="33%">
<col width="33%">
<col width="33%">
</colgroup>
<thead><tr>
<th align="left">Piperacillin/tazobactam</th>
@@ -190,9 +188,9 @@
<th align="left">Piperacillin/tazobactam + Tobramycin</th>
</tr></thead>
<tbody><tr>
<td align="left">70.1% (65.1-75.4%)</td>
<td align="left">93.6% (92.1-95%)</td>
<td align="left">89.8% (87.3-92.4%)</td>
<td align="left">70% (64.8-75.2%)</td>
<td align="left">93.6% (92-95.1%)</td>
<td align="left">89.9% (87.1-92.5%)</td>
</tr></tbody>
</table>
<p>WISCA supports stratification by any clinical variable, so you can generate syndrome-specific or ward-specific coverage estimates:</p>
@@ -204,10 +202,10 @@
<span><span class="co">#&gt; Warning: invalid microorganism code, NA generated</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="14%">
<col width="21%">
<col width="32%">
<col width="32%">
<col width="25%">
<col width="25%">
<col width="25%">
<col width="25%">
</colgroup>
<thead><tr>
<th align="left">Syndromic Group</th>
@@ -218,21 +216,21 @@
<tbody>
<tr>
<td align="left">Clinical</td>
<td align="left">74.4% (68.2-79.9%)</td>
<td align="left">93.6% (91.9-95.1%)</td>
<td align="left">90.4% (86.9-93.3%)</td>
<td align="left">74.6% (69.3-80.3%)</td>
<td align="left">93.6% (92.1-95%)</td>
<td align="left">90.4% (87-93.2%)</td>
</tr>
<tr>
<td align="left">ICU</td>
<td align="left">57% (48.6-65.9%)</td>
<td align="left">86.8% (83.4-89.8%)</td>
<td align="left">82.9% (77.5-87.1%)</td>
<td align="left">56.9% (48.2-66.3%)</td>
<td align="left">86.7% (83.4-89.7%)</td>
<td align="left">82.9% (78.1-87.3%)</td>
</tr>
<tr>
<td align="left">Outpatient</td>
<td align="left">57.5% (45.9-69.3%)</td>
<td align="left">76.6% (70.6-82.3%)</td>
<td align="left">67.9% (57.6-77.2%)</td>
<td align="left">57.3% (45.8-69.1%)</td>
<td align="left">76.6% (70.6-81.9%)</td>
<td align="left">67.9% (58-76.9%)</td>
</tr>
</tbody>
</table>
@@ -241,15 +239,14 @@
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"TZP"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM</span></span>
<span><span class="co">#&gt; (meropenem)</span></span></code></pre></div>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="13%">
<col width="25%">
<col width="18%">
<col width="19%">
<col width="22%">
<col width="20%">
<col width="20%">
<col width="20%">
<col width="20%">
<col width="20%">
</colgroup>
<thead><tr>
<th align="left">Pathogen</th>
@@ -282,10 +279,10 @@
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="12%">
<col width="21%">
<col width="32%">
<col width="32%">
<col width="25%">
<col width="25%">
<col width="25%">
<col width="25%">
</colgroup>
<thead><tr>
<th align="left">Pathogen</th>
@@ -407,16 +404,15 @@
<span> <span class="co"># calculate AMR using resistance(), over all aminoglycosides and polymyxins:</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
<span> <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB</span></span>
<span><span class="co">#&gt; (tobramycin), AMK (amikacin), and KAN (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN</span></span>
<span><span class="co">#&gt; (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `polymyxins()` using column COL (colistin)</span></span>
<span><span class="co">#&gt; Warning: There was 1 warning in `summarise()`.</span></span>
<span><span class="co">#&gt; ℹ In argument: `across(c(aminoglycosides(), polymyxins()),</span></span>
<span><span class="co">#&gt; resistance)`.</span></span>
<span><span class="co">#&gt; ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.</span></span>
<span><span class="co">#&gt; ℹ In group 3: `ward = "Outpatient"`.</span></span>
<span><span class="co">#&gt; Caused by warning:</span></span>
<span><span class="co">#&gt; ! Introducing NA: only 23 results available for KAN in group:</span></span>
<span><span class="co">#&gt; ward = "Outpatient" (whilst `minimum = 30`).</span></span>
<span><span class="co">#&gt; ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (whilst `minimum =</span></span>
<span><span class="co">#&gt; 30`).</span></span>
<span><span class="va">out</span></span>
<span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
<span><span class="co">#&gt; ward GEN TOB AMK KAN COL</span></span>

36
index.md
View File

@@ -48,7 +48,7 @@ in scientific research.
After installing this package, R knows [**~97 000 distinct microbial
species**](https://amr-for-r.org/reference/microorganisms.md) (updated
mei 2026) and all [**~620 antimicrobial and antiviral
May 2026) and all [**~620 antimicrobial and antiviral
drugs**](https://amr-for-r.org/reference/antimicrobials.md) by name and
code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
CT), and knows all about valid SIR and MIC values. The integral clinical
@@ -114,13 +114,11 @@ example_isolates %>%
#> ℹ Using column mo as input for `mo_fullname()`
#> ℹ Using column mo as input for `mo_is_gram_negative()`
#> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected
#> Resistant Phenotypes' v1.2 (2023). This note will be shown
#> once per session.
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
#> (tobramycin), AMK (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
#> (meropenem)
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023).
#> This note will be shown once per session.
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
#> (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 35 × 7
#> bacteria GEN TOB AMK KAN IPM MEM
#> <chr> <sir> <sir> <sir> <sir> <sir> <sir>
@@ -179,7 +177,7 @@ wisca(example_isolates,
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|
| 70.1% (65.1-75.4%) | 93.6% (92.1-95%) | 89.8% (87.3-92.4%) |
| 70% (64.8-75.2%) | 93.6% (92-95.1%) | 89.9% (87.1-92.5%) |
WISCA supports stratification by any clinical variable, so you can
generate syndrome-specific or ward-specific coverage estimates:
@@ -195,9 +193,9 @@ wisca(example_isolates,
| Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|:---|
| Clinical | 74.4% (68.2-79.9%) | 93.6% (91.9-95.1%) | 90.4% (86.9-93.3%) |
| ICU | 57% (48.6-65.9%) | 86.8% (83.4-89.8%) | 82.9% (77.5-87.1%) |
| Outpatient | 57.5% (45.9-69.3%) | 76.6% (70.6-82.3%) | 67.9% (57.6-77.2%) |
| Clinical | 74.6% (69.3-80.3%) | 93.6% (92.1-95%) | 90.4% (87-93.2%) |
| ICU | 56.9% (48.2-66.3%) | 86.7% (83.4-89.7%) | 82.9% (78.1-87.3%) |
| Outpatient | 57.3% (45.8-69.1%) | 76.6% (70.6-81.9%) | 67.9% (58-76.9%) |
**For AMR surveillance**, traditional antibiograms remain the right tool
for tracking resistance per species over time:
@@ -207,8 +205,7 @@ for tracking resistance per species over time:
antibiogram(example_isolates,
mo_transform = "gramstain",
antimicrobials = c("AMC", carbapenems(), "TZP"))
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
#> (meropenem)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
```
| Pathogen | Amoxicillin/clavulanic acid | Imipenem | Meropenem | Piperacillin/tazobactam |
@@ -329,16 +326,15 @@ out <- example_isolates %>%
# calculate AMR using resistance(), over all aminoglycosides and polymyxins:
summarise(across(c(aminoglycosides(), polymyxins()),
resistance))
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
#> (tobramycin), AMK (amikacin), and KAN (kanamycin)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
#> (kanamycin)
#> ℹ For `polymyxins()` using column COL (colistin)
#> Warning: There was 1 warning in `summarise()`.
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()),
#> resistance)`.
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
#> ℹ In group 3: `ward = "Outpatient"`.
#> Caused by warning:
#> ! Introducing NA: only 23 results available for KAN in group:
#> ward = "Outpatient" (whilst `minimum = 30`).
#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (whilst `minimum =
#> 30`).
out
#> # A tibble: 3 × 6
#> ward GEN TOB AMK KAN COL

36
llms.txt
View File

@@ -48,7 +48,7 @@ in scientific research.
After installing this package, R knows [**~97 000 distinct microbial
species**](https://amr-for-r.org/reference/microorganisms.md) (updated
mei 2026) and all [**~620 antimicrobial and antiviral
May 2026) and all [**~620 antimicrobial and antiviral
drugs**](https://amr-for-r.org/reference/antimicrobials.md) by name and
code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
CT), and knows all about valid SIR and MIC values. The integral clinical
@@ -114,13 +114,11 @@ example_isolates %>%
#> ℹ Using column mo as input for `mo_fullname()`
#> ℹ Using column mo as input for `mo_is_gram_negative()`
#> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected
#> Resistant Phenotypes' v1.2 (2023). This note will be shown
#> once per session.
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
#> (tobramycin), AMK (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
#> (meropenem)
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023).
#> This note will be shown once per session.
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
#> (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 35 × 7
#> bacteria GEN TOB AMK KAN IPM MEM
#> <chr> <sir> <sir> <sir> <sir> <sir> <sir>
@@ -179,7 +177,7 @@ wisca(example_isolates,
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|
| 70.1% (65.1-75.4%) | 93.6% (92.1-95%) | 89.8% (87.3-92.4%) |
| 70% (64.8-75.2%) | 93.6% (92-95.1%) | 89.9% (87.1-92.5%) |
WISCA supports stratification by any clinical variable, so you can
generate syndrome-specific or ward-specific coverage estimates:
@@ -195,9 +193,9 @@ wisca(example_isolates,
| Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|:---|
| Clinical | 74.4% (68.2-79.9%) | 93.6% (91.9-95.1%) | 90.4% (86.9-93.3%) |
| ICU | 57% (48.6-65.9%) | 86.8% (83.4-89.8%) | 82.9% (77.5-87.1%) |
| Outpatient | 57.5% (45.9-69.3%) | 76.6% (70.6-82.3%) | 67.9% (57.6-77.2%) |
| Clinical | 74.6% (69.3-80.3%) | 93.6% (92.1-95%) | 90.4% (87-93.2%) |
| ICU | 56.9% (48.2-66.3%) | 86.7% (83.4-89.7%) | 82.9% (78.1-87.3%) |
| Outpatient | 57.3% (45.8-69.1%) | 76.6% (70.6-81.9%) | 67.9% (58-76.9%) |
**For AMR surveillance**, traditional antibiograms remain the right tool
for tracking resistance per species over time:
@@ -207,8 +205,7 @@ for tracking resistance per species over time:
antibiogram(example_isolates,
mo_transform = "gramstain",
antimicrobials = c("AMC", carbapenems(), "TZP"))
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
#> (meropenem)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
```
| Pathogen | Amoxicillin/clavulanic acid | Imipenem | Meropenem | Piperacillin/tazobactam |
@@ -329,16 +326,15 @@ out <- example_isolates %>%
# calculate AMR using resistance(), over all aminoglycosides and polymyxins:
summarise(across(c(aminoglycosides(), polymyxins()),
resistance))
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
#> (tobramycin), AMK (amikacin), and KAN (kanamycin)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
#> (kanamycin)
#> ℹ For `polymyxins()` using column COL (colistin)
#> Warning: There was 1 warning in `summarise()`.
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()),
#> resistance)`.
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
#> ℹ In group 3: `ward = "Outpatient"`.
#> Caused by warning:
#> ! Introducing NA: only 23 results available for KAN in group:
#> ward = "Outpatient" (whilst `minimum = 30`).
#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (whilst `minimum =
#> 30`).
out
#> # A tibble: 3 × 6
#> ward GEN TOB AMK KAN COL

12
news/index.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">
@@ -49,15 +49,15 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9083" id="amr-3019083">AMR 3.0.1.9083<a class="anchor" aria-label="anchor" href="#amr-3019083"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9084" id="amr-3019084">AMR 3.0.1.9084<a class="anchor" aria-label="anchor" href="#amr-3019084"></a></h2>
<p>Planned as v3.1.0, end of June 2026.</p>
<div class="section level4">
<h4 id="breaking-changes-3-0-1-9083">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9083"></a></h4>
<h4 id="breaking-changes-3-0-1-9084">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9084"></a></h4>
<ul><li>The former <em>kingdoms</em> Bacteria and Archaea are now each divided into four kingdoms with new top-level <em>domains</em> ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new <code>domain</code> column in the <code>microorganisms</code> data set was added, and more importantly, <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal kingdom (e.g. <code>"Pseudomonadati"</code> instead of <code>"Bacteria"</code>). Use <code><a href="../reference/mo_property.html">mo_domain()</a></code> for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), <code>kingdom</code> and <code>domain</code> are identical.</li>
<li>Faster parallel computing via the <code>future</code> package for <code><a href="../reference/as.sir.html">as.sir()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>.</li>
</ul></div>
<div class="section level4">
<h4 id="new-3-0-1-9083">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9083"></a></h4>
<h4 id="new-3-0-1-9084">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9084"></a></h4>
<ul><li>EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the <code>clinical_breakpoints</code> data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations</li>
<li>Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting <code>breakpoint_type = "ECOFF"</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code>; WT/NWT results are fully supported in all resistance/susceptibility functions and plots (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li>
<li>
@@ -74,7 +74,7 @@
<li>New <code><a href="../reference/antibiogram.html">wisca_plot()</a></code> to assess the susceptibility and incidence distributions from the Monte Carlo simulations</li>
</ul></div>
<div class="section level4">
<h4 id="fixed-3-0-1-9083">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9083"></a></h4>
<h4 id="fixed-3-0-1-9084">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9084"></a></h4>
<ul><li>Setting <code>options(AMR_guideline = "EUCAST 2012")</code> or any year-qualified value no longer causes errors or silent wrong behaviour in <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, <code><a href="../reference/proportion.html">resistance()</a></code>, <code><a href="../reference/proportion.html">susceptibility()</a></code>, <code><a href="../reference/count.html">count_resistant()</a></code>, <code><a href="../reference/count.html">count_susceptible()</a></code>, and SIR plotting/printing functions (<a href="https://github.com/msberends/AMR/issues/298" class="external-link">#298</a>)</li>
<li>
<code><a href="../reference/as.sir.html">as.sir()</a></code>
@@ -103,7 +103,7 @@
</li>
</ul></div>
<div class="section level4">
<h4 id="updated-3-0-1-9083">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9083"></a></h4>
<h4 id="updated-3-0-1-9084">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9084"></a></h4>
<ul><li>
<code><a href="../reference/top_n_microorganisms.html">top_n_microorganisms()</a></code>: new <code>property_for_each</code> argument for sub-grouping within top <em>n</em> groups; rank ordering enforced (only lower taxonomic ranks allowed); fixed <code>property = NULL</code> not being accepted; inner filter now tracks original row indices to prevent cross-group contamination</li>
<li>Taxonomic update for all microorganisms, now updated to June 2026</li>

2
news/index.md
View File

@@ -1,6 +1,6 @@
# Changelog
## AMR 3.0.1.9083
## AMR 3.0.1.9084
Planned as v3.1.0, end of June 2026.

4
pkgdown.yml
View File

@@ -1,5 +1,5 @@
pandoc: 3.8.3
pkgdown: 2.2.0
pkgdown: 2.2.1
pkgdown_sha: ~
articles:
AMR_for_Python: AMR_for_Python.html
@@ -10,7 +10,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2026-07-03T17:47Z
last_built: 2026-07-09T15:23Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles

2
reference/AMR-deprecated.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/AMR-options.html
View File

@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

8
reference/AMR.html
View File

@@ -5,14 +5,14 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~97 000 distinct microbial species (updated mei 2026) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
After installing this package, R knows ~97 000 distinct microbial species (updated May 2026) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:description" content="Welcome to the AMR package.
The AMR package is a peer-reviewed, free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of many different researchers from around the globe to make this a successful and durable project!
This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~97 000 distinct microbial species (updated mei 2026) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
After installing this package, R knows ~97 000 distinct microbial species (updated May 2026) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -70,7 +70,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">doi:10.33612/diss.177417131</a>
and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a>
).</p>
<p>After installing this package, R knows <a href="https://amr-for-r.org/reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated mei 2026) and all <a href="https://amr-for-r.org/reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<p>After installing this package, R knows <a href="https://amr-for-r.org/reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated May 2026) and all <a href="https://amr-for-r.org/reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<p>The <code>AMR</code> package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
</div>

2
reference/AMR.md
View File

@@ -25,7 +25,7 @@ and
After installing this package, R knows [**~97 000 distinct microbial
species**](https://amr-for-r.org/reference/microorganisms.html) (updated
mei 2026) and all [**~620 antimicrobial and antiviral
May 2026) and all [**~620 antimicrobial and antiviral
drugs**](https://amr-for-r.org/reference/antimicrobials.html) by name
and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
CT), and knows all about valid SIR and MIC values. The integral clinical

2
reference/WHOCC.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/WHONET.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/ab_from_text.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/ab_property.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/add_custom_antimicrobials.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/add_custom_microorganisms.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

22
reference/age.html
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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -112,16 +112,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 27 27.00822 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.42466 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.57534 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.33973 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.66849 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.38082 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.36712 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.47671 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.84932 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.43288 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 27 27.02466 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.44110 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.59178 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.35616 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.68493 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.39726 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.38356 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.49315 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.86575 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.44932 21</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

20
reference/age.md
View File

@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
df
#> birth_date age age_exact age_at_y2k
#> 1 1999-06-30 27 27.00822 0
#> 2 1968-01-29 58 58.42466 31
#> 3 1965-12-05 60 60.57534 34
#> 4 1980-03-01 46 46.33973 19
#> 5 1949-11-01 76 76.66849 50
#> 6 1947-02-14 79 79.38082 52
#> 7 1940-02-19 86 86.36712 59
#> 8 1988-01-10 38 38.47671 11
#> 9 1997-08-27 28 28.84932 2
#> 10 1978-01-26 48 48.43288 21
#> 1 1999-06-30 27 27.02466 0
#> 2 1968-01-29 58 58.44110 31
#> 3 1965-12-05 60 60.59178 34
#> 4 1980-03-01 46 46.35616 19
#> 5 1949-11-01 76 76.68493 50
#> 6 1947-02-14 79 79.39726 52
#> 7 1940-02-19 86 86.38356 59
#> 8 1988-01-10 38 38.49315 11
#> 9 1997-08-27 28 28.86575 2
#> 10 1978-01-26 48 48.44932 21
```

2
reference/age_groups.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/amr-tidymodels.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/amr_course.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/antibiogram.html
View File

@@ -13,7 +13,7 @@ All antibiogram types adhere to previously described approaches (see Source), an
<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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/antimicrobial_selectors.html
View File

@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/antimicrobials.html
View File

@@ -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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/as.ab.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/as.av.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/as.disk.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/as.mic.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/as.mo.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">

10
reference/as.sir.html
View File

@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">
@@ -462,10 +462,10 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-07-03 <span style="color: #949494;">17:49:48</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> 2026-07-03 <span style="color: #949494;">17:49:49</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> 2026-07-03 <span style="color: #949494;">17:49:49</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> 2026-07-03 <span style="color: #949494;">17:49:49</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> 2026-07-09 <span style="color: #949494;">15:26:20</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> 2026-07-09 <span style="color: #949494;">15:26:21</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> 2026-07-09 <span style="color: #949494;">15:26:21</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> 2026-07-09 <span style="color: #949494;">15:26:21</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>

8
reference/as.sir.md
View File

@@ -712,10 +712,10 @@ 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 2026-07-03 17:49:48 1 MIC amoxicillin Escherich… human 8
#> 2 2026-07-03 17:49:49 1 MIC cipro Escherich… human 0.256
#> 3 2026-07-03 17:49:49 1 DISK tobra Escherich… human 16
#> 4 2026-07-03 17:49:49 1 DISK genta Escherich… human 18
#> 1 2026-07-09 15:26:20 1 MIC amoxicillin Escherich… human 8
#> 2 2026-07-09 15:26:21 1 MIC cipro Escherich… human 0.256
#> 3 2026-07-09 15:26:21 1 DISK tobra Escherich… human 16
#> 4 2026-07-09 15:26:21 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr>

2
reference/atc_online.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/av_from_text.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/av_property.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/availability.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/bug_drug_combinations.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

8
reference/clinical_breakpoints.html
View File

@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">
@@ -78,7 +78,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 45 555 observations and 14 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 45 735 observations and 14 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
<li><p><code>type</code><br> Breakpoint type, either <code>"ECOFF"</code>, <code>"animal"</code>, or <code>"human"</code></p></li>
<li><p><code>host</code><br> Host of infectious agent. This is mostly useful for veterinary breakpoints and is either <code>"ECOFF"</code>, <code>"aquatic"</code>, <code>"cats"</code>, <code>"cattle"</code>, <code>"dogs"</code>, <code>"horse"</code>, <code>"human"</code>, <code>"poultry"</code>, or <code>"swine"</code></p></li>
<li><p><code>method</code><br> Testing method, either <code>"DISK"</code> or <code>"MIC"</code></p></li>
@@ -143,7 +143,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">clinical_breakpoints</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 45,555 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 45,735 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> guideline type host method site mo rank_index ab ref_tbl </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2026 human human DISK <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS 2 MEM A. xylo…</span>
@@ -156,7 +156,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2026 human human DISK Uncomp… <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2026 human human MIC <span style="color: #BB0000;">NA</span> <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EUCAST 2026 human human MIC Uncomp… <span style="color: #949494;">B_</span>ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 45,545 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 45,725 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5 more variables: disk_dose &lt;chr&gt;, breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># uti &lt;lgl&gt;, is_SDD &lt;lgl&gt;</span></span>
</code></pre></div>

6
reference/clinical_breakpoints.md
View File

@@ -26,7 +26,7 @@ clinical_breakpoints
## Format
A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 45
555 observations and 14 variables:
735 observations and 14 variables:
- `guideline`
Name of the guideline
@@ -154,7 +154,7 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
``` r
clinical_breakpoints
#> # A tibble: 45,555 × 14
#> # A tibble: 45,735 × 14
#> guideline type host method site mo rank_index ab ref_tbl
#> <chr> <chr> <chr> <chr> <chr> <mo> <dbl> <ab> <chr>
#> 1 EUCAST 2026 human human DISK NA B_ACHRMB_XYLS 2 MEM A. xylo…
@@ -167,7 +167,7 @@ clinical_breakpoints
#> 8 EUCAST 2026 human human DISK Uncomp… B_ACNTB 3 AMK Acineto…
#> 9 EUCAST 2026 human human MIC NA B_ACNTB 3 AMK Acineto…
#> 10 EUCAST 2026 human human MIC Uncomp… B_ACNTB 3 AMK Acineto…
#> # ℹ 45,545 more rows
#> # ℹ 45,725 more rows
#> # ℹ 5 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>,
#> # uti <lgl>, is_SDD <lgl>
```

2
reference/count.html
View File

@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/custom_interpretive_rules.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/custom_mdro_guideline.html
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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/dosage.html
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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/esbl_isolates.html
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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/example_isolates.html
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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/example_isolates_unclean.html
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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/export_ncbi_biosample.html
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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/first_isolate.html
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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
reference/g.test.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">
@@ -125,7 +125,7 @@
<dt>stdres</dt>
<dd><p>standardized residuals,
<code>(observed - expected) / sqrt(V)</code>, where <code>V</code> is the
residual cell variance (<a href="#reference+chisq.test.Rd+R+3AAgresti+3A2007" class="citation">Agresti 2007</a>, section 2.4.5)
residual cell variance (Agresti, 2007, section 2.4.5
for the case where <code>x</code> is a matrix, <code>n * p * (1 - p)</code> otherwise).</p></dd>
</dl></div>

5
reference/g.test.md
View File

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

2
reference/get_episode.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

7
reference/ggplot_pca.html
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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">
@@ -113,9 +113,8 @@
<dt id="arg-pc-biplot">pc.biplot<a class="anchor" aria-label="anchor" href="#arg-pc-biplot"></a></dt>
<dd><p>If true, use what <cite></cite><a href="#reference+biplot.princomp.Rd+R+3AGabriel+3A1971" class="citation">Gabriel (1971)</a> refers to as a
“principal component biplot”,
with <code>lambda = 1</code> and observations scaled up by sqrt(n) and
<dd><p>If true, use what Gabriel (1971) refers to as a "principal component
biplot", with <code>lambda = 1</code> and observations scaled up by sqrt(n) and
variables scaled down by sqrt(n). Then inner products between
variables approximate covariances and distances between observations
approximate Mahalanobis distance.</p></dd>

11
reference/ggplot_pca.md
View File

@@ -85,12 +85,11 @@ the changes made based on the source code were:
- pc.biplot:
If true, use what [Gabriel
(1971)](#reference+biplot.princomp.Rd+R+3AGabriel+3A1971) refers to as
a “principal component biplot”, with `lambda = 1` and observations
scaled up by sqrt(n) and variables scaled down by sqrt(n). Then inner
products between variables approximate covariances and distances
between observations approximate Mahalanobis distance.
If true, use what Gabriel (1971) refers to as a "principal component
biplot", with `lambda = 1` and observations scaled up by sqrt(n) and
variables scaled down by sqrt(n). Then inner products between
variables approximate covariances and distances between observations
approximate Mahalanobis distance.
- labels:

2
reference/ggplot_sir.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/guess_ab_col.html
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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/index.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">

11
reference/interpretive_rules.html
View File

@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</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">
@@ -212,13 +212,8 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
<ul><li><p>EUCAST Expert Rules. Version 2.0, 2012.<br>
Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60; <a href="https://doi.org/10.1111/j.1469-0691.2011.03703.x" class="external-link">doi:10.1111/j.1469-0691.2011.03703.x</a></p></li>
<li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf" class="external-link">(link)</a></p></li>
<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf" class="external-link">(link)</a></p></li>
<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf" class="external-link">(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx" class="external-link">(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx" class="external-link">(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx" class="external-link">(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 12.0, 2022. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.xlsx" class="external-link">(link)</a></p></li>
<li><p>EUCAST Expected Phenotypes. <a href="https://www.eucast.org/bacteria/important-additional-information/expected-phenotypes/" class="external-link">(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. <a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" class="external-link">(link)</a></p></li>
</ul></div>
<div class="section level2">

27
reference/interpretive_rules.md
View File

@@ -280,31 +280,12 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
testing.** *Clin Microbiol Infect.* 2013;19(2):141-60;
[doi:10.1111/j.1469-0691.2011.03703.x](https://doi.org/10.1111/j.1469-0691.2011.03703.x)
- EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes
Tables. Version 3.1, 2016.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf)
- EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf)
- EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf)
- EUCAST Expected Phenotypes.
[(link)](https://www.eucast.org/bacteria/important-additional-information/expected-phenotypes/)
- EUCAST Breakpoint tables for interpretation of MICs and zone
diameters. Version 9.0, 2019.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx)
- EUCAST Breakpoint tables for interpretation of MICs and zone
diameters. Version 10.0, 2020.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx)
- EUCAST Breakpoint tables for interpretation of MICs and zone
diameters. Version 11.0, 2021.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx)
- EUCAST Breakpoint tables for interpretation of MICs and zone
diameters. Version 12.0, 2022.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.xlsx)
diameters.
[(link)](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/)
## Examples

2
reference/intrinsic_resistant.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/italicise_taxonomy.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/join.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/key_antimicrobials.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/kurtosis.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/like.html
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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/mdro.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/mean_amr_distance.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/microorganisms.codes.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/microorganisms.groups.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/microorganisms.html
View File

@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/mo_matching_score.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/mo_property.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/mo_source.html
View File

@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/pca.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/plot.html
View File

@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/proportion.html
View File

@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/random.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/resistance_predict.html
View File

@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
<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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/skewness.html
View File

@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<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="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/top_n_microorganisms.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/translate.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9084</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
search.json
View File

File diff suppressed because one or more lines are too long