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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="">3.0.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9045</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">
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</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9044" id="amr-3019044">AMR 3.0.1.9044<a class="anchor" aria-label="anchor" href="#amr-3019044"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9045" id="amr-3019045">AMR 3.0.1.9045<a class="anchor" aria-label="anchor" href="#amr-3019045"></a></h2>
<div class="section level4">
<h4 id="new-3-0-1-9044">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9044"></a></h4>
<h4 id="new-3-0-1-9045">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9045"></a></h4>
<ul><li>Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the <code>clinical_breakpoints</code> data set for usage in <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations.</li>
<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>
@@ -80,11 +80,13 @@
<li>Function <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>
<li>Gained argument <code>add_if_missing</code> (default: <code>TRUE</code>). When set to <code>FALSE</code>, rules are only applied to cells that already contain an SIR value; <code>NA</code> cells are left untouched. This is useful with <code>overwrite = TRUE</code> to update reported results without imputing values for drugs that were not tested (<a href="https://github.com/msberends/AMR/issues/259" class="external-link">#259</a>)</li>
</ul></li>
<li>Function <code><a href="../reference/amr_course.html">amr_course()</a></code>, which allows for automated download and unpacking of a GitHub repository for e.g. webinar use</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-3-0-1-9044">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9044"></a></h4>
<h4 id="fixes-3-0-1-9045">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9045"></a></h4>
<ul><li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where values that were purely numeric (e.g., <code>"1"</code>) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter</li>
<li>Fixed a bug in <code><a href="../reference/as.mic.html">as.mic()</a></code> where MIC values in scientific notation (e.g., <code>"1e-3"</code>) were incorrectly handled because the letter <code>e</code> was removed along with other Unicode letters; scientific notation <code>e</code> is now preserved</li>
<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>
@@ -99,7 +101,7 @@
<li>Fixed SIR and MIC coercion of combined values, e.g. <code>as.sir("&lt;= 0.002; S")</code> or <code>as.mic("S; 0.002")</code> (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li>
</ul></div>
<div class="section level4">
<h4 id="updates-3-0-1-9044">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9044"></a></h4>
<h4 id="updates-3-0-1-9045">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9045"></a></h4>
<ul><li>Extensive <code>cli</code> integration for better message handling and clickable links in messages and warnings (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li>
<li>
<code><a href="../reference/mdro.html">mdro()</a></code> now infers resistance for a <em>missing</em> base drug column from an <em>available</em> corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument <code>infer_from_combinations</code>, which defaults to <code>TRUE</code> (<a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a>). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).</li>

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# Changelog
## AMR 3.0.1.9044
## AMR 3.0.1.9045
#### New
@@ -47,10 +47,19 @@
([\#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
- Gained argument `add_if_missing` (default: `TRUE`). When set to
`FALSE`, rules are only applied to cells that already contain an SIR
value; `NA` cells are left untouched. This is useful with
`overwrite = TRUE` to update reported results without imputing
values for drugs that were not tested
([\#259](https://github.com/msberends/AMR/issues/259))
- Function
[`amr_course()`](https://amr-for-r.org/reference/amr_course.md), which
allows for automated download and unpacking of a GitHub repository for
e.g. webinar use
- 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