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404.html
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<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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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="">3.0.1.9023</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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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 04 March 2026.</p>
generated on 06 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">2026-03-04</td>
<td align="center">2026-03-06</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">2026-03-04</td>
<td align="center">2026-03-06</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">2026-03-04</td>
<td align="center">2026-03-06</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 04 March 2026.
methodology remains unchanged. This page was generated on 06 March 2026.
## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-03-04 | abcd | Escherichia coli | S | S |
| 2026-03-04 | abcd | Escherichia coli | S | R |
| 2026-03-04 | efgh | Escherichia coli | R | S |
| 2026-03-06 | abcd | Escherichia coli | S | S |
| 2026-03-06 | abcd | Escherichia coli | S | R |
| 2026-03-06 | 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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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">
@@ -198,7 +198,7 @@ function:</p>
<span><span class="co">#&gt; [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co">#&gt; Importance of components:</span></span>
<span><span class="co">#&gt; PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
<span><span class="co">#&gt; Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co">#&gt; Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>

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@@ -117,7 +117,7 @@ summary(pca_result)
#> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"
#> Importance of components:
#> PC1 PC2 PC3 PC4 PC5 PC6 PC7
#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16
#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17
#> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00
#> Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00
```

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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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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">04 March 2026</h4>
<h4 data-toc-skip class="date">06 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>

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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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
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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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
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llms.txt
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@@ -501,8 +501,9 @@ to add your own custom microorganisms to this package.
[`mo_renamed()`](https://amr-for-r.org/reference/as.mo.md)
[`mo_failures()`](https://amr-for-r.org/reference/as.mo.md)
[`mo_reset_session()`](https://amr-for-r.org/reference/as.mo.md)
[`mo_cleaning_regex()`](https://amr-for-r.org/reference/as.mo.md) :
Transform Arbitrary Input to Valid Microbial Taxonomy
[`mo_cleaning_regex()`](https://amr-for-r.org/reference/as.mo.md)
[`NA_mo_`](https://amr-for-r.org/reference/as.mo.md) : Transform
Arbitrary Input to Valid Microbial Taxonomy
- [`mo_name()`](https://amr-for-r.org/reference/mo_property.md)
[`mo_fullname()`](https://amr-for-r.org/reference/mo_property.md)
[`mo_shortname()`](https://amr-for-r.org/reference/mo_property.md)
@@ -557,8 +558,9 @@ from clinical text records, using
- [`as.ab()`](https://amr-for-r.org/reference/as.ab.md)
[`is.ab()`](https://amr-for-r.org/reference/as.ab.md)
[`ab_reset_session()`](https://amr-for-r.org/reference/as.ab.md) :
Transform Input to an Antibiotic ID
[`ab_reset_session()`](https://amr-for-r.org/reference/as.ab.md)
[`NA_ab_`](https://amr-for-r.org/reference/as.ab.md) : Transform Input
to an Antibiotic ID
- [`ab_name()`](https://amr-for-r.org/reference/ab_property.md)
[`ab_cid()`](https://amr-for-r.org/reference/ab_property.md)
[`ab_synonyms()`](https://amr-for-r.org/reference/ab_property.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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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="3.0.1.9023" id="amr-3019023">AMR 3.0.1.9023<a class="anchor" aria-label="anchor" href="#amr-3019023"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9026" id="amr-3019026">AMR 3.0.1.9026<a class="anchor" aria-label="anchor" href="#amr-3019026"></a></h2>
<div class="section level4">
<h4 id="new-3-0-1-9023">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9023"></a></h4>
<h4 id="new-3-0-1-9026">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9026"></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>
@@ -70,7 +70,6 @@
<li>Data set <code>esbl_isolates</code> to practise with AMR modelling</li>
<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>
@@ -80,11 +79,12 @@
<li>
<code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, which allows future implementation of CLSI interpretive rules (<a href="https://github.com/msberends/AMR/issues/235" class="external-link">#235</a>)
<ul><li>
<code><a href="../reference/interpretive_rules.html">eucast_rules()</a></code> has become a wrapper around that function.</li>
<code><a href="../reference/interpretive_rules.html">eucast_rules()</a></code> has become a wrapper around that function</li>
</ul></li>
<li>Two new <code>NA</code> objects, <code>NA_ab_</code> and <code>NA_mo_</code>, analogous to base R’s <code>NA_character_</code> and <code>NA_integer_</code>, for use in pipelines that require typed missing values</li>
</ul></div>
<div class="section level4">
<h4 id="fixes-3-0-1-9023">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9023"></a></h4>
<h4 id="fixes-3-0-1-9026">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9026"></a></h4>
<ul><li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> where certain AB codes containing “PH” or “TH” (such as <code>ETH</code>, <code>MTH</code>, <code>PHE</code>, <code>PHN</code>, <code>STH</code>, <code>THA</code>, <code>THI1</code>) would incorrectly return <code>NA</code> when combined in a vector with any untranslatable value (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
<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>
@@ -94,7 +94,7 @@
<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-3-0-1-9023">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9023"></a></h4>
<h4 id="updates-3-0-1-9026">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9026"></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>
@@ -103,7 +103,7 @@
<code>antimicrobials$group</code> is now a <code>list</code> instead of a <code>character</code>, to contain any group the drug is in (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<li>
<code><a href="../reference/ab_property.html">ab_group()</a></code> gained an argument <code>all_groups</code> to return all groups the antimicrobial drug is in (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<li>Added taniborbactam (<code>TAN</code>) and cefepime/taniborbactam (<code>FTA</code>) to the <code>antimicrobials</code> data set</li>
<li>Added to the <code>antimicrobials</code> data set: cefepime/taniborbactam (<code>FTA</code>), ceftibuten/avibactam (<code>CTA</code>), kasugamycin (<code>KAS</code>), ostreogrycin (<code>OST</code>), taniborbactam (<code>TAN</code>), thiostrepton (<code>THS</code>), xeruborbactam (<code>XER</code>), and zorbamycin (<code>ZOR</code>)</li>
<li>Added explaining message to <code><a href="../reference/as.sir.html">as.sir()</a></code> when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
<li>Updated handling of capped MIC values (<code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, <code>&gt;=</code>) in <code><a href="../reference/as.sir.html">as.sir()</a></code> in the argument <code>capped_mic_handling</code>: (<a href="https://github.com/msberends/AMR/issues/243" class="external-link">#243</a>)
<ul><li>Introduced four clearly defined options: <code>"none"</code>, <code>"conservative"</code> (default), <code>"standard"</code>, and <code>"lenient"</code>

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@@ -1,6 +1,6 @@
# Changelog
## AMR 3.0.1.9023
## AMR 3.0.1.9026
#### New
@@ -23,9 +23,6 @@
[`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.
@@ -41,7 +38,10 @@
which allows future implementation of CLSI interpretive rules
([\#235](https://github.com/msberends/AMR/issues/235))
- [`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
has become a wrapper around that function.
has become a wrapper around that function
- Two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R’s
`NA_character_` and `NA_integer_`, for use in pipelines that require
typed missing values
#### Fixes
@@ -82,8 +82,10 @@
- [`ab_group()`](https://amr-for-r.org/reference/ab_property.md) gained
an argument `all_groups` to return all groups the antimicrobial drug
is in ([\#246](https://github.com/msberends/AMR/issues/246))
- Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the
`antimicrobials` data set
- Added to the `antimicrobials` data set: cefepime/taniborbactam
(`FTA`), ceftibuten/avibactam (`CTA`), kasugamycin (`KAS`),
ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`),
xeruborbactam (`XER`), and zorbamycin (`ZOR`)
- Added explaining message to
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) when
interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R)

2
pkgdown.yml
View File

@@ -10,7 +10,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2026-03-04T08:06Z
last_built: 2026-03-06T11:51Z
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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/AMR-options.html
View File

@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/AMR.html
View File

@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

8
reference/NA_ab_.html Normal file
View File

@@ -0,0 +1,8 @@
<html>
<head>
<meta http-equiv="refresh" content="0;URL=https://amr-for-r.org/reference/as.ab.html" />
<meta name="robots" content="noindex">
<link rel="canonical" href="https://amr-for-r.org/reference/as.ab.html">
</head>
</html>

8
reference/NA_mo_.html Normal file
View File

@@ -0,0 +1,8 @@
<html>
<head>
<meta http-equiv="refresh" content="0;URL=https://amr-for-r.org/reference/as.mo.html" />
<meta name="robots" content="noindex">
<link rel="canonical" href="https://amr-for-r.org/reference/as.mo.html">
</head>
</html>

2
reference/WHOCC.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/WHONET.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/ab_from_text.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/ab_property.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/add_custom_antimicrobials.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/add_custom_microorganisms.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

22
reference/age.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -112,16 +112,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 46 46.01370 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.60548 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.50137 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.58356 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.28767 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.92877 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.69589 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.46301 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.80000 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.30137 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 46 46.01918 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.61096 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.50685 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.58904 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.29315 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.93425 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.70137 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.46849 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.80548 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.30685 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 46.01370 19
#> 2 1953-07-26 72 72.60548 46
#> 3 1949-09-02 76 76.50137 50
#> 4 1986-08-03 39 39.58356 13
#> 5 1932-11-19 93 93.28767 67
#> 6 1949-03-30 76 76.92877 50
#> 7 1996-06-23 29 29.69589 3
#> 8 1963-09-16 62 62.46301 36
#> 9 1952-05-16 73 73.80000 47
#> 10 1952-11-14 73 73.30137 47
#> 1 1980-02-27 46 46.01918 19
#> 2 1953-07-26 72 72.61096 46
#> 3 1949-09-02 76 76.50685 50
#> 4 1986-08-03 39 39.58904 13
#> 5 1932-11-19 93 93.29315 67
#> 6 1949-03-30 76 76.93425 50
#> 7 1996-06-23 29 29.70137 3
#> 8 1963-09-16 62 62.46849 36
#> 9 1952-05-16 73 73.80548 47
#> 10 1952-11-14 73 73.30685 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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/amr-tidymodels.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/antibiogram.html
View File

@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/antimicrobial_selectors.html
View File

@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/antimicrobials.html
View File

@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

7
reference/as.ab.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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">
@@ -60,7 +60,9 @@
<span></span>
<span><span class="fu">is.ab</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">ab_reset_session</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">ab_reset_session</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="va">NA_ab_</span></span></code></pre></div>
</div>
<div class="section level2">
@@ -101,6 +103,7 @@
</ul><p>Use the <code><a href="ab_property.html">ab_*</a></code> functions to get properties based on the returned antibiotic ID, see <em>Examples</em>.</p>
<p>Note: the <code>as.ab()</code> and <code><a href="ab_property.html">ab_*</a></code> functions may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.</p>
<p>You can add your own manual codes to be considered by <code>as.ab()</code> and all <code><a href="ab_property.html">ab_*</a></code> functions, see <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p>
<p><code>NA_ab_</code> is a missing value of the new <code>ab</code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>

5
reference/as.ab.md
View File

@@ -15,6 +15,8 @@ as.ab(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
is.ab(x)
ab_reset_session()
NA_ab_
```
## Arguments
@@ -91,6 +93,9 @@ You can add your own manual codes to be considered by `as.ab()` and all
[`ab_*`](https://amr-for-r.org/reference/ab_property.md) functions, see
[`add_custom_antimicrobials()`](https://amr-for-r.org/reference/add_custom_antimicrobials.md).
`NA_ab_` is a missing value of the new `ab` class, analogous to e.g.
base R's [`NA_character_`](https://rdrr.io/r/base/NA.html).
## Source
World Health Organization (WHO) Collaborating Centre for Drug Statistics

2
reference/as.av.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/as.disk.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/as.mic.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

7
reference/as.mo.html
View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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">
@@ -74,7 +74,9 @@
<span></span>
<span><span class="fu">mo_reset_session</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_cleaning_regex</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">mo_cleaning_regex</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="va">NA_mo_</span></span></code></pre></div>
</div>
<div class="section level2">
@@ -201,6 +203,7 @@
</ul><p>This is based on:</p><ul><li><p>Lancefield RC (1933). <strong>A serological differentiation of human and other groups of hemolytic streptococci.</strong> <em>J Exp Med.</em> 57(4): 571-95; <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
</ul></div>
<p><code>NA_mo_</code> is a missing value of the new <code>mo</code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>

5
reference/as.mo.md
View File

@@ -32,6 +32,8 @@ mo_failures()
mo_reset_session()
mo_cleaning_regex()
NA_mo_
```
## Arguments
@@ -338,6 +340,9 @@ This is based on:
other groups of hemolytic streptococci.** *J Exp Med.* 57(4): 571-95;
[doi:10.1084/jem.57.4.571](https://doi.org/10.1084/jem.57.4.571)
`NA_mo_` is a missing value of the new `mo` class, analogous to e.g.
base R's [`NA_character_`](https://rdrr.io/r/base/NA.html).
## Source
- Berends MS *et al.* (2022). **AMR: An R Package for Working with

10
reference/as.sir.html
View File

@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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">
@@ -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> 2026-03-04 <span style="color: #949494;">08:07:22</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> 2026-03-04 <span style="color: #949494;">08:07:22</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> 2026-03-04 <span style="color: #949494;">08:07:23</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> 2026-03-04 <span style="color: #949494;">08:07:23</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> 2026-03-06 <span style="color: #949494;">11:51:54</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> 2026-03-06 <span style="color: #949494;">11:51:54</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> 2026-03-06 <span style="color: #949494;">11:51:55</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> 2026-03-06 <span style="color: #949494;">11:51:55</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>

8
reference/as.sir.md
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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 2026-03-04 08:07:22 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-04 08:07:22 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-04 08:07:23 1 DISK tobra Escherich… human 16
#> 4 2026-03-04 08:07:23 1 DISK genta Escherich… human 18
#> 1 2026-03-06 11:51:54 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-06 11:51:54 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-06 11:51:55 1 DISK tobra Escherich… human 16
#> 4 2026-03-06 11:51:55 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr>

2
reference/atc_online.html
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@@ -7,7 +7,7 @@
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@@ -7,7 +7,7 @@
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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 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/clinical_breakpoints.html
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@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -7,7 +7,7 @@
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@@ -7,7 +7,7 @@
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@@ -7,7 +7,7 @@
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@@ -7,7 +7,7 @@
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reference/example_isolates.html
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@@ -7,7 +7,7 @@
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reference/example_isolates_unclean.html
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@@ -7,7 +7,7 @@
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reference/export_ncbi_biosample.html
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@@ -7,7 +7,7 @@
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@@ -9,7 +9,7 @@
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@@ -7,7 +7,7 @@
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reference/get_episode.html
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@@ -7,7 +7,7 @@
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reference/ggplot_pca.html
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@@ -7,7 +7,7 @@
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reference/ggplot_sir.html
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@@ -7,7 +7,7 @@
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reference/guess_ab_col.html
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@@ -7,7 +7,7 @@
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6
reference/index.html
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@@ -7,7 +7,7 @@
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@@ -75,7 +75,7 @@
<dl><dt>
<code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_reset_session()</a></code> <code><a href="as.mo.html">mo_cleaning_regex()</a></code>
<code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_reset_session()</a></code> <code><a href="as.mo.html">mo_cleaning_regex()</a></code> <code><a href="as.mo.html">NA_mo_</a></code>
</dt>
<dd>Transform Arbitrary Input to Valid Microbial Taxonomy</dd>
@@ -112,7 +112,7 @@
<dl><dt>
<code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> <code><a href="as.ab.html">ab_reset_session()</a></code>
<code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> <code><a href="as.ab.html">ab_reset_session()</a></code> <code><a href="as.ab.html">NA_ab_</a></code>
</dt>
<dd>Transform Input to an Antibiotic ID</dd>

10
reference/index.md
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@@ -29,8 +29,9 @@ to add your own custom microorganisms to this package.
[`mo_renamed()`](https://amr-for-r.org/reference/as.mo.md)
[`mo_failures()`](https://amr-for-r.org/reference/as.mo.md)
[`mo_reset_session()`](https://amr-for-r.org/reference/as.mo.md)
[`mo_cleaning_regex()`](https://amr-for-r.org/reference/as.mo.md) :
Transform Arbitrary Input to Valid Microbial Taxonomy
[`mo_cleaning_regex()`](https://amr-for-r.org/reference/as.mo.md)
[`NA_mo_`](https://amr-for-r.org/reference/as.mo.md) : Transform
Arbitrary Input to Valid Microbial Taxonomy
- [`mo_name()`](https://amr-for-r.org/reference/mo_property.md)
[`mo_fullname()`](https://amr-for-r.org/reference/mo_property.md)
[`mo_shortname()`](https://amr-for-r.org/reference/mo_property.md)
@@ -85,8 +86,9 @@ from clinical text records, using
- [`as.ab()`](https://amr-for-r.org/reference/as.ab.md)
[`is.ab()`](https://amr-for-r.org/reference/as.ab.md)
[`ab_reset_session()`](https://amr-for-r.org/reference/as.ab.md) :
Transform Input to an Antibiotic ID
[`ab_reset_session()`](https://amr-for-r.org/reference/as.ab.md)
[`NA_ab_`](https://amr-for-r.org/reference/as.ab.md) : Transform Input
to an Antibiotic ID
- [`ab_name()`](https://amr-for-r.org/reference/ab_property.md)
[`ab_cid()`](https://amr-for-r.org/reference/ab_property.md)
[`ab_synonyms()`](https://amr-for-r.org/reference/ab_property.md)

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@@ -13,7 +13,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -7,7 +7,7 @@
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@@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
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reference/mdro.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="">3.0.1.9023</small>
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reference/mean_amr_distance.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="">3.0.1.9023</small>
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reference/microorganisms.codes.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="">3.0.1.9023</small>
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reference/microorganisms.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/microorganisms.html
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
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reference/mo_matching_score.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/mo_property.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/mo_source.html
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@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
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reference/pca.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="">3.0.1.9023</small>
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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
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
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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
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
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reference/random.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="">3.0.1.9023</small>
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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
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
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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
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
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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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@@ -7,7 +7,7 @@
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search.json
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