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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9086</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
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<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>
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<div class="section level2">
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<h2 class="pkg-version" data-toc-text="3.0.1.9086" id="amr-3019086">AMR 3.0.1.9086<a class="anchor" aria-label="anchor" href="#amr-3019086"></a></h2>
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<p>Planned as v3.1.0, end of June 2026.</p>
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<h2 class="pkg-version" data-toc-text="3.0.1.9087" id="amr-3019087">AMR 3.0.1.9087<a class="anchor" aria-label="anchor" href="#amr-3019087"></a></h2>
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<p>Planned as v3.1.0, end of September 2026.</p>
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<div class="section level4">
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<h4 id="breaking-changes-3-0-1-9086">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9086"></a></h4>
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<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>
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<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>
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<h4 id="breaking-changes-3-0-1-9087">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9087"></a></h4>
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<ul><li>
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<p>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.</p>
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<table class="table"><colgroup><col width="33%"><col width="29%"><col width="37%"></colgroup><thead><tr><th>
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<code><a href="../reference/mo_property.html">mo_kingdom()</a></code> < 3.1.0</th>
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<th>
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<code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now</th>
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<th>
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<code><a href="../reference/mo_property.html">mo_domain()</a></code> (unchanged)</th>
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</tr></thead><tbody><tr><td>Bacteria</td>
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<td>Bacillati</td>
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<td>Bacteria</td>
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</tr><tr><td></td>
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<td>Fusobacteriati</td>
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<td>Bacteria</td>
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</tr><tr><td></td>
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<td>Pseudomonadati</td>
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<td>Bacteria</td>
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</tr><tr><td></td>
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<td>Thermotogati</td>
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<td>Bacteria</td>
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</tr><tr><td></td>
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<td></td>
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<td></td>
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</tr><tr><td>Archaea</td>
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<td>Methanobacteriati</td>
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<td>Archaea</td>
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</tr><tr><td></td>
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<td>Nanobdellati</td>
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<td>Archaea</td>
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</tr><tr><td></td>
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<td>Promethearchaeati</td>
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<td>Archaea</td>
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</tr><tr><td></td>
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<td>Thermoproteati</td>
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<td>Archaea</td>
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</tr><tr><td></td>
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<td></td>
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<td></td>
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</tr><tr><td>Fungi</td>
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<td>Fungi</td>
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<td>Fungi</td>
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</tr><tr><td></td>
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<td></td>
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<td></td>
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</tr><tr><td>Protozoa</td>
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<td>Protozoa</td>
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<td>Protozoa</td>
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</tr></tbody></table><p>Thus, <code><a href="../reference/mo_property.html">mo_domain()</a></code> was previously an alias of <code><a href="../reference/mo_property.html">mo_kingdom()</a></code>; it is now a distinct function returning the domain. Output of <code><a href="../reference/mo_property.html">mo_domain()</a></code> is therefore unchanged, while <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal, new kingdom.</p>
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</li>
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<li><p>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>.</p></li>
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</ul></div>
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<div class="section level4">
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<h4 id="new-3-0-1-9086">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9086"></a></h4>
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<h4 id="new-3-0-1-9087">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9087"></a></h4>
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<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>
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<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>
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<li>
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@@ -74,7 +122,7 @@
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<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>
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</ul></div>
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<div class="section level4">
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<h4 id="fixed-3-0-1-9086">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9086"></a></h4>
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<h4 id="fixed-3-0-1-9087">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9087"></a></h4>
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<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>
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<li>
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<code><a href="../reference/as.sir.html">as.sir()</a></code>
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</li>
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</ul></div>
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<div class="section level4">
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<h4 id="updated-3-0-1-9086">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9086"></a></h4>
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<h4 id="updated-3-0-1-9087">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9087"></a></h4>
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<ul><li>
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<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>
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<li>Taxonomic update for all microorganisms, now updated to June 2026</li>
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@@ -345,7 +393,7 @@
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<footer><div class="pkgdown-footer-left">
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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</div>
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<div class="pkgdown-footer-right">
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@@ -1,8 +1,8 @@
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# Changelog
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## AMR 3.0.1.9086
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## AMR 3.0.1.9087
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Planned as v3.1.0, end of June 2026.
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Planned as v3.1.0, end of September 2026.
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#### Breaking Changes
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@@ -17,6 +17,32 @@ Planned as v3.1.0, end of June 2026.
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[`mo_domain()`](https://amr-for-r.org/reference/mo_property.md) for
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the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa,
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etc.), `kingdom` and `domain` are identical.
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| [`mo_kingdom()`](https://amr-for-r.org/reference/mo_property.md) \< 3.1.0 | [`mo_kingdom()`](https://amr-for-r.org/reference/mo_property.md) now | [`mo_domain()`](https://amr-for-r.org/reference/mo_property.md) (unchanged) |
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|----|----|----|
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| Bacteria | Bacillati | Bacteria |
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| | Fusobacteriati | Bacteria |
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| | Pseudomonadati | Bacteria |
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| | Thermotogati | Bacteria |
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| | | |
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| Archaea | Methanobacteriati | Archaea |
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| | Nanobdellati | Archaea |
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| | Promethearchaeati | Archaea |
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| | Thermoproteati | Archaea |
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| | | |
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| Fungi | Fungi | Fungi |
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| | | |
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| Protozoa | Protozoa | Protozoa |
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Thus, [`mo_domain()`](https://amr-for-r.org/reference/mo_property.md)
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was previously an alias of
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[`mo_kingdom()`](https://amr-for-r.org/reference/mo_property.md); it
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is now a distinct function returning the domain. Output of
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[`mo_domain()`](https://amr-for-r.org/reference/mo_property.md) is
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therefore unchanged, while
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[`mo_kingdom()`](https://amr-for-r.org/reference/mo_property.md) now
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returns the formal, new kingdom.
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- Faster parallel computing via the `future` package for
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[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) and
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[`wisca()`](https://amr-for-r.org/reference/antibiogram.md): a
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