P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-02-09 03:12:57 +01:00
Code Releases Activity

Built site for AMR@3.0.1.9018: 2df2911

Browse Source
This commit is contained in:
github-actions
2026-01-16 10:08:12 +00:00
parent 86f19c7576
commit 0551ea51cb
100 changed files with 264 additions and 236 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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">

12
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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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 08 January 2026.</p>
generated on 16 January 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">2026-01-08</td>
<td align="center">2026-01-16</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">2026-01-08</td>
<td align="center">2026-01-16</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">2026-01-08</td>
<td align="center">2026-01-16</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -401,6 +401,8 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #BB0000;">ℹ Determining first isolates using an episode length of </span><span style="color: #BB0000; font-weight: bold;">365 days</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #444444;">`col_mo`</span><span style="color: #0000BB;">.</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">first</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; it seems to be cefozopran (ZOP)</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">date</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #444444;">`col_date`</span><span style="color: #0000BB;">.</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">patient_id</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #444444;">`col_patient_id`</span><span style="color: #0000BB;">.</span></span></span>
<span><span class="co">#&gt; <span style="color: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span></span>

10
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 08 January
methodology remains unchanged. This page was generated on 16 January
2026.
## Introduction
@@ -52,9 +52,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-01-08 | abcd | Escherichia coli | S | S |
| 2026-01-08 | abcd | Escherichia coli | S | R |
| 2026-01-08 | efgh | Escherichia coli | R | S |
| 2026-01-16 | abcd | Escherichia coli | S | S |
| 2026-01-16 | abcd | Escherichia coli | S | R |
| 2026-01-16 | efgh | Escherichia coli | R | S |
### Needed R packages
@@ -318,6 +318,8 @@ our_data <- our_data %>%
mutate(first = first_isolate(info = TRUE))
#> ℹ Determining first isolates using an episode length of 365 days
#> ℹ Using column 'bacteria' as input for `col_mo`.
#> ℹ Column 'first' is SIR eligible (despite only having empty values), since
#> it seems to be cefozopran (ZOP)
#> ℹ Using column 'date' as input for `col_date`.
#> ℹ Using column 'patient_id' as input for `col_patient_id`.
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold

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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
articles/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">08 January 2026</h4>
<h4 data-toc-skip class="date">16 January 2026</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@@ -424,7 +424,7 @@ 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 6 January 2026 22:08:50 UTC. Find more info
<p>It was last updated on 16 January 2026 09:57:03 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>

4
articles/datasets.md
View File

@@ -100,8 +100,8 @@ names:
This data set is in R available as `antimicrobials`, after you load the
`AMR` package.
It was last updated on 6 January 2026 22:08:50 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
It was last updated on 16 January 2026 09:57:03 UTC. Find more info
about the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/antimicrobials.html).
**Direct download links:**

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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
index.html
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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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
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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,9 +49,9 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9017" id="amr-3019017">AMR 3.0.1.9017<a class="anchor" aria-label="anchor" href="#amr-3019017"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9018" id="amr-3019018">AMR 3.0.1.9018<a class="anchor" aria-label="anchor" href="#amr-3019018"></a></h2>
<div class="section level4">
<h4 id="new-3-0-1-9017">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9017"></a></h4>
<h4 id="new-3-0-1-9018">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9018"></a></h4>
<ul><li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
<ul><li>
<code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code> to transform <code>&lt;mic&gt;</code> columns with log2, and <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code> to convert <code>&lt;sir&gt;</code> columns to numeric</li>
@@ -71,13 +71,20 @@
<li>AMR selectors <code><a href="../reference/antimicrobial_selectors.html">phosphonics()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">spiropyrimidinetriones()</a></code>
</li>
<li>
<code><a href="../reference/ab_property.html">ab_group()</a></code> gained an argument <code>all_groups</code> to return all groups the antimicrobial drug is in (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<code>antimicrobials$group</code> is now a <code>list</code> instead of a <code>character</code>, to contain any group the drug is in (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
</ul></div>
<div class="section level4">
<h4 id="changed-3-0-1-9017">Changed<a class="anchor" aria-label="anchor" href="#changed-3-0-1-9017"></a></h4>
<h4 id="fixes-3-0-1-9018">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9018"></a></h4>
<ul><li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li>
<li>Added taniborbactam (<code>TAN</code>) and cefepime/taniborbactam (<code>FTA</code>) to the <code>antimicrobials</code> data set</li>
<li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where for numeric input the arguments <code>S</code>, <code>i</code>, and <code>R</code> would not be considered (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
<li>Fixed some foreign translations of antimicrobial drugs</li>
<li>Fixed a bug for printing column names to the console when using <code>mutate_at(vars(...), as.mic)</code> (<a href="https://github.com/msberends/AMR/issues/249" class="external-link">#249</a>)</li>
</ul></div>
<div class="section level4">
<h4 id="updates-3-0-1-9018">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9018"></a></h4>
<ul><li>
<code><a href="../reference/ab_property.html">ab_group()</a></code> gained an argument <code>all_groups</code> to return all groups the antimicrobial drug is in (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<li>Added taniborbactam (<code>TAN</code>) and cefepime/taniborbactam (<code>FTA</code>) to the <code>antimicrobials</code> data set</li>
<li>Added explaining message to <code><a href="../reference/as.sir.html">as.sir()</a></code> when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
<li>Updated handling of capped MIC values (<code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, <code>&gt;=</code>) in <code><a href="../reference/as.sir.html">as.sir()</a></code> in the argument <code>capped_mic_handling</code>: (<a href="https://github.com/msberends/AMR/issues/243" class="external-link">#243</a>)
<ul><li>Introduced four clearly defined options: <code>"none"</code>, <code>"conservative"</code> (default), <code>"standard"</code>, and <code>"lenient"</code>
@@ -86,9 +93,6 @@
<li>This results in more reliable behaviour compared to previous versions for capped MIC values</li>
<li>Removed the <code>"inverse"</code> option, which has now become redundant</li>
</ul></li>
<li>Fixed some foreign translations of antimicrobial drugs</li>
<li>
<code>antimicrobials$group</code> is now a <code>list</code> instead of a <code>character</code>, to contain any group the drug is in (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<li>
<code><a href="../reference/ab_property.html">ab_group()</a></code> now returns values consist with the AMR selectors (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
</ul></div>

28
news/index.md
View File

@@ -1,6 +1,6 @@
# Changelog
## AMR 3.0.1.9017
## AMR 3.0.1.9018
#### New
@@ -22,20 +22,30 @@
[`phosphonics()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
and
[`spiropyrimidinetriones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
- [`ab_group()`](https://amr-for-r.org/reference/ab_property.md) gained
an argument `all_groups` to return all groups the antimicrobial drug
is in ([\#246](https://github.com/msberends/AMR/issues/246))
- `antimicrobials$group` is now a `list` instead of a `character`, to
contain any group the drug is in
([\#246](https://github.com/msberends/AMR/issues/246))
#### Changed
#### Fixes
- Fixed a bug in
[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) for
when no antimicrobials are set
- Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the
`antimicrobials` data set
- Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
where for numeric input the arguments `S`, `i`, and `R` would not be
considered ([\#244](https://github.com/msberends/AMR/issues/244))
- Fixed some foreign translations of antimicrobial drugs
- Fixed a bug for printing column names to the console when using
`mutate_at(vars(...), as.mic)`
([\#249](https://github.com/msberends/AMR/issues/249))
#### Updates
- [`ab_group()`](https://amr-for-r.org/reference/ab_property.md) gained
an argument `all_groups` to return all groups the antimicrobial drug
is in ([\#246](https://github.com/msberends/AMR/issues/246))
- Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the
`antimicrobials` data set
- Added explaining message to
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) when
interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R)
@@ -52,10 +62,6 @@
- This results in more reliable behaviour compared to previous
versions for capped MIC values
- Removed the `"inverse"` option, which has now become redundant
- Fixed some foreign translations of antimicrobial drugs
- `antimicrobials$group` is now a `list` instead of a `character`, to
contain any group the drug is in
([\#246](https://github.com/msberends/AMR/issues/246))
- [`ab_group()`](https://amr-for-r.org/reference/ab_property.md) now
returns values consist with the AMR selectors
([\#246](https://github.com/msberends/AMR/issues/246))

2
pkgdown.yml
View File

@@ -10,7 +10,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2026-01-08T13:07Z
last_built: 2026-01-16T10:03Z
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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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

@@ -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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/AMR.html
View File

@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/WHOCC.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">
@@ -155,7 +155,7 @@
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href="https://atcddd.fhi.no/atc_ddd_index/" class="external-link">https://atcddd.fhi.no/atc_ddd_index/</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm</a></p>
</div>
<div class="section level2">
<h2 id="download-our-reference-data">Download Our Reference Data<a class="anchor" aria-label="anchor" href="#download-our-reference-data"></a></h2>

2
reference/ab_property.md
View File

@@ -155,7 +155,7 @@ World Health Organization (WHO) Collaborating Centre for Drug Statistics
Methodology: <https://atcddd.fhi.no/atc_ddd_index/>
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER:
<https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>
<https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm>
## Download Our Reference Data

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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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 1980-02-27 45 45.86301 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.45479 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.35068 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.43288 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.13699 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.77808 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.54521 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.31233 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.64932 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.15068 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 45 45.88493 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.47671 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.37260 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.45479 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.15890 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.80000 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.56712 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.33425 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.67123 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.17260 47</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

20
reference/age.md
View File

@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
df
#> birth_date age age_exact age_at_y2k
#> 1 1980-02-27 45 45.86301 19
#> 2 1953-07-26 72 72.45479 46
#> 3 1949-09-02 76 76.35068 50
#> 4 1986-08-03 39 39.43288 13
#> 5 1932-11-19 93 93.13699 67
#> 6 1949-03-30 76 76.77808 50
#> 7 1996-06-23 29 29.54521 3
#> 8 1963-09-16 62 62.31233 36
#> 9 1952-05-16 73 73.64932 47
#> 10 1952-11-14 73 73.15068 47
#> 1 1980-02-27 45 45.88493 19
#> 2 1953-07-26 72 72.47671 46
#> 3 1949-09-02 76 76.37260 50
#> 4 1986-08-03 39 39.45479 13
#> 5 1932-11-19 93 93.15890 67
#> 6 1949-03-30 76 76.80000 50
#> 7 1996-06-23 29 29.56712 3
#> 8 1963-09-16 62 62.33425 36
#> 9 1952-05-16 73 73.67123 47
#> 10 1952-11-14 73 73.17260 47
```

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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">
@@ -191,8 +191,8 @@ may affect the computations for subsequent operations.</p></dd>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials </span> 1.4.2 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tailor </span> 0.1.0 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer </span> 1.1.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr </span> 1.3.2 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata </span> 1.5.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune </span> 2.0.1 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip </span> 1.4.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows </span> 1.3.0 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr </span> 1.2.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.1 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip </span> 1.4.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows </span> 1.3.0 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr </span> 1.2.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.1 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes </span> 1.3.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick </span> 1.3.2 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Conflicts</span> ───────────────────────────────────────── tidymodels_conflicts() ──</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">purrr</span>::<span style="color: #00BB00;">discard()</span> masks <span style="color: #0000BB;">scales</span>::discard()</span>

4
reference/amr-tidymodels.md
View File

@@ -170,8 +170,8 @@ if (require("tidymodels")) {
#> ✔ dials 1.4.2 ✔ tailor 0.1.0
#> ✔ infer 1.1.0 ✔ tidyr 1.3.2
#> ✔ modeldata 1.5.1 ✔ tune 2.0.1
#> ✔ parsnip 1.4.0 ✔ workflows 1.3.0
#> ✔ purrr 1.2.0 ✔ workflowsets 1.1.1
#> ✔ parsnip 1.4.1 ✔ workflows 1.3.0
#> ✔ purrr 1.2.1 ✔ workflowsets 1.1.1
#> ✔ recipes 1.3.1 ✔ yardstick 1.3.2
#> ── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ──
#> ✖ purrr::discard() masks scales::discard()

2
reference/antibiogram.html
View File

@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">
@@ -211,7 +211,7 @@ my_data_with_all_these_columns %&amp;gt;%
<p>The <code>amr_class()</code> function can be used to filter/select on a manually defined antimicrobial class. It searches for results in the <a href="antimicrobials.html">antimicrobials</a> data set within the columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code>.</p>
<p>The <code>administrable_per_os()</code> and <code>administrable_iv()</code> functions also rely on the <a href="antimicrobials.html">antimicrobials</a> data set - antimicrobials will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the <a href="antimicrobials.html">antimicrobials</a> data set.</p>
<p>The <code>amr_selector()</code> function can be used to internally filter the <a href="antimicrobials.html">antimicrobials</a> data set on any results, see <em>Examples</em>. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.</p>
<p>The <code>not_intrinsic_resistant()</code> function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of <em>E. coli</em> and <em>K. pneumoniae</em> and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023) to determine intrinsic resistance, using the <code><a href="eucast_rules.html">eucast_rules()</a></code> function internally. Because of this determination, this function is quite slow in terms of performance.</p>
<p>The <code>not_intrinsic_resistant()</code> function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of <em>E. coli</em> and <em>K. pneumoniae</em> and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023) to determine intrinsic resistance, using the <code><a href="eucast_rules.html">eucast_rules()</a></code> function internally. Because of this determination, this function is quite slow in terms of performance.</p>
</div>
<div class="section level2">
<h2 id="full-list-of-supported-antimicrobial-classes">Full list of supported (antimicrobial) classes<a class="anchor" aria-label="anchor" href="#full-list-of-supported-antimicrobial-classes"></a></h2>
@@ -247,9 +247,9 @@ my_data_with_all_these_columns %&amp;gt;%
<li><p><code>rifamycins()</code> can select: <br> rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), and rifapentine (RFP)</p></li>
<li><p><code>spiropyrimidinetriones()</code> can select: <br> zoliflodacin (ZFD)</p></li>
<li><p><code>streptogramins()</code> can select: <br> pristinamycin (PRI) and quinupristin/dalfopristin (QDA)</p></li>
<li><p><code>sulfonamides()</code> can select: <br> brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfamoxole (SLF8), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), and sulfathiourea (SLF13)</p></li>
<li><p><code>tetracyclines()</code> can select: <br> cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), tetracycline screening test (TCY-S), and tigecycline (TGC)</p></li>
<li><p><code>trimethoprims()</code> can select: <br> brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT)</p></li>
<li><p><code>sulfonamides()</code> can select: <br> isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), ormetroprim/sulfamethoxazole (ORS), sulfachlorpyridazine (SUP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethazine (SUM), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfasuccinamide (SNA), sulfathiazole (SUT), sulfathiourea (SLF13), sulfisoxazole (SOX), sulfonamide (SSS), and trimethoprim/sulfamethoxazole (SXT)</p></li>
<li><p><code>tetracyclines()</code> can select: <br> cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), tetracycline screening test (TCY-S), tetracycline/oleandomycin (TOL), and tigecycline (TGC)</p></li>
<li><p><code>trimethoprims()</code> can select: <br> brodimoprim (BDP), iclaprim (ICL), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), ormetroprim/sulfamethoxazole (ORS), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT)</p></li>
<li><p><code>ureidopenicillins()</code> can select: <br> azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), and piperacillin/tazobactam (TZP)</p></li>
</ul></div>
<div class="section level2">

36
reference/antimicrobial_selectors.md
View File

@@ -231,7 +231,7 @@ codes or names of *E. coli* and *K. pneumoniae* and contains a column
"vancomycin", this column will be removed (or rather, unselected) using
this function. It currently applies ['EUCAST Expected Resistant
Phenotypes'
v1.2](https://www.eucast.org/expert_rules_and_expected_phenotypes)
v1.2](https://www.eucast.org/bacteria/important-additional-information/expert-rules/)
(2023) to determine intrinsic resistance, using the
[`eucast_rules()`](https://amr-for-r.org/reference/eucast_rules.md)
function internally. Because of this determination, this function is
@@ -559,14 +559,21 @@ quite slow in terms of performance.
pristinamycin (PRI) and quinupristin/dalfopristin (QDA)
- `sulfonamides()` can select:
brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT),
sulfadimethoxine (SUD), sulfadimidine (SDM), sulfafurazole (SLF),
sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO),
sulfamerazine (SLF3), sulfamethizole (SLF4), sulfamethoxazole (SMX),
isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST),
ormetroprim/sulfamethoxazole (ORS), sulfachlorpyridazine (SUP),
sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT),
sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD),
sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole
(SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO),
sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3),
sulfamethazine (SUM), sulfamethizole (SLF4), sulfamethoxazole (SMX),
sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6),
sulfametoxydiazine (SLF7), sulfamoxole (SLF8), sulfanilamide (SLF9),
sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12),
sulfathiazole (SUT), and sulfathiourea (SLF13)
sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4),
sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide
(SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine
(SLF12), sulfasuccinamide (SNA), sulfathiazole (SUT), sulfathiourea
(SLF13), sulfisoxazole (SOX), sulfonamide (SSS), and
trimethoprim/sulfamethoxazole (SXT)
- `tetracyclines()` can select:
cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1),
@@ -574,13 +581,16 @@ quite slow in terms of performance.
lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline
(OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline
(RLT), sarecycline (SRC), tetracycline (TCY), tetracycline screening
test (TCY-S), and tigecycline (TGC)
test (TCY-S), tetracycline/oleandomycin (TOL), and tigecycline (TGC)
- `trimethoprims()` can select:
brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT),
sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD),
sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole
(SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO),
brodimoprim (BDP), iclaprim (ICL),
isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST),
ormetroprim/sulfamethoxazole (ORS), sulfadiazine (SDI),
sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1),
sulfadimethoxine (SUD), sulfadimidine (SDM),
sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF),
sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO),
sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3),
sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine
(SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7),

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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -107,7 +107,7 @@
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href="https://atcddd.fhi.no/atc_ddd_index/" class="external-link">https://atcddd.fhi.no/atc_ddd_index/</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm</a></p>
</div>
<div class="section level2">
<h2 id="whocc">WHOCC<a class="anchor" aria-label="anchor" href="#whocc"></a></h2>

2
reference/as.ab.md
View File

@@ -97,7 +97,7 @@ World Health Organization (WHO) Collaborating Centre for Drug Statistics
Methodology: <https://atcddd.fhi.no/atc_ddd_index/>
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER:
<https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>
<https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm>
## WHOCC

4
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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">
@@ -99,7 +99,7 @@
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href="https://atcddd.fhi.no/atc_ddd_index/" class="external-link">https://atcddd.fhi.no/atc_ddd_index/</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm</a></p>
</div>
<div class="section level2">
<h2 id="whocc">WHOCC<a class="anchor" aria-label="anchor" href="#whocc"></a></h2>

2
reference/as.av.md
View File

@@ -83,7 +83,7 @@ World Health Organization (WHO) Collaborating Centre for Drug Statistics
Methodology: <https://atcddd.fhi.no/atc_ddd_index/>
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER:
<https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>
<https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm>
## WHOCC

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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">

24
reference/as.sir.html
View File

@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">
@@ -117,7 +117,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2011-2025, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
<li><p><strong>CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2025, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
<li><p><strong>CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals</strong>, 2019-2025, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/veterinary-medicine/documents/vet01/" class="external-link">https://clsi.org/standards/products/veterinary-medicine/documents/vet01/</a>.</p></li>
<li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2025, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/clinical_breakpoints" class="external-link">https://www.eucast.org/clinical_breakpoints</a>.</p></li>
<li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2025, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" class="external-link">https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/</a>.</p></li>
<li><p><strong>WHONET</strong> as a source for machine-reading the clinical breakpoints (<a href="https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet">read more here</a>), 1989-2025, <em>WHO Collaborating Centre for Surveillance of Antimicrobial Resistance</em>. <a href="https://whonet.org/" class="external-link">https://whonet.org/</a>.</p></li>
</ul></div>
<div class="section level2">
@@ -175,7 +175,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<dt id="arg-add-intrinsic-resistance">add_intrinsic_resistance<a class="anchor" aria-label="anchor" href="#arg-add-intrinsic-resistance"></a></dt>
<dd><p><em>(only useful when using a EUCAST guideline)</em> a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in <em>Klebsiella</em> species. Determination is based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, that itself is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021).</p></dd>
<dd><p><em>(only useful when using a EUCAST guideline)</em> a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in <em>Klebsiella</em> species. Determination is based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, that itself is based on <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021).</p></dd>
<dt id="arg-reference-data">reference_data<a class="anchor" aria-label="anchor" href="#arg-reference-data"></a></dt>
@@ -321,7 +321,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<h2 id="interpretation-of-sir">Interpretation of SIR<a class="anchor" aria-label="anchor" href="#interpretation-of-sir"></a></h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<a href="https://www.eucast.org/newsiandr" class="external-link">https://www.eucast.org/newsiandr</a>).</p>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/" class="external-link">https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/</a>).</p>
<p>This AMR package follows insight; use <code><a href="proportion.html">susceptibility()</a></code> (equal to <code><a href="proportion.html">proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code><a href="count.html">count_susceptible()</a></code> (equal to <code><a href="count.html">count_SI()</a></code>) to count susceptible isolates.</p>
</div>
<div class="section level2">
@@ -416,10 +416,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-01-08 <span style="color: #949494;">13:08:47</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> 2026-01-08 <span style="color: #949494;">13:08:47</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> 2026-01-08 <span style="color: #949494;">13:08:48</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> 2026-01-08 <span style="color: #949494;">13:08:48</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> 2026-01-16 <span style="color: #949494;">10:04:38</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> 2026-01-16 <span style="color: #949494;">10:04:39</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> 2026-01-16 <span style="color: #949494;">10:04:39</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> 2026-01-16 <span style="color: #949494;">10:04:39</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>
@@ -620,13 +620,13 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-in"><span><span class="co"># For CLEANING existing SIR values -------------------------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.sir</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="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #444444;">`as.sir()`</span>: 3 results in index '21' truncated (38%) that were invalid</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial interpretations: "A", "B", and "C"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #444444;">`as.sir()`</span>: 3 results truncated (38%) that were invalid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretations: "A", "B", and "C"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S SDD I R NI &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="st">"&lt;= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #444444;">`as.sir()`</span>: 1 result in index '21' truncated (100%) that were invalid</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial interpretations: "&lt;= 0.002; S"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #444444;">`as.sir()`</span>: 1 result truncated (100%) that were invalid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretations: "&lt;= 0.002; S"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;NA&gt;</span>
<span class="r-in"><span></span></span>

23
reference/as.sir.md
View File

@@ -93,7 +93,7 @@ disk diffusion diameters:
- **EUCAST Breakpoint tables for interpretation of MICs and zone
diameters**, 2011-2025, *European Committee on Antimicrobial
Susceptibility Testing* (EUCAST).
<https://www.eucast.org/clinical_breakpoints>.
<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/>.
- **WHONET** as a source for machine-reading the clinical breakpoints
([read more
@@ -228,7 +228,7 @@ disk diffusion diameters:
[intrinsic_resistant](https://amr-for-r.org/reference/intrinsic_resistant.md)
data set, that itself is based on ['EUCAST Expert Rules' and 'EUCAST
Intrinsic Resistance and Unusual Phenotypes'
v3.3](https://www.eucast.org/expert_rules_and_expected_phenotypes)
v3.3](https://www.eucast.org/bacteria/important-additional-information/expert-rules/)
(2021).
- reference_data:
@@ -537,7 +537,8 @@ base R's [`NA_character_`](https://rdrr.io/r/base/NA.html).
In 2019, the European Committee on Antimicrobial Susceptibility Testing
(EUCAST) has decided to change the definitions of susceptibility testing
categories S, I, and R (<https://www.eucast.org/newsiandr>).
categories S, I, and R
(<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/>).
This AMR package follows insight; use
[`susceptibility()`](https://amr-for-r.org/reference/proportion.md)
@@ -650,10 +651,10 @@ 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 2026-01-08 13:08:47 1 MIC amoxicillin Escherich… human 8
#> 2 2026-01-08 13:08:47 1 MIC cipro Escherich… human 0.256
#> 3 2026-01-08 13:08:48 1 DISK tobra Escherich… human 16
#> 4 2026-01-08 13:08:48 1 DISK genta Escherich… human 18
#> 1 2026-01-16 10:04:38 1 MIC amoxicillin Escherich… human 8
#> 2 2026-01-16 10:04:39 1 MIC cipro Escherich… human 0.256
#> 3 2026-01-16 10:04:39 1 DISK tobra Escherich… human 16
#> 4 2026-01-16 10:04:39 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>
@@ -854,13 +855,13 @@ as.sir(
# For CLEANING existing SIR values -------------------------------------
as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C"))
#> Warning: in `as.sir()`: 3 results in index '21' truncated (38%) that were invalid
#> antimicrobial interpretations: "A", "B", and "C"
#> Warning: in `as.sir()`: 3 results truncated (38%) that were invalid antimicrobial
#> interpretations: "A", "B", and "C"
#> Class 'sir'
#> [1] S SDD I R NI <NA> <NA> <NA>
as.sir("<= 0.002; S") # will return "S"
#> Warning: in `as.sir()`: 1 result in index '21' truncated (100%) that were invalid
#> antimicrobial interpretations: "<= 0.002; S"
#> Warning: in `as.sir()`: 1 result truncated (100%) that were invalid antimicrobial
#> interpretations: "<= 0.002; S"
#> Class 'sir'
#> [1] <NA>

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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">
@@ -130,7 +130,7 @@
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href="https://atcddd.fhi.no/atc_ddd_index/" class="external-link">https://atcddd.fhi.no/atc_ddd_index/</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm</a></p>
</div>
<div class="section level2">
<h2 id="download-our-reference-data">Download Our Reference Data<a class="anchor" aria-label="anchor" href="#download-our-reference-data"></a></h2>

2
reference/av_property.md
View File

@@ -104,7 +104,7 @@ World Health Organization (WHO) Collaborating Centre for Drug Statistics
Methodology: <https://atcddd.fhi.no/atc_ddd_index/>
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER:
<https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>
<https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm>
## Download Our Reference Data

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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/clinical_breakpoints.html
View File

@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">
@@ -123,7 +123,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<h2 id="interpretation-of-sir">Interpretation of SIR<a class="anchor" aria-label="anchor" href="#interpretation-of-sir"></a></h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<a href="https://www.eucast.org/newsiandr" class="external-link">https://www.eucast.org/newsiandr</a>).</p>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/" class="external-link">https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/</a>).</p>
<p>This AMR package follows insight; use <code><a href="proportion.html">susceptibility()</a></code> (equal to <code><a href="proportion.html">proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code>count_susceptible()</code> (equal to <code>count_SI()</code>) to count susceptible isolates.</p>
</div>
<div class="section level2">

3
reference/count.md
View File

@@ -110,7 +110,8 @@ works exactly like `count_df()`, but adds the percentage of S, I and R.
In 2019, the European Committee on Antimicrobial Susceptibility Testing
(EUCAST) has decided to change the definitions of susceptibility testing
categories S, I, and R (<https://www.eucast.org/newsiandr>).
categories S, I, and R
(<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/>).
This AMR package follows insight; use
[`susceptibility()`](https://amr-for-r.org/reference/proportion.md)

10
reference/custom_eucast_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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">
@@ -180,10 +180,10 @@
<li><p>rifamycins<br>(rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine)</p></li>
<li><p>spiropyrimidinetriones<br>(zoliflodacin)</p></li>
<li><p>streptogramins<br>(pristinamycin and quinupristin/dalfopristin)</p></li>
<li><p>sulfonamides<br>(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea)</p></li>
<li><p>tetracyclines<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tigecycline)</p></li>
<li><p>tetracyclines_except_tgc<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, and tetracycline screening test)</p></li>
<li><p>trimethoprims<br>(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole)</p></li>
<li><p>sulfonamides<br>(isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea, sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole)</p></li>
<li><p>tetracyclines<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, tetracycline/oleandomycin, and tigecycline)</p></li>
<li><p>tetracyclines_except_tgc<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tetracycline/oleandomycin)</p></li>
<li><p>trimethoprims<br>(brodimoprim, iclaprim, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole)</p></li>
<li><p>ureidopenicillins<br>(azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam)</p></li>
</ul></div>

26
reference/custom_eucast_rules.md
View File

@@ -431,28 +431,36 @@ These 38 antimicrobial groups are allowed in the rules
(pristinamycin and quinupristin/dalfopristin)
- sulfonamides
(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim,
sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine,
sulfalene, sulfamazone, sulfamerazine, sulfamethizole,
(isoniazid/sulfamethoxazole/trimethoprim/pyridoxine,
ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine,
sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine,
sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole,
sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine,
sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole,
sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine,
sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin,
sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea)
sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole,
sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole,
sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea,
sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole)
- tetracyclines
(cetocycline, chlortetracycline, clomocycline, demeclocycline,
doxycycline, eravacycline, lymecycline, metacycline, minocycline,
omadacycline, oxytetracycline, penimepicycline, rolitetracycline,
sarecycline, tetracycline, tetracycline screening test, and
tigecycline)
sarecycline, tetracycline, tetracycline screening test,
tetracycline/oleandomycin, and tigecycline)
- tetracyclines_except_tgc
(cetocycline, chlortetracycline, clomocycline, demeclocycline,
doxycycline, eravacycline, lymecycline, metacycline, minocycline,
omadacycline, oxytetracycline, penimepicycline, rolitetracycline,
sarecycline, tetracycline, and tetracycline screening test)
sarecycline, tetracycline, tetracycline screening test, and
tetracycline/oleandomycin)
- trimethoprims
(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim,
(brodimoprim, iclaprim,
isoniazid/sulfamethoxazole/trimethoprim/pyridoxine,
ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim,
sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine,
sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine,
sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim,

16
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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">
@@ -174,9 +174,9 @@
<li><p><code><a href="antimicrobial_selectors.html">rifamycins()</a></code> can select: <br> rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine</p></li>
<li><p><code><a href="antimicrobial_selectors.html">spiropyrimidinetriones()</a></code> can select: <br> zoliflodacin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">streptogramins()</a></code> can select: <br> pristinamycin and quinupristin/dalfopristin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">sulfonamides()</a></code> can select: <br> brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea</p></li>
<li><p><code><a href="antimicrobial_selectors.html">tetracyclines()</a></code> can select: <br> cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tigecycline</p></li>
<li><p><code><a href="antimicrobial_selectors.html">trimethoprims()</a></code> can select: <br> brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole</p></li>
<li><p><code><a href="antimicrobial_selectors.html">sulfonamides()</a></code> can select: <br> isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea, sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole</p></li>
<li><p><code><a href="antimicrobial_selectors.html">tetracyclines()</a></code> can select: <br> cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, tetracycline/oleandomycin, and tigecycline</p></li>
<li><p><code><a href="antimicrobial_selectors.html">trimethoprims()</a></code> can select: <br> brodimoprim, iclaprim, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole</p></li>
<li><p><code><a href="antimicrobial_selectors.html">ureidopenicillins()</a></code> can select: <br> azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam</p></li>
</ul></div>
@@ -243,14 +243,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> Results will be of class 'factor', with ordered levels: Negative &lt; Custom MDRO 1 &lt; Custom MDRO 2</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">out</span> <span class="op">&lt;-</span> <span class="fu"><a href="mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">my_guideline</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">esbl</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> it seems to be tazobactam (TAZ)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">mecC</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> it seems to be mecillinam (MEC)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">vanA</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> it seems to be lenampicillin (LEN)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">vanB</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> it seems to be metronidazole (MTR)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`cephalosporins_2nd()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">' (cefuroxime) and '</span><span style="color: #0000BB; font-weight: bold;">FOX</span><span style="color: #0000BB;">'</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (cefoxitin)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Assuming a filter on all 2 cephalosporins_2nd. Wrap around </span><span style="color: #0000BB; background-color: #444444;">`all()`</span><span style="color: #0000BB;"> or</span></span>

33
reference/custom_mdro_guideline.md
View File

@@ -413,24 +413,31 @@ All 38 antimicrobial selectors are supported for use in the rules:
- [`sulfonamides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine,
sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene,
sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole,
sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine,
sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine,
sulfathiazole, and sulfathiourea
isoniazid/sulfamethoxazole/trimethoprim/pyridoxine,
ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine,
sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine,
sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole,
sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine,
sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole,
sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine,
sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole,
sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole,
sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea,
sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole
- [`tetracyclines()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
cetocycline, chlortetracycline, clomocycline, demeclocycline,
doxycycline, eravacycline, lymecycline, metacycline, minocycline,
omadacycline, oxytetracycline, penimepicycline, rolitetracycline,
sarecycline, tetracycline, tetracycline screening test, and
tigecycline
sarecycline, tetracycline, tetracycline screening test,
tetracycline/oleandomycin, and tigecycline
- [`trimethoprims()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim,
brodimoprim, iclaprim,
isoniazid/sulfamethoxazole/trimethoprim/pyridoxine,
ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim,
sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine,
sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine,
sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim,
@@ -506,14 +513,6 @@ my_guideline
#> Results will be of class 'factor', with ordered levels: Negative < Custom MDRO 1 < Custom MDRO 2
out <- mdro(example_isolates, guideline = my_guideline)
#> ℹ Column 'esbl' is SIR eligible (despite only having empty values), since
#> it seems to be tazobactam (TAZ)
#> ℹ Column 'mecC' is SIR eligible (despite only having empty values), since
#> it seems to be mecillinam (MEC)
#> ℹ Column 'vanA' is SIR eligible (despite only having empty values), since
#> it seems to be lenampicillin (LEN)
#> ℹ Column 'vanB' is SIR eligible (despite only having empty values), since
#> it seems to be metronidazole (MTR)
#> ℹ For `cephalosporins_2nd()` using columns 'CXM' (cefuroxime) and 'FOX'
#> (cefoxitin)
#> ℹ Assuming a filter on all 2 cephalosporins_2nd. Wrap around `all()` or

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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/eucast_rules.html
View File

@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/g.test.html
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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/get_episode.html
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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">
@@ -65,7 +65,7 @@
</ul></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>This data set is currently based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023).</p>
<p>This data set is currently based on <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023).</p>
<p>This data set is internally used by:</p><ul><li><p><code><a href="antimicrobial_selectors.html">not_intrinsic_resistant()</a></code> (an <a href="antimicrobial_selectors.html">antimicrobial selector</a>)</p></li>
<li><p><code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code></p></li>
</ul></div>

2
reference/intrinsic_resistant.md
View File

@@ -33,7 +33,7 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 271
This data set is currently based on ['EUCAST Expected Resistant
Phenotypes'
v1.2](https://www.eucast.org/expert_rules_and_expected_phenotypes)
v1.2](https://www.eucast.org/bacteria/important-additional-information/expert-rules/)
(2023).
This data set is internally used by:

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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">
@@ -194,7 +194,7 @@ Ordered <a href="https://rdatatable.gitlab.io/data.table/reference/fctr.html" cl
<h2 id="interpretation-of-sir">Interpretation of SIR<a class="anchor" aria-label="anchor" href="#interpretation-of-sir"></a></h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<a href="https://www.eucast.org/newsiandr" class="external-link">https://www.eucast.org/newsiandr</a>).</p>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/" class="external-link">https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/</a>).</p>
<p>This AMR package follows insight; use <code><a href="proportion.html">susceptibility()</a></code> (equal to <code><a href="proportion.html">proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code><a href="count.html">count_susceptible()</a></code> (equal to <code><a href="count.html">count_SI()</a></code>) to count susceptible isolates.</p>
</div>
<div class="section level2">

3
reference/mdro.md
View File

@@ -269,7 +269,8 @@ function.
In 2019, the European Committee on Antimicrobial Susceptibility Testing
(EUCAST) has decided to change the definitions of susceptibility testing
categories S, I, and R (<https://www.eucast.org/newsiandr>).
categories S, I, and R
(<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/>).
This AMR package follows insight; use
[`susceptibility()`](https://amr-for-r.org/reference/proportion.md)

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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">
@@ -220,7 +220,7 @@
). This function returns a <a href="https://rdatatable.gitlab.io/data.table/reference/fctr.html" class="external-link">factor</a> with the levels <em>Pathogenic</em>, <em>Potentially pathogenic</em>, <em>Non-pathogenic</em>, and <em>Unknown</em>.</p>
<p>Determination of the Gram stain (<code>mo_gramstain()</code>) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318/" class="external-link">PMID 11837318</a>), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, <a href="https://pubmed.ncbi.nlm.nih.gov/34694987/" class="external-link">PMID 34694987</a>). Bacteria in these phyla are considered Gram-positive in this <code>AMR</code> package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
<p>Determination of yeasts (<code>mo_is_yeast()</code>) will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. <em>True yeasts</em> quite specifically refers to yeasts in the underlying order Saccharomycetales (such as <em>Saccharomyces cerevisiae</em>). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
<p>Determination of intrinsic resistance (<code>mo_is_intrinsic_resistant()</code>) will be based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023). The <code>mo_is_intrinsic_resistant()</code> function can be vectorised over both argument <code>x</code> (input for microorganisms) and <code>ab</code> (input for antimicrobials).</p>
<p>Determination of intrinsic resistance (<code>mo_is_intrinsic_resistant()</code>) will be based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023). The <code>mo_is_intrinsic_resistant()</code> function can be vectorised over both argument <code>x</code> (input for microorganisms) and <code>ab</code> (input for antimicrobials).</p>
<p>Determination of bacterial oxygen tolerance (<code>mo_oxygen_tolerance()</code>) will be based on BacDive, see <em>Source</em>. The function <code>mo_is_anaerobic()</code> only returns <code>TRUE</code> if the oxygen tolerance is <code>"anaerobe"</code>, indicting an obligate anaerobic species or genus. It always returns <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. <a href="https://www.mycobank.org" class="external-link">This MycoBank URL</a> will be used for fungi wherever available , <a href="https://www.mycobank.org" class="external-link">this LPSN URL</a> for bacteria wherever available, and <a href="https://www.gbif.org" class="external-link">this GBIF link</a> otherwise.</p>
<p>SNOMED codes (<code>mo_snomed()</code>) was last updated on July 16th, 2024. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>

2
reference/mo_property.md
View File

@@ -277,7 +277,7 @@ Determination of intrinsic resistance (`mo_is_intrinsic_resistant()`)
will be based on the
[intrinsic_resistant](https://amr-for-r.org/reference/intrinsic_resistant.md)
data set, which is based on ['EUCAST Expected Resistant Phenotypes'
v1.2](https://www.eucast.org/expert_rules_and_expected_phenotypes)
v1.2](https://www.eucast.org/bacteria/important-additional-information/expert-rules/)
(2023). The `mo_is_intrinsic_resistant()` function can be vectorised
over both argument `x` (input for microorganisms) and `ab` (input for
antimicrobials).

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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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">
@@ -194,7 +194,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<h2 id="interpretation-of-sir">Interpretation of SIR<a class="anchor" aria-label="anchor" href="#interpretation-of-sir"></a></h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<a href="https://www.eucast.org/newsiandr" class="external-link">https://www.eucast.org/newsiandr</a>).</p>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/" class="external-link">https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/</a>).</p>
<p>This AMR package follows insight; use <code>susceptibility()</code> (equal to <code>proportion_SI()</code>) to determine antimicrobial susceptibility and <code><a href="count.html">count_susceptible()</a></code> (equal to <code><a href="count.html">count_SI()</a></code>) to count susceptible isolates.</p>
</div>
<div class="section level2">

3
reference/proportion.md
View File

@@ -236,7 +236,8 @@ input.
In 2019, the European Committee on Antimicrobial Susceptibility Testing
(EUCAST) has decided to change the definitions of susceptibility testing
categories S, I, and R (<https://www.eucast.org/newsiandr>).
categories S, I, and R
(<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/>).
This AMR package follows insight; use `susceptibility()` (equal to
`proportion_SI()`) to determine antimicrobial susceptibility and

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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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/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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -163,7 +163,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
<h2 id="interpretation-of-sir">Interpretation of SIR<a class="anchor" aria-label="anchor" href="#interpretation-of-sir"></a></h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<a href="https://www.eucast.org/newsiandr" class="external-link">https://www.eucast.org/newsiandr</a>).</p>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/" class="external-link">https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/</a>).</p>
<p>This AMR package follows insight; use <code><a href="proportion.html">susceptibility()</a></code> (equal to <code><a href="proportion.html">proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code><a href="count.html">count_susceptible()</a></code> (equal to <code><a href="count.html">count_SI()</a></code>) to count susceptible isolates.</p>
</div>
<div class="section level2">

3
reference/resistance_predict.md
View File

@@ -163,7 +163,8 @@ Valid options for the statistical model (argument `model`) are:
In 2019, the European Committee on Antimicrobial Susceptibility Testing
(EUCAST) has decided to change the definitions of susceptibility testing
categories S, I, and R (<https://www.eucast.org/newsiandr>).
categories S, I, and R
(<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/>).
This AMR package follows insight; use
[`susceptibility()`](https://amr-for-r.org/reference/proportion.md)

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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</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