Built site for AMR@3.0.1.9070: 637ada9

news/index.html

@@ -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="">3.0.1.9069</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9070</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="3.0.1.9069" id="amr-3019069">AMR 3.0.1.9069<a class="anchor" aria-label="anchor" href="#amr-3019069"></a></h2>
+<h2 class="pkg-version" data-toc-text="3.0.1.9070" id="amr-3019070">AMR 3.0.1.9070<a class="anchor" aria-label="anchor" href="#amr-3019070"></a></h2>
 <p>Planned as v3.1.0, end of June 2026.</p>
 <div class="section level4">
-<h4 id="breaking-changes-3-0-1-9069">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9069"></a></h4>
+<h4 id="breaking-changes-3-0-1-9070">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9070"></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-3-0-1-9069">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9069"></a></h4>
+<h4 id="new-3-0-1-9070">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9070"></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>
@@ -74,7 +74,7 @@
 <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-3-0-1-9069">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9069"></a></h4>
+<h4 id="fixed-3-0-1-9070">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9070"></a></h4>
 <ul><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>
@@ -101,7 +101,7 @@
 </li>
 </ul></div>
 <div class="section level4">
-<h4 id="updated-3-0-1-9069">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9069"></a></h4>
+<h4 id="updated-3-0-1-9070">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9070"></a></h4>
 <ul><li>Taxonomic update for all microorganisms, now updated to June 2026</li>
 <li>
 <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal taxonomic kingdom; a one-time note per session explains the change when querying bacterial or archaeal records.</li>
@@ -125,6 +125,8 @@
 <li>Improved console messages with clickable links throughout, powered by <code>cli</code> if it is installed (<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/as.disk.html">as.disk()</a></code>: input validation is now more strict, rejecting values that are not recognisable as a numeric disk zone diameter</li>
+<li>
+<code><a href="../reference/as.sir.html">as.sir()</a></code> gains an <code>enforce_method</code> argument (<code>"auto"</code>, <code>"mic"</code>, or <code>"disk"</code>) to force the interpretation method when S3 class information is lost, e.g. when called from Python (<a href="https://github.com/msberends/AMR/issues/291" class="external-link">#291</a>)</li>
 </ul></div>
 </div>
     <div class="section level2">

news/index.md

@@ -1,6 +1,6 @@
 # Changelog
 
-## AMR 3.0.1.9069
+## AMR 3.0.1.9070
 
 Planned as v3.1.0, end of June 2026.
 
@@ -175,6 +175,11 @@ Planned as v3.1.0, end of June 2026.
 - [`as.disk()`](https://amr-for-r.org/reference/as.disk.md): input
   validation is now more strict, rejecting values that are not
   recognisable as a numeric disk zone diameter
+- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) gains an
+  `enforce_method` argument (`"auto"`, `"mic"`, or `"disk"`) to force
+  the interpretation method when S3 class information is lost, e.g. when
+  called from Python
+  ([\#291](https://github.com/msberends/AMR/issues/291))
 
 ## AMR 3.0.1