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news/index.html
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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="">3.0.1.9077</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9078</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,15 +49,15 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9077" id="amr-3019077">AMR 3.0.1.9077<a class="anchor" aria-label="anchor" href="#amr-3019077"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9078" id="amr-3019078">AMR 3.0.1.9078<a class="anchor" aria-label="anchor" href="#amr-3019078"></a></h2>
<p>Planned as v3.1.0, end of June 2026.</p>
<div class="section level4">
<h4 id="breaking-changes-3-0-1-9077">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9077"></a></h4>
<h4 id="breaking-changes-3-0-1-9078">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9078"></a></h4>
<ul><li>The former <em>kingdoms</em> Bacteria and Archaea are now each divided into four kingdoms with new top-level <em>domains</em> ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new <code>domain</code> column in the <code>microorganisms</code> data set was added, and more importantly, <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal kingdom (e.g. <code>"Pseudomonadati"</code> instead of <code>"Bacteria"</code>). Use <code><a href="../reference/mo_property.html">mo_domain()</a></code> for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), <code>kingdom</code> and <code>domain</code> are identical.</li>
<li>Faster parallel computing via the <code>future</code> package for <code><a href="../reference/as.sir.html">as.sir()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>.</li>
</ul></div>
<div class="section level4">
<h4 id="new-3-0-1-9077">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9077"></a></h4>
<h4 id="new-3-0-1-9078">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9078"></a></h4>
<ul><li>EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the <code>clinical_breakpoints</code> data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations</li>
<li>Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting <code>breakpoint_type = "ECOFF"</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code>; WT/NWT results are fully supported in all resistance/susceptibility functions and plots (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li>
<li>
@@ -74,8 +74,9 @@
<li>New <code><a href="../reference/antibiogram.html">wisca_plot()</a></code> to assess the susceptibility and incidence distributions from the Monte Carlo simulations</li>
</ul></div>
<div class="section level4">
<h4 id="fixed-3-0-1-9077">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9077"></a></h4>
<ul><li>
<h4 id="fixed-3-0-1-9078">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9078"></a></h4>
<ul><li>Setting <code>options(AMR_guideline = "EUCAST 2012")</code> or any year-qualified value no longer causes errors or silent wrong behaviour in <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, <code><a href="../reference/proportion.html">resistance()</a></code>, <code><a href="../reference/proportion.html">susceptibility()</a></code>, <code><a href="../reference/count.html">count_resistant()</a></code>, <code><a href="../reference/count.html">count_susceptible()</a></code>, and SIR plotting/printing functions (<a href="https://github.com/msberends/AMR/issues/298" class="external-link">#298</a>)</li>
<li>
<code><a href="../reference/as.sir.html">as.sir()</a></code>
<ul><li>On data frames: already-converted SIR columns no longer dropped on re-run (<a href="https://github.com/msberends/AMR/issues/278" class="external-link">#278</a>)</li>
<li>Metadata columns (e.g. <code>patient</code>, <code>ward</code>) no longer misidentified as antibiotic columns</li>
@@ -101,7 +102,7 @@
</li>
</ul></div>
<div class="section level4">
<h4 id="updated-3-0-1-9077">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9077"></a></h4>
<h4 id="updated-3-0-1-9078">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9078"></a></h4>
<ul><li>
<code><a href="../reference/top_n_microorganisms.html">top_n_microorganisms()</a></code>: new <code>property_for_each</code> argument for sub-grouping within top <em>n</em> groups; rank ordering enforced (only lower taxonomic ranks allowed); fixed <code>property = NULL</code> not being accepted; inner filter now tracks original row indices to prevent cross-group contamination</li>
<li>Taxonomic update for all microorganisms, now updated to June 2026</li>

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# Changelog
## AMR 3.0.1.9077
## AMR 3.0.1.9078
Planned as v3.1.0, end of June 2026.
@@ -77,6 +77,15 @@ Planned as v3.1.0, end of June 2026.
#### Fixed
- Setting `options(AMR_guideline = "EUCAST 2012")` or any year-qualified
value no longer causes errors or silent wrong behaviour in
[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md),
[`resistance()`](https://amr-for-r.org/reference/proportion.md),
[`susceptibility()`](https://amr-for-r.org/reference/proportion.md),
[`count_resistant()`](https://amr-for-r.org/reference/count.md),
[`count_susceptible()`](https://amr-for-r.org/reference/count.md), and
SIR plotting/printing functions
([\#298](https://github.com/msberends/AMR/issues/298))
- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
- On data frames: already-converted SIR columns no longer dropped on
re-run ([\#278](https://github.com/msberends/AMR/issues/278))