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404.html
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@@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
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@@ -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 27 February 2026.</p>
generated on 03 March 2026.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2026-02-27</td>
<td align="center">2026-03-03</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2026-02-27</td>
<td align="center">2026-03-03</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2026-02-27</td>
<td align="center">2026-03-03</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

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**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 27 February
2026.
methodology remains unchanged. This page was generated on 03 March 2026.
## Introduction
@@ -52,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-02-27 | abcd | Escherichia coli | S | S |
| 2026-02-27 | abcd | Escherichia coli | S | R |
| 2026-02-27 | efgh | Escherichia coli | R | S |
| 2026-03-03 | abcd | Escherichia coli | S | S |
| 2026-03-03 | abcd | Escherichia coli | S | R |
| 2026-03-03 | efgh | Escherichia coli | R | S |
### Needed R packages

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
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@@ -30,7 +30,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
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articles/datasets.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
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@@ -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">27 February 2026</h4>
<h4 data-toc-skip class="date">03 March 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>
@@ -417,14 +417,14 @@ all SNOMED codes as comma separated values.</p>
<h2 id="antimicrobials-antibiotic-and-antifungal-drugs">
<code>antimicrobials</code>: Antibiotic and Antifungal Drugs<a class="anchor" aria-label="anchor" href="#antimicrobials-antibiotic-and-antifungal-drugs"></a>
</h2>
<p>A data set with 498 rows and 14 columns, containing the following
<p>A data set with 504 rows and 14 columns, containing the following
column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
<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 16 January 2026 09:57:03 UTC. Find more info
<p>It was last updated on 3 March 2026 14:41:08 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>
@@ -436,7 +436,7 @@ R Data Structure (RDS) file</a> (46 kB)<br>
text file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.xlsx" class="external-link">Microsoft
Excel workbook</a> (78 kB)<br>
Excel workbook</a> (79 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.feather" class="external-link">Apache
Feather file</a> (0.1 MB)<br>

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@@ -91,7 +91,7 @@ First 6 rows when filtering on genus *Escherichia*:
## `antimicrobials`: Antibiotic and Antifungal Drugs
A data set with 498 rows and 14 columns, containing the following column
A data set with 504 rows and 14 columns, containing the following column
names:
*ab*, *cid*, *name*, *group*, *atc*, *atc_group1*, *atc_group2*,
*abbreviations*, *synonyms*, *oral_ddd*, *oral_units*, *iv_ddd*,
@@ -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 16 January 2026 09:57:03 UTC. Find more info
about the contents, (scientific) source, and structure of this [data set
It was last updated on 3 March 2026 14:41:08 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:**
@@ -114,7 +114,7 @@ here](https://amr-for-r.org/reference/antimicrobials.html).
(0.1 MB)
- Download as [Microsoft Excel
workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.xlsx)
(78 kB)
(79 kB)
- Download as [Apache Feather
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.feather)
(0.1 MB)

2
articles/index.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
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authors.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
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6
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@@ -33,7 +33,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</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">
@@ -404,6 +404,10 @@
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">GEN</span>, <span class="va">TOB</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>total_R <span class="op">=</span> <span class="va">resistance</span>,</span>
<span> conf_int <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="reference/proportion.html">sir_confidence_interval</a></span><span class="op">(</span><span class="va">x</span>, collapse <span class="op">=</span> <span class="st">"-"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
<span><span class="co">#&gt; category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
<span><span class="co">#&gt; option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
<span><span class="co">#&gt; ℹ This message will be shown once per session.</span></span>
<span><span class="co">#&gt; # A tibble: 3 × 5</span></span>
<span><span class="co">#&gt; ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int</span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; </span></span>

4
index.md
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@@ -266,6 +266,10 @@ example_isolates %>%
summarise(across(c(GEN, TOB),
list(total_R = resistance,
conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
#> # A tibble: 3 × 5
#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
#> <chr> <dbl> <chr> <dbl> <chr>

7
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@@ -266,6 +266,10 @@ example_isolates %>%
summarise(across(c(GEN, TOB),
list(total_R = resistance,
conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
#> # A tibble: 3 × 5
#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
#> <chr> <dbl> <chr> <dbl> <chr>
@@ -726,6 +730,7 @@ or determine multi-drug resistant microorganisms (MDRO,
[`nitrofurans()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`oxazolidinones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`penicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`peptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`phenicols()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`phosphonics()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`polymyxins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
@@ -858,7 +863,7 @@ information about how to work with functions in this package.
- [`antimicrobials`](https://amr-for-r.org/reference/antimicrobials.md)
[`antibiotics`](https://amr-for-r.org/reference/antimicrobials.md)
[`antivirals`](https://amr-for-r.org/reference/antimicrobials.md) :
Data Sets with 618 Antimicrobial Drugs
Data Sets with 624 Antimicrobial Drugs
- [`clinical_breakpoints`](https://amr-for-r.org/reference/clinical_breakpoints.md)
: Data Set with Clinical Breakpoints for SIR Interpretation
- [`example_isolates`](https://amr-for-r.org/reference/example_isolates.md)

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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</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="3.0.1.9021" id="amr-3019021">AMR 3.0.1.9021<a class="anchor" aria-label="anchor" href="#amr-3019021"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9022" id="amr-3019022">AMR 3.0.1.9022<a class="anchor" aria-label="anchor" href="#amr-3019022"></a></h2>
<div class="section level4">
<h4 id="new-3-0-1-9021">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9021"></a></h4>
<h4 id="new-3-0-1-9022">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9022"></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>
@@ -68,8 +68,9 @@
</ul></li>
</ul></li>
<li>Data set <code>esbl_isolates</code> to practise with AMR modelling</li>
<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>AMR selectors <code><a href="../reference/antimicrobial_selectors.html">peptides()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">phosphonics()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">spiropyrimidinetriones()</a></code>
</li>
<li>Antimicrobials in the <code>antimicrobials</code> data set: ceftibuten/avibactam (<code>CTA</code>), kasugamycin (<code>KAS</code>), ostreogrycin (<code>OST</code>), thiostrepton (<code>THS</code>), xeruborbactam (<code>XER</code>), zorbamycin (<code>ZOR</code>)</li>
<li>Support for Wildtype (WT) / Non-wildtype (NWT) in <code><a href="../reference/as.sir.html">as.sir()</a></code>, all plotting functions, and all susceptibility/resistance functions.
<ul><li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> gained an argument <code>as_wt_nwt</code>, which defaults to <code>TRUE</code> only when <code>breakpoint_type = "ECOFF"</code> (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li>
@@ -83,7 +84,7 @@
</ul></li>
</ul></div>
<div class="section level4">
<h4 id="fixes-3-0-1-9021">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9021"></a></h4>
<h4 id="fixes-3-0-1-9022">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9022"></a></h4>
<ul><li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li>
<li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where for numeric input the arguments <code>S</code>, <code>I</code>, and <code>R</code> would not be considered (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
<li>Fixed some foreign translations of antimicrobial drugs</li>
@@ -92,7 +93,7 @@
<li>Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (<a href="https://github.com/msberends/AMR/issues/256" class="external-link">#256</a>)</li>
</ul></div>
<div class="section level4">
<h4 id="updates-3-0-1-9021">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9021"></a></h4>
<h4 id="updates-3-0-1-9022">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9022"></a></h4>
<ul><li>
<code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> gained the argument <code>guideline</code>, which defaults to EUCAST, for interpreting the ‘I’ category correctly.</li>
<li>

6
news/index.md
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@@ -1,6 +1,6 @@
# Changelog
## AMR 3.0.1.9021
## AMR 3.0.1.9022
#### New
@@ -19,9 +19,13 @@
[`all_disk_predictors()`](https://amr-for-r.org/reference/amr-tidymodels.md)
- Data set `esbl_isolates` to practise with AMR modelling
- AMR selectors
[`peptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
[`phosphonics()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
and
[`spiropyrimidinetriones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
- Antimicrobials in the `antimicrobials` data set: ceftibuten/avibactam
(`CTA`), kasugamycin (`KAS`), ostreogrycin (`OST`), thiostrepton
(`THS`), xeruborbactam (`XER`), zorbamycin (`ZOR`)
- Support for Wildtype (WT) / Non-wildtype (NWT) in
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md), all plotting
functions, and all susceptibility/resistance functions.

2
pkgdown.yml
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@@ -10,7 +10,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2026-02-27T16:21Z
last_built: 2026-03-03T14:47Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles

2
reference/AMR-deprecated.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/AMR-options.html
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@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/AMR.html
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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
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2
reference/WHOCC.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
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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="">3.0.1.9021</small>
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2
reference/ab_from_text.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
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2
reference/ab_property.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
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2
reference/add_custom_antimicrobials.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
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2
reference/add_custom_microorganisms.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
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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="">3.0.1.9021</small>
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@@ -112,16 +112,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 46 46.00000 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.59178 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.48767 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.56986 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.27397 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.91507 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.68219 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.44932 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.78630 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.28767 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 46 46.01096 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.60274 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.49863 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.58082 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.28493 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.92603 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.69315 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.46027 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.79726 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.29863 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 46 46.00000 19
#> 2 1953-07-26 72 72.59178 46
#> 3 1949-09-02 76 76.48767 50
#> 4 1986-08-03 39 39.56986 13
#> 5 1932-11-19 93 93.27397 67
#> 6 1949-03-30 76 76.91507 50
#> 7 1996-06-23 29 29.68219 3
#> 8 1963-09-16 62 62.44932 36
#> 9 1952-05-16 73 73.78630 47
#> 10 1952-11-14 73 73.28767 47
#> 1 1980-02-27 46 46.01096 19
#> 2 1953-07-26 72 72.60274 46
#> 3 1949-09-02 76 76.49863 50
#> 4 1986-08-03 39 39.58082 13
#> 5 1932-11-19 93 93.28493 67
#> 6 1949-03-30 76 76.92603 50
#> 7 1996-06-23 29 29.69315 3
#> 8 1963-09-16 62 62.46027 36
#> 9 1952-05-16 73 73.79726 47
#> 10 1952-11-14 73 73.29863 47
```

2
reference/age_groups.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/amr-tidymodels.html
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@@ -7,7 +7,7 @@
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2
reference/antibiogram.html
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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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19
reference/antimicrobial_selectors.html
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -124,6 +124,8 @@ my_data_with_all_these_columns %&amp;gt;%
<span></span>
<span><span class="fu">penicillins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">peptides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">phenicols</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">phosphonics</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
@@ -217,21 +219,21 @@ my_data_with_all_these_columns %&amp;gt;%
<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>
<ul><li><p><code>aminoglycosides()</code> can select: <br> amikacin (AMK), amikacin/fosfomycin (AKF), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB), and tobramycin-high (TOH)</p></li>
<ul><li><p><code>aminoglycosides()</code> can select: <br> amikacin (AMK), amikacin/fosfomycin (AKF), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), kasugamycin (KAS), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB), and tobramycin-high (TOH)</p></li>
<li><p><code>aminopenicillins()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), and ampicillin (AMP)</p></li>
<li><p><code>antifungals()</code> can select: <br> amorolfine (AMO), amphotericin B (AMB), amphotericin B-high (AMH), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), and voriconazole (VOR)</p></li>
<li><p><code>antimycobacterials()</code> can select: <br> 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)</p></li>
<li><p><code>betalactams()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), carumonam (CAR), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), taniborbactam (TAN), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC), and tigemonam (TMN)</p></li>
<li><p><code>betalactams_with_inhibitor()</code> can select: <br> amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>betalactams()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), carumonam (CAR), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftibuten/avibactam (CTA), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), taniborbactam (TAN), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC), and tigemonam (TMN)</p></li>
<li><p><code>betalactams_with_inhibitor()</code> can select: <br> amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftibuten/avibactam (CTA), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>carbapenems()</code> can select: <br> biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), taniborbactam (TAN), and tebipenem (TBP)</p></li>
<li><p><code>cephalosporins()</code> can select: <br> cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)</p></li>
<li><p><code>cephalosporins()</code> can select: <br> cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftibuten/avibactam (CTA), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)</p></li>
<li><p><code>cephalosporins_1st()</code> can select: <br> cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), and cephradine (CED)</p></li>
<li><p><code>cephalosporins_2nd()</code> can select: <br> cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA), and loracarbef (LOR)</p></li>
<li><p><code>cephalosporins_3rd()</code> can select: <br> cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), and latamoxef (LTM)</p></li>
<li><p><code>cephalosporins_3rd()</code> can select: <br> cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftibuten/avibactam (CTA), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), and latamoxef (LTM)</p></li>
<li><p><code>cephalosporins_4th()</code> can select: <br> cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO), and cefquinome (CEQ)</p></li>
<li><p><code>cephalosporins_5th()</code> can select: <br> ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)</p></li>
<li><p><code>fluoroquinolones()</code> can select: <br> besifloxacin (BES), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)</p></li>
<li><p><code>glycopeptides()</code> can select: <br> avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), and vancomycin-macromethod (VAM)</p></li>
<li><p><code>glycopeptides()</code> can select: <br> avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), vancomycin-macromethod (VAM), and zorbamycin (ZOR)</p></li>
<li><p><code>isoxazolylpenicillins()</code> can select: <br> cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC), meticillin (MET), oxacillin (OXA), and oxacillin screening test (OXA-S)</p></li>
<li><p><code>lincosamides()</code> can select: <br> clindamycin (CLI), clindamycin inducible screening test (CLI-S), lincomycin (LIN), and pirlimycin (PRL)</p></li>
<li><p><code>lipoglycopeptides()</code> can select: <br> dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)</p></li>
@@ -240,13 +242,14 @@ my_data_with_all_these_columns %&amp;gt;%
<li><p><code>nitrofurans()</code> can select: <br> furazidin (FUR), furazolidone (FRZ), nifurtoinol (NFR), nitrofurantoin (NIT), and nitrofurazone (NIZ)</p></li>
<li><p><code>oxazolidinones()</code> can select: <br> cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD), and thiacetazone (THA)</p></li>
<li><p><code>penicillins()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), carbenicillin (CRB), carindacillin (CRN), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>peptides()</code> can select: <br> avoparcin (AVO), bacitracin (BAC), bleomycin (BLM), dalbavancin (DAL), daptomycin (DAP), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), thiostrepton (THS), vancomycin (VAN), vancomycin-macromethod (VAM), and zorbamycin (ZOR)</p></li>
<li><p><code>phenicols()</code> can select: <br> chloramphenicol (CHL), florfenicol (FLR), and thiamphenicol (THI)</p></li>
<li><p><code>phosphonics()</code> can select: <br> amikacin/fosfomycin (AKF) and fosfomycin (FOS)</p></li>
<li><p><code>polymyxins()</code> can select: <br> colistin (COL), polymyxin B (PLB), and polymyxin B/polysorbate 80 (POP)</p></li>
<li><p><code>quinolones()</code> can select: <br> besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nalidixic acid screening test (NAL-S), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), oxolinic acid (OXO), ozenoxacin (OZN), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)</p></li>
<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>streptogramins()</code> can select: <br> ostreogrycin (OST), pristinamycin (PRI), quinupristin/dalfopristin (QDA), and virginiamycine (VIR)</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>

91
reference/antimicrobial_selectors.md
View File

@@ -73,6 +73,8 @@ oxazolidinones(only_sir_columns = FALSE, return_all = TRUE, ...)
penicillins(only_sir_columns = FALSE, return_all = TRUE, ...)
peptides(only_sir_columns = FALSE, return_all = TRUE, ...)
phenicols(only_sir_columns = FALSE, return_all = TRUE, ...)
phosphonics(only_sir_columns = FALSE, return_all = TRUE, ...)
@@ -244,11 +246,11 @@ quite slow in terms of performance.
(ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB),
framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin
(HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN),
kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR),
neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin
(PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS),
streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH),
tobramycin (TOB), and tobramycin-high (TOH)
kanamycin-high (KAH), kanamycin/cephalexin (KAC), kasugamycin (KAS),
micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin
(PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST),
sisomicin (SIS), streptoduocin (STR), streptomycin (STR1),
streptomycin-high (STH), tobramycin (TOB), and tobramycin-high (TOH)
- `aminopenicillins()` can select:
amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), and ampicillin
@@ -312,22 +314,23 @@ quite slow in terms of performance.
cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT),
ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam
(CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram
pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO),
ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR),
ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT),
ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB),
cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED),
ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO),
dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem
(ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM),
imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM),
lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem
(MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV),
metampicillin (MTM), meticillin (MET), mezlocillin (MEZ),
mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA),
oxacillin screening test (OXA-S), panipenem (PAN), penamecillin (PNM),
penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin
(PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP),
pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftibuten/avibactam
(CTA), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil
(CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1),
ceftolozane/tazobactam (CZT), ceftriaxone (CRO),
ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM),
cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC),
clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem
(DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC),
hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE),
imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN),
loracarbef (LOR), mecillinam (MEC), meropenem (MEM),
meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin
(MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam
(MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test
(OXA-S), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin
(PNO), penicillin/sulbactam (PSU), pheneticillin (PHE),
phenoxymethylpenicillin (PHN), piperacillin (PIP),
piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP),
piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine
benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem
@@ -346,12 +349,13 @@ quite slow in terms of performance.
cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC),
cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC),
ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA),
ceftazidime/clavulanic acid (CCV), ceftolozane/tazobactam (CZT),
ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR),
meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV),
mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO),
penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS),
piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)
ceftazidime/clavulanic acid (CCV), ceftibuten/avibactam (CTA),
ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor
(CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC),
meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU),
penicillin/novobiocin (PNO), penicillin/sulbactam (PSU),
piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and
ticarcillin/clavulanic acid (TCC)
- `carbapenems()` can select:
biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM),
@@ -383,12 +387,13 @@ quite slow in terms of performance.
cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT),
ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam
(CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram
pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO),
ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR),
ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT),
ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB),
cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef
(LTM), and loracarbef (LOR)
pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftibuten/avibactam
(CTA), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil
(CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1),
ceftolozane/tazobactam (CZT), ceftriaxone (CRO),
ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM),
cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and
loracarbef (LOR)
- `cephalosporins_1st()` can select:
cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine
@@ -413,9 +418,9 @@ quite slow in terms of performance.
proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS),
ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic
acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB),
ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP),
ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), and
latamoxef (LTM)
ceftibuten/avibactam (CTA), ceftiofur (TIO), ceftizoxime (CZX),
ceftizoxime alapivoxil (CZP), ceftriaxone (CRO),
ceftriaxone/beta-lactamase inhibitor (CEB), and latamoxef (LTM)
- `cephalosporins_4th()` can select:
cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid
@@ -451,8 +456,8 @@ quite slow in terms of performance.
- `glycopeptides()` can select:
avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin
(NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC),
teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), and
vancomycin-macromethod (VAM)
teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN),
vancomycin-macromethod (VAM), and zorbamycin (ZOR)
- `isoxazolylpenicillins()` can select:
cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC),
@@ -512,6 +517,13 @@ quite slow in terms of performance.
temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid
(TCC)
- `peptides()` can select:
avoparcin (AVO), bacitracin (BAC), bleomycin (BLM), dalbavancin (DAL),
daptomycin (DAP), norvancomycin (NVA), oritavancin (ORI), ramoplanin
(RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin
(TLV), thiostrepton (THS), vancomycin (VAN), vancomycin-macromethod
(VAM), and zorbamycin (ZOR)
- `phenicols()` can select:
chloramphenicol (CHL), florfenicol (FLR), and thiamphenicol (THI)
@@ -556,7 +568,8 @@ quite slow in terms of performance.
zoliflodacin (ZFD)
- `streptogramins()` can select:
pristinamycin (PRI) and quinupristin/dalfopristin (QDA)
ostreogrycin (OST), pristinamycin (PRI), quinupristin/dalfopristin
(QDA), and virginiamycine (VIR)
- `sulfonamides()` can select:
isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST),

14
reference/antimicrobials.html
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@@ -1,5 +1,5 @@
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Sets with 618 Antimicrobial Drugs — antimicrobials • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Sets with 618 Antimicrobial Drugs — antimicrobials"><meta name="description" content="Two data sets containing all antimicrobials and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antimicrobials data set. Three identifiers are included in this data set: an antimicrobial ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
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The antibiotics data set has been renamed to antimicrobials. The old name will be removed in a future version."><meta property="og:description" content="Two data sets containing all antimicrobials and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antimicrobials data set. Three identifiers are included in this data set: an antimicrobial ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -46,7 +46,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
</nav><div class="container template-reference-topic">
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data Sets with 618 Antimicrobial Drugs</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Data Sets with 624 Antimicrobial Drugs</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="d-none name"><code>antimicrobials.Rd</code></div>
</div>
@@ -69,7 +69,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<div class="section">
<h3 id="for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-">For the antimicrobials data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 498 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-"></a></h3>
<h3 id="for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-">For the antimicrobials data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 504 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-"></a></h3>
<ul><li><p><code>ab</code><br> antimicrobial ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>cid</code><br> Compound ID as found in PubChem. <em><strong>This is a unique identifier.</strong></em></p></li>
@@ -103,7 +103,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<li><p><code>loinc</code><br> All codes associated with the name of the antiviral drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use <code><a href="av_property.html">av_loinc()</a></code> to retrieve them quickly, see <code><a href="av_property.html">av_property()</a></code>.</p></li>
</ul></div>
<p>An object of class <code>deprecated_amr_dataset</code> (inherits from <code>tbl_df</code>, <code>tbl</code>, <code>data.frame</code>) with 498 rows and 14 columns.</p>
<p>An object of class <code>deprecated_amr_dataset</code> (inherits from <code>tbl_df</code>, <code>tbl</code>, <code>data.frame</code>) with 504 rows and 14 columns.</p>
<p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 120 rows and 11 columns.</p>
</div>
<div class="section level2">
@@ -145,7 +145,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">antimicrobials</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 498 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 504 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab cid name group atc atc_group1 atc_group2 abbreviations synonyms</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lis&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lis&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;list&gt;</span> <span style="color: #949494; font-style: italic;">&lt;named &gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> AMA <span style="text-decoration: underline;">4</span>649 4-ami… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> Drugs for… Aminosali… <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
@@ -158,7 +158,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> AMX <span style="text-decoration: underline;">33</span>613 Amoxi… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Penicilli… <span style="color: #949494;">&lt;chr [4]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> AMC 23<span style="text-decoration: underline;">665</span>637 Amoxi… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Combinati… <span style="color: #949494;">&lt;chr [6]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> AXS <span style="text-decoration: underline;">465</span>441 Amoxi… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 488 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 494 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5 more variables: oral_ddd &lt;dbl&gt;, oral_units &lt;chr&gt;, iv_ddd &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># iv_units &lt;chr&gt;, loinc &lt;list&gt;</span></span>
<span class="r-in"><span><span class="va">antivirals</span></span></span>

10
reference/antimicrobials.md
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@@ -1,4 +1,4 @@
# Data Sets with 618 Antimicrobial Drugs
# Data Sets with 624 Antimicrobial Drugs
Two data sets containing all antimicrobials and antivirals. Use
[`as.ab()`](https://amr-for-r.org/reference/as.ab.md) or one of the
@@ -25,7 +25,7 @@ antivirals
## Format
### For the antimicrobials data set: a [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 498 observations and 14 variables:
### For the antimicrobials data set: a [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 504 observations and 14 variables:
- `ab`
antimicrobial ID as used in this package (such as `AMC`), using the
@@ -138,7 +138,7 @@ LOINC:
[`av_property()`](https://amr-for-r.org/reference/av_property.md).
An object of class `deprecated_amr_dataset` (inherits from `tbl_df`,
`tbl`, `data.frame`) with 498 rows and 14 columns.
`tbl`, `data.frame`) with 504 rows and 14 columns.
An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with 120
rows and 11 columns.
@@ -219,7 +219,7 @@ unlike any other info from this package.** See
``` r
antimicrobials
#> # A tibble: 498 × 14
#> # A tibble: 504 × 14
#> ab cid name group atc atc_group1 atc_group2 abbreviations synonyms
#> <ab> <dbl> <chr> <lis> <lis> <chr> <chr> <list> <named >
#> 1 AMA 4649 4-ami… <chr> <chr> Drugs for… Aminosali… <chr [1]> <chr>
@@ -232,7 +232,7 @@ antimicrobials
#> 8 AMX 33613 Amoxi… <chr> <chr> Beta-lact… Penicilli… <chr [4]> <chr>
#> 9 AMC 23665637 Amoxi… <chr> <chr> Beta-lact… Combinati… <chr [6]> <chr>
#> 10 AXS 465441 Amoxi… <chr> <chr> NA NA <chr [1]> <chr>
#> # ℹ 488 more rows
#> # ℹ 494 more rows
#> # ℹ 5 more variables: oral_ddd <dbl>, oral_units <chr>, iv_ddd <dbl>,
#> # iv_units <chr>, loinc <list>
antivirals

2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/as.disk.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

11
reference/as.mic.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</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">
@@ -168,7 +168,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.002</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># mathematical processing treats MICs as numeric values</span></span></span>
<span class="r-in"><span><span class="co"># mathematical processing treats MICs as, and returns, numeric values</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/fivenum.html" class="external-link">fivenum</a></span><span class="op">(</span><span class="va">mic_data</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.128 1.000 8.000 16.000 32.000</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/quantile.html" class="external-link">quantile</a></span><span class="op">(</span><span class="va">mic_data</span><span class="op">)</span></span></span>
@@ -182,6 +182,13 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=16 &lt;=4 &lt;=4 &lt;=4 8 &lt;=4 8 &gt;=16 &gt;=16</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># round up to nearest log2 level, e.g. for CLSI breakpoint interpretation:</span></span></span>
<span class="r-in"><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="fl">1</span><span class="op">:</span><span class="fl">8</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 3 4 5 6 7 8</span>
<span class="r-in"><span><span class="fu">as.mic</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="fl">1</span><span class="op">:</span><span class="fl">8</span><span class="op">)</span>, round_to_next_log2 <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 4 4 8 8 8 8</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># interpret MIC values</span></span></span>
<span class="r-in"><span><span class="fu"><a href="as.sir.html">as.sir</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> x <span class="op">=</span> <span class="fu">as.mic</span><span class="op">(</span><span class="fl">2</span><span class="op">)</span>,</span></span>

9
reference/as.mic.md
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@@ -197,7 +197,7 @@ as.mic("<=0.002; S")
#> Class 'mic'
#> [1] <=0.002
# mathematical processing treats MICs as numeric values
# mathematical processing treats MICs as, and returns, numeric values
fivenum(mic_data)
#> [1] 0.128 1.000 8.000 16.000 32.000
quantile(mic_data)
@@ -211,6 +211,13 @@ rescale_mic(mic_data, mic_range = c(4, 16))
#> Class 'mic'
#> [1] >=16 <=4 <=4 <=4 8 <=4 8 >=16 >=16
# round up to nearest log2 level, e.g. for CLSI breakpoint interpretation:
c(1:8)
#> [1] 1 2 3 4 5 6 7 8
as.mic(c(1:8), round_to_next_log2 = TRUE)
#> Class 'mic'
#> [1] 1 2 4 4 8 8 8 8
# interpret MIC values
as.sir(
x = as.mic(2),

2
reference/as.mo.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</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">

17
reference/as.sir.html
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</small>
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@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-02-27 <span style="color: #949494;">16:22:03</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-02-27 <span style="color: #949494;">16:22:03</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-02-27 <span style="color: #949494;">16:22:03</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-02-27 <span style="color: #949494;">16:22:03</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> 2026-03-03 <span style="color: #949494;">14:48:38</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> 2026-03-03 <span style="color: #949494;">14:48:39</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> 2026-03-03 <span style="color: #949494;">14:48:39</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> 2026-03-03 <span style="color: #949494;">14:48:39</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>
@@ -583,10 +583,11 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> CLSI interpretation guideline.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (ASP, acetylspiramycin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (ASP, acetylspiramycin),</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (TESTAB, test Antibiotic), </span><span style="color: #0000BB; font-weight: bold;">CLSI</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (TESTAB, test Antibiotic),</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (ASP, acetylspiramycin),</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (TESTAB, test Antibiotic),</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span>

15
reference/as.sir.md
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@@ -660,10 +660,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2026-02-27 16:22:03 1 MIC amoxicillin Escherich… human 8
#> 2 2026-02-27 16:22:03 1 MIC cipro Escherich… human 0.256
#> 3 2026-02-27 16:22:03 1 DISK tobra Escherich… human 16
#> 4 2026-02-27 16:22:03 1 DISK genta Escherich… human 18
#> 1 2026-03-03 14:48:38 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-03 14:48:39 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-03 14:48:39 1 DISK tobra Escherich… human 16
#> 4 2026-03-03 14:48:39 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>
@@ -819,10 +819,11 @@ if (require("dplyr")) {
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the
#> CLSI interpretation guideline.
#> Interpreting MIC values: 'antibiotic' (ASP, acetylspiramycin), CLSI 2025...
#> Interpreting disk diffusion zones: 'antibiotic' (ASP, acetylspiramycin),
#> Interpreting MIC values: 'antibiotic' (TESTAB, test Antibiotic), CLSI
#> 2025...
#> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic),
#> CLSI 2025...
#> Interpreting disk diffusion zones: 'antibiotic' (ASP, acetylspiramycin),
#> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic),
#> CLSI 2025...
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `cipro = (function (x, ...) ...`.

2
reference/atc_online.html
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@@ -7,7 +7,7 @@
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reference/av_from_text.html
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@@ -7,7 +7,7 @@
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reference/av_property.html
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@@ -7,7 +7,7 @@
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reference/availability.html
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@@ -7,7 +7,7 @@
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reference/bug_drug_combinations.html
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@@ -7,7 +7,7 @@
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2
reference/clinical_breakpoints.html
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@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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reference/count.html
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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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reference/custom_eucast_rules.html
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@@ -7,7 +7,7 @@
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@@ -147,24 +147,26 @@
<span><span class="co">#&gt;</span></span>
<span><span class="co">#&gt; 1. If TZP is "R" then set to "R":</span></span>
<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)</span></span></code></pre><p></p></div>
<p>These 38 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
<p>These 42 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
<li><p>aminopenicillins<br>(amoxicillin, amoxicillin/clavulanic acid, and ampicillin)</p></li>
<li><p>antifungals<br>(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
<li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>
<li><p>betalactamase_inhibitors<br>(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, avibactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/sulbactam, ceftaroline/avibactam, ceftazidime/avibactam, ceftolozane/tazobactam, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, nacubactam, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, sulbactam, sultamicillin, taniborbactam, tazobactam, ticarcillin/clavulanic acid, and zidebactam)</p></li>
<li><p>betalactams<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, taniborbactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)</p></li>
<li><p>betalactams_with_inhibitor<br>(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)</p></li>
<li><p>betalactamase_inhibitors<br>(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, avibactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/sulbactam, ceftaroline/avibactam, ceftazidime/avibactam, ceftibuten/avibactam, ceftolozane/tazobactam, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, nacubactam, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, sulbactam, sultamicillin, taniborbactam, tazobactam, ticarcillin/clavulanic acid, xeruborbactam, and zidebactam)</p></li>
<li><p>betalactams<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, taniborbactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)</p></li>
<li><p>betalactams_with_inhibitor<br>(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftibuten/avibactam, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)</p></li>
<li><p>carbapenems<br>(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, taniborbactam, and tebipenem)</p></li>
<li><p>cephalosporins<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>cephalosporins<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>cephalosporins_1st<br>(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine)</p></li>
<li><p>cephalosporins_2nd<br>(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening test, cefprozil, cefuroxime, cefuroxime axetil, and loracarbef)</p></li>
<li><p>cephalosporins_3rd<br>(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef)</p></li>
<li><p>cephalosporins_3rd<br>(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef)</p></li>
<li><p>cephalosporins_4th<br>(cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)</p></li>
<li><p>cephalosporins_5th<br>(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam)</p></li>
<li><p>cephalosporins_except_caz<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>cephalosporins_except_caz<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>fluoroquinolones<br>(besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>glycopeptides<br>(avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod)</p></li>
<li><p>glycopeptides_except_lipo<br>(avoparcin, bleomycin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, and vancomycin-macromethod)</p></li>
<li><p>fusidanes<br>(fusidic acid)</p></li>
<li><p>glycopeptides<br>(avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod, and zorbamycin)</p></li>
<li><p>glycopeptides_except_lipo<br>(avoparcin, bleomycin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, vancomycin-macromethod, and zorbamycin)</p></li>
<li><p>ionophores<br>(lasalocid, monensin sodium, narasin, nystatin, and salinomycin)</p></li>
<li><p>isoxazolylpenicillins<br>(cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test)</p></li>
<li><p>lincosamides<br>(clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin)</p></li>
<li><p>lipoglycopeptides<br>(dalbavancin, oritavancin, and telavancin)</p></li>
@@ -173,13 +175,15 @@
<li><p>nitrofurans<br>(furazidin, furazolidone, nifurtoinol, nitrofurantoin, and nitrofurazone)</p></li>
<li><p>oxazolidinones<br>(cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone)</p></li>
<li><p>penicillins<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic acid)</p></li>
<li><p>peptides<br>(avoparcin, bacitracin, bleomycin, dalbavancin, daptomycin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, thiostrepton, vancomycin, vancomycin-macromethod, and zorbamycin)</p></li>
<li><p>phenicols<br>(chloramphenicol, florfenicol, and thiamphenicol)</p></li>
<li><p>phosphonics<br>(amikacin/fosfomycin and fosfomycin)</p></li>
<li><p>pleuromutilins<br>(retapamulin and tiamulin)</p></li>
<li><p>polymyxins<br>(colistin, polymyxin B, and polymyxin B/polysorbate 80)</p></li>
<li><p>quinolones<br>(besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, ozenoxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<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>streptogramins<br>(ostreogrycin, pristinamycin, quinupristin/dalfopristin, and virginiamycine)</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>

83
reference/custom_eucast_rules.md
View File

@@ -135,14 +135,14 @@ TZP (piperacillin/tazobactam) is "R":
#> 1. If TZP is "R" then set to "R":
#> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
These 38 antimicrobial groups are allowed in the rules
These 42 antimicrobial groups are allowed in the rules
(case-insensitive) and can be used in any combination:
- aminoglycosides
(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin,
bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high,
habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high,
kanamycin/cephalexin, micronomicin, neomycin, netilmicin,
kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin,
pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin,
streptoduocin, streptomycin, streptomycin-high, tobramycin, and
tobramycin-high)
@@ -177,11 +177,12 @@ These 38 antimicrobial groups are allowed in the rules
aztreonam/nacubactam, cefepime/enmetazobactam, cefepime/nacubactam,
cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam,
cefoperazone/sulbactam, cefotaxime/sulbactam, ceftaroline/avibactam,
ceftazidime/avibactam, ceftolozane/tazobactam, imipenem/relebactam,
meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam,
nacubactam, penicillin/sulbactam, piperacillin/sulbactam,
piperacillin/tazobactam, sulbactam, sultamicillin, taniborbactam,
tazobactam, ticarcillin/clavulanic acid, and zidebactam)
ceftazidime/avibactam, ceftibuten/avibactam, ceftolozane/tazobactam,
imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam,
mezlocillin/sulbactam, nacubactam, penicillin/sulbactam,
piperacillin/sulbactam, piperacillin/tazobactam, sulbactam,
sultamicillin, taniborbactam, tazobactam, ticarcillin/clavulanic acid,
xeruborbactam, and zidebactam)
- betalactams
(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam,
@@ -206,12 +207,12 @@ These 38 antimicrobial groups are allowed in the rules
cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline,
ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam,
ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole,
ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil,
ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam,
ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime,
cefuroxime axetil, cephradine, ciclacillin, clometocillin,
cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem,
flucloxacillin, hetacillin, imipenem, imipenem/EDTA,
ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime
alapivoxil, ceftobiprole, ceftobiprole medocaril,
ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase
inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin,
clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin,
ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA,
imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam,
meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin,
meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin,
@@ -232,11 +233,11 @@ These 38 antimicrobial groups are allowed in the rules
cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic
acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid,
ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic
acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor,
imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam,
mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam,
piperacillin/sulbactam, piperacillin/tazobactam, and
ticarcillin/clavulanic acid)
acid, ceftibuten/avibactam, ceftolozane/tazobactam,
ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam,
meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam,
penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam,
piperacillin/tazobactam, and ticarcillin/clavulanic acid)
- carbapenems
(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA,
@@ -261,11 +262,11 @@ These 38 antimicrobial groups are allowed in the rules
cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide,
ceftaroline, ceftaroline/avibactam, ceftazidime,
ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram
pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime
alapivoxil, ceftobiprole, ceftobiprole medocaril,
ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase
inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and
loracarbef)
pivoxil, ceftezole, ceftibuten, ceftibuten/avibactam, ceftiofur,
ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole
medocaril, ceftolozane/tazobactam, ceftriaxone,
ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil,
cephradine, latamoxef, and loracarbef)
- cephalosporins_1st
(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin,
@@ -286,8 +287,8 @@ These 38 antimicrobial groups are allowed in the rules
cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic
acid, cefsulodin, ceftazidime, ceftazidime/avibactam,
ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten,
ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone,
ceftriaxone/beta-lactamase inhibitor, and latamoxef)
ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil,
ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef)
- cephalosporins_4th
(cefepime, cefepime/amikacin, cefepime/clavulanic acid,
@@ -316,10 +317,11 @@ These 38 antimicrobial groups are allowed in the rules
cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide,
ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam,
ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole,
ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil,
ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam,
ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime,
cefuroxime axetil, cephradine, latamoxef, and loracarbef)
ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime
alapivoxil, ceftobiprole, ceftobiprole medocaril,
ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase
inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and
loracarbef)
- fluoroquinolones
(besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole,
@@ -336,14 +338,21 @@ These 38 antimicrobial groups are allowed in the rules
sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and
trovafloxacin)
- fusidanes
(fusidic acid)
- glycopeptides
(avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin,
ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin,
vancomycin, and vancomycin-macromethod)
vancomycin, vancomycin-macromethod, and zorbamycin)
- glycopeptides_except_lipo
(avoparcin, bleomycin, norvancomycin, ramoplanin, teicoplanin,
teicoplanin-macromethod, vancomycin, and vancomycin-macromethod)
teicoplanin-macromethod, vancomycin, vancomycin-macromethod, and
zorbamycin)
- ionophores
(lasalocid, monensin sodium, narasin, nystatin, and salinomycin)
- isoxazolylpenicillins
(cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin,
@@ -393,12 +402,21 @@ These 38 antimicrobial groups are allowed in the rules
talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic
acid)
- peptides
(avoparcin, bacitracin, bleomycin, dalbavancin, daptomycin,
norvancomycin, oritavancin, ramoplanin, teicoplanin,
teicoplanin-macromethod, telavancin, thiostrepton, vancomycin,
vancomycin-macromethod, and zorbamycin)
- phenicols
(chloramphenicol, florfenicol, and thiamphenicol)
- phosphonics
(amikacin/fosfomycin and fosfomycin)
- pleuromutilins
(retapamulin and tiamulin)
- polymyxins
(colistin, polymyxin B, and polymyxin B/polysorbate 80)
@@ -428,7 +446,8 @@ These 38 antimicrobial groups are allowed in the rules
(zoliflodacin)
- streptogramins
(pristinamycin and quinupristin/dalfopristin)
(ostreogrycin, pristinamycin, quinupristin/dalfopristin, and
virginiamycine)
- sulfonamides
(isoniazid/sulfamethoxazole/trimethoprim/pyridoxine,

17
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="">3.0.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9022</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">
@@ -144,21 +144,21 @@
<span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">cephalosporins_2nd</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span> <span class="op">~</span> <span class="st">"My MDRO #2"</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">glycopeptides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span> <span class="op">~</span> <span class="st">"My MDRO #3"</span></span>
<span><span class="op">)</span></span></code></pre><p></p></div>
<p>All 38 antimicrobial selectors are supported for use in the rules:</p><ul><li><p><code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> can select: <br> amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high</p></li>
<p>All 42 antimicrobial selectors are supported for use in the rules:</p><ul><li><p><code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> can select: <br> amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high</p></li>
<li><p><code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> can select: <br> amoxicillin, amoxicillin/clavulanic acid, and ampicillin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">antifungals()</a></code> can select: <br> amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole</p></li>
<li><p><code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> can select: <br> 4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">betalactams()</a></code> can select: <br> amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, taniborbactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam</p></li>
<li><p><code><a href="antimicrobial_selectors.html">betalactams_with_inhibitor()</a></code> can select: <br> amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid</p></li>
<li><p><code><a href="antimicrobial_selectors.html">betalactams()</a></code> can select: <br> amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, taniborbactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam</p></li>
<li><p><code><a href="antimicrobial_selectors.html">betalactams_with_inhibitor()</a></code> can select: <br> amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftibuten/avibactam, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid</p></li>
<li><p><code><a href="antimicrobial_selectors.html">carbapenems()</a></code> can select: <br> biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, taniborbactam, and tebipenem</p></li>
<li><p><code><a href="antimicrobial_selectors.html">cephalosporins()</a></code> can select: <br> cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef</p></li>
<li><p><code><a href="antimicrobial_selectors.html">cephalosporins()</a></code> can select: <br> cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef</p></li>
<li><p><code><a href="antimicrobial_selectors.html">cephalosporins_1st()</a></code> can select: <br> cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine</p></li>
<li><p><code><a href="antimicrobial_selectors.html">cephalosporins_2nd()</a></code> can select: <br> cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening test, cefprozil, cefuroxime, cefuroxime axetil, and loracarbef</p></li>
<li><p><code><a href="antimicrobial_selectors.html">cephalosporins_3rd()</a></code> can select: <br> cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef</p></li>
<li><p><code><a href="antimicrobial_selectors.html">cephalosporins_3rd()</a></code> can select: <br> cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef</p></li>
<li><p><code><a href="antimicrobial_selectors.html">cephalosporins_4th()</a></code> can select: <br> cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome</p></li>
<li><p><code><a href="antimicrobial_selectors.html">cephalosporins_5th()</a></code> can select: <br> ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam</p></li>
<li><p><code><a href="antimicrobial_selectors.html">fluoroquinolones()</a></code> can select: <br> besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">glycopeptides()</a></code> can select: <br> avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod</p></li>
<li><p><code><a href="antimicrobial_selectors.html">glycopeptides()</a></code> can select: <br> avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod, and zorbamycin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">isoxazolylpenicillins()</a></code> can select: <br> cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test</p></li>
<li><p><code><a href="antimicrobial_selectors.html">lincosamides()</a></code> can select: <br> clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">lipoglycopeptides()</a></code> can select: <br> dalbavancin, oritavancin, and telavancin</p></li>
@@ -167,13 +167,14 @@
<li><p><code><a href="antimicrobial_selectors.html">nitrofurans()</a></code> can select: <br> furazidin, furazolidone, nifurtoinol, nitrofurantoin, and nitrofurazone</p></li>
<li><p><code><a href="antimicrobial_selectors.html">oxazolidinones()</a></code> can select: <br> cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone</p></li>
<li><p><code><a href="antimicrobial_selectors.html">penicillins()</a></code> can select: <br> amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic acid</p></li>
<li><p><code><a href="antimicrobial_selectors.html">peptides()</a></code> can select: <br> avoparcin, bacitracin, bleomycin, dalbavancin, daptomycin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, thiostrepton, vancomycin, vancomycin-macromethod, and zorbamycin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">phenicols()</a></code> can select: <br> chloramphenicol, florfenicol, and thiamphenicol</p></li>
<li><p><code><a href="antimicrobial_selectors.html">phosphonics()</a></code> can select: <br> amikacin/fosfomycin and fosfomycin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">polymyxins()</a></code> can select: <br> colistin, polymyxin B, and polymyxin B/polysorbate 80</p></li>
<li><p><code><a href="antimicrobial_selectors.html">quinolones()</a></code> can select: <br> besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, ozenoxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin</p></li>
<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">streptogramins()</a></code> can select: <br> ostreogrycin, pristinamycin, quinupristin/dalfopristin, and virginiamycine</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>

51
reference/custom_mdro_guideline.md
View File

@@ -126,14 +126,14 @@ antimicrobial group:
all(glycopeptides() == "R") ~ "My MDRO #3"
)
All 38 antimicrobial selectors are supported for use in the rules:
All 42 antimicrobial selectors are supported for use in the rules:
- [`aminoglycosides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin,
bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high,
habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high,
kanamycin/cephalexin, micronomicin, neomycin, netilmicin,
kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin,
pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin,
streptoduocin, streptomycin, streptomycin-high, tobramycin, and
tobramycin-high
@@ -189,12 +189,12 @@ All 38 antimicrobial selectors are supported for use in the rules:
cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline,
ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam,
ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole,
ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil,
ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam,
ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime,
cefuroxime axetil, cephradine, ciclacillin, clometocillin,
cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem,
flucloxacillin, hetacillin, imipenem, imipenem/EDTA,
ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime
alapivoxil, ceftobiprole, ceftobiprole medocaril,
ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase
inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin,
clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin,
ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA,
imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam,
meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin,
meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin,
@@ -216,11 +216,11 @@ All 38 antimicrobial selectors are supported for use in the rules:
cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic
acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid,
ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic
acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor,
imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam,
mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam,
piperacillin/sulbactam, piperacillin/tazobactam, and
ticarcillin/clavulanic acid
acid, ceftibuten/avibactam, ceftolozane/tazobactam,
ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam,
meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam,
penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam,
piperacillin/tazobactam, and ticarcillin/clavulanic acid
- [`carbapenems()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
@@ -247,10 +247,11 @@ All 38 antimicrobial selectors are supported for use in the rules:
cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline,
ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam,
ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole,
ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil,
ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam,
ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime,
cefuroxime axetil, cephradine, latamoxef, and loracarbef
ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime
alapivoxil, ceftobiprole, ceftobiprole medocaril,
ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase
inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and
loracarbef
- [`cephalosporins_1st()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
@@ -274,8 +275,8 @@ All 38 antimicrobial selectors are supported for use in the rules:
cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic
acid, cefsulodin, ceftazidime, ceftazidime/avibactam,
ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten,
ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone,
ceftriaxone/beta-lactamase inhibitor, and latamoxef
ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil,
ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef
- [`cephalosporins_4th()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
@@ -309,7 +310,7 @@ All 38 antimicrobial selectors are supported for use in the rules:
can select:
avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin,
ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin,
vancomycin, and vancomycin-macromethod
vancomycin, vancomycin-macromethod, and zorbamycin
- [`isoxazolylpenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
@@ -367,6 +368,13 @@ All 38 antimicrobial selectors are supported for use in the rules:
talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic
acid
- [`peptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
avoparcin, bacitracin, bleomycin, dalbavancin, daptomycin,
norvancomycin, oritavancin, ramoplanin, teicoplanin,
teicoplanin-macromethod, telavancin, thiostrepton, vancomycin,
vancomycin-macromethod, and zorbamycin
- [`phenicols()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
chloramphenicol, florfenicol, and thiamphenicol
@@ -409,7 +417,8 @@ All 38 antimicrobial selectors are supported for use in the rules:
- [`streptogramins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
pristinamycin and quinupristin/dalfopristin
ostreogrycin, pristinamycin, quinupristin/dalfopristin, and
virginiamycine
- [`sulfonamides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:

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="">3.0.1.9021</small>
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reference/example_isolates.html
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reference/index.html
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@@ -263,7 +263,7 @@
<dt>
<code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> <code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">antifungals()</a></code> <code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> <code><a href="antimicrobial_selectors.html">betalactams()</a></code> <code><a href="antimicrobial_selectors.html">betalactams_with_inhibitor()</a></code> <code><a href="antimicrobial_selectors.html">carbapenems()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_1st()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_4th()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_5th()</a></code> <code><a href="antimicrobial_selectors.html">fluoroquinolones()</a></code> <code><a href="antimicrobial_selectors.html">glycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">isoxazolylpenicillins()</a></code> <code><a href="antimicrobial_selectors.html">lincosamides()</a></code> <code><a href="antimicrobial_selectors.html">lipoglycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">macrolides()</a></code> <code><a href="antimicrobial_selectors.html">monobactams()</a></code> <code><a href="antimicrobial_selectors.html">nitrofurans()</a></code> <code><a href="antimicrobial_selectors.html">oxazolidinones()</a></code> <code><a href="antimicrobial_selectors.html">penicillins()</a></code> <code><a href="antimicrobial_selectors.html">phenicols()</a></code> <code><a href="antimicrobial_selectors.html">phosphonics()</a></code> <code><a href="antimicrobial_selectors.html">polymyxins()</a></code> <code><a href="antimicrobial_selectors.html">quinolones()</a></code> <code><a href="antimicrobial_selectors.html">rifamycins()</a></code> <code><a href="antimicrobial_selectors.html">spiropyrimidinetriones()</a></code> <code><a href="antimicrobial_selectors.html">streptogramins()</a></code> <code><a href="antimicrobial_selectors.html">sulfonamides()</a></code> <code><a href="antimicrobial_selectors.html">tetracyclines()</a></code> <code><a href="antimicrobial_selectors.html">trimethoprims()</a></code> <code><a href="antimicrobial_selectors.html">ureidopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">amr_class()</a></code> <code><a href="antimicrobial_selectors.html">amr_selector()</a></code> <code><a href="antimicrobial_selectors.html">administrable_per_os()</a></code> <code><a href="antimicrobial_selectors.html">administrable_iv()</a></code> <code><a href="antimicrobial_selectors.html">not_intrinsic_resistant()</a></code>
<code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> <code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">antifungals()</a></code> <code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> <code><a href="antimicrobial_selectors.html">betalactams()</a></code> <code><a href="antimicrobial_selectors.html">betalactams_with_inhibitor()</a></code> <code><a href="antimicrobial_selectors.html">carbapenems()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_1st()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_4th()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_5th()</a></code> <code><a href="antimicrobial_selectors.html">fluoroquinolones()</a></code> <code><a href="antimicrobial_selectors.html">glycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">isoxazolylpenicillins()</a></code> <code><a href="antimicrobial_selectors.html">lincosamides()</a></code> <code><a href="antimicrobial_selectors.html">lipoglycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">macrolides()</a></code> <code><a href="antimicrobial_selectors.html">monobactams()</a></code> <code><a href="antimicrobial_selectors.html">nitrofurans()</a></code> <code><a href="antimicrobial_selectors.html">oxazolidinones()</a></code> <code><a href="antimicrobial_selectors.html">penicillins()</a></code> <code><a href="antimicrobial_selectors.html">peptides()</a></code> <code><a href="antimicrobial_selectors.html">phenicols()</a></code> <code><a href="antimicrobial_selectors.html">phosphonics()</a></code> <code><a href="antimicrobial_selectors.html">polymyxins()</a></code> <code><a href="antimicrobial_selectors.html">quinolones()</a></code> <code><a href="antimicrobial_selectors.html">rifamycins()</a></code> <code><a href="antimicrobial_selectors.html">spiropyrimidinetriones()</a></code> <code><a href="antimicrobial_selectors.html">streptogramins()</a></code> <code><a href="antimicrobial_selectors.html">sulfonamides()</a></code> <code><a href="antimicrobial_selectors.html">tetracyclines()</a></code> <code><a href="antimicrobial_selectors.html">trimethoprims()</a></code> <code><a href="antimicrobial_selectors.html">ureidopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">amr_class()</a></code> <code><a href="antimicrobial_selectors.html">amr_selector()</a></code> <code><a href="antimicrobial_selectors.html">administrable_per_os()</a></code> <code><a href="antimicrobial_selectors.html">administrable_iv()</a></code> <code><a href="antimicrobial_selectors.html">not_intrinsic_resistant()</a></code>
</dt>
<dd>Antimicrobial Selectors</dd>
@@ -393,7 +393,7 @@
<code><a href="antimicrobials.html">antimicrobials</a></code> <code><a href="antimicrobials.html">antibiotics</a></code> <code><a href="antimicrobials.html">antivirals</a></code>
</dt>
<dd>Data Sets with 618 Antimicrobial Drugs</dd>
<dd>Data Sets with 624 Antimicrobial Drugs</dd>
<dt>

3
reference/index.md
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@@ -258,6 +258,7 @@ or determine multi-drug resistant microorganisms (MDRO,
[`nitrofurans()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`oxazolidinones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`penicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`peptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`phenicols()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`phosphonics()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`polymyxins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
@@ -390,7 +391,7 @@ information about how to work with functions in this package.
- [`antimicrobials`](https://amr-for-r.org/reference/antimicrobials.md)
[`antibiotics`](https://amr-for-r.org/reference/antimicrobials.md)
[`antivirals`](https://amr-for-r.org/reference/antimicrobials.md) :
Data Sets with 618 Antimicrobial Drugs
Data Sets with 624 Antimicrobial Drugs
- [`clinical_breakpoints`](https://amr-for-r.org/reference/clinical_breakpoints.md)
: Data Set with Clinical Breakpoints for SIR Interpretation
- [`example_isolates`](https://amr-for-r.org/reference/example_isolates.md)

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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
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reference/peptides.html Normal file
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@@ -0,0 +1,8 @@
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reference/plot.html
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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reference/proportion.html
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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@@ -7,7 +7,7 @@
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reference/resistance_predict.html
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@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
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reference/skewness.html
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@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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reference/top_n_microorganisms.html
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@@ -7,7 +7,7 @@
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reference/translate.html
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search.json
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