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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="">3.0.1.9057</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9061</small>
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</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9057" id="amr-3019057">AMR 3.0.1.9057<a class="anchor" aria-label="anchor" href="#amr-3019057"></a></h2>
<p>Planned as v3.1.0, May 2026.</p>
<h2 class="pkg-version" data-toc-text="3.0.1.9061" id="amr-3019061">AMR 3.0.1.9061<a class="anchor" aria-label="anchor" href="#amr-3019061"></a></h2>
<p>Planned as v3.1.0, end of June 2026.</p>
<div class="section level4">
<h4 id="new-3-0-1-9057">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9057"></a></h4>
<h4 id="breaking-changes-3-0-1-9061">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9061"></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-3-0-1-9061">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9061"></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>Faster parallel computing via the <code>future</code> package; <strong>breaking change</strong>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>; <code><a href="../reference/antibiogram.html">antibiogram()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code> now also support <code>parallel = TRUE</code> (<a href="https://github.com/msberends/AMR/issues/281" class="external-link">#281</a>)</li>
<li>
<em>tidymodels</em> integration for using SIR, MIC and disk data in modelling pipelines: <code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code>, <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code>, and new column selectors <code><a href="../reference/amr-tidymodels.html">all_sir()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_mic()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_disk()</a></code>
</li>
<li>New <code>esbl_isolates</code> data set for practising AMR modelling</li>
<li>New antimicrobial selectors: <code><a href="../reference/antimicrobial_selectors.html">ionophores()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">peptides()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">phosphonics()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">spiropyrimidinetriones()</a></code>
</li>
<li>New antimicrobials: cefepime/taniborbactam (<code>FTA</code>), ceftibuten/avibactam (<code>CTA</code>), clorobiocin (<code>CLB</code>), kasugamycin (<code>KAS</code>), ostreogrycin (<code>OST</code>), taniborbactam (<code>TAN</code>), thiostrepton (<code>THS</code>), xeruborbactam (<code>XER</code>), zorbamycin (<code>ZOR</code>)</li>
<li>New <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, a unified function for EUCAST and CLSI interpretive rules; <code><a href="../reference/interpretive_rules.html">eucast_rules()</a></code> is now a wrapper around it (<a href="https://github.com/msberends/AMR/issues/235" class="external-link">#235</a>, <a href="https://github.com/msberends/AMR/issues/259" class="external-link">#259</a>)</li>
<li>New <code>morphology</code> column in the <code>microorganisms</code> data set and corresponding <code><a href="../reference/mo_property.html">mo_morphology()</a></code> function, returning the cell shape of bacteria. Data sourced from BacDive; values prefixed with “likely” are extrapolated from genus-level consensus. New <code>add_morphology</code> argument was added to <code><a href="../reference/mo_property.html">mo_gramstain()</a></code> to return combined results such as <code>"Gram-negative rods"</code>.</li>
<li>New <code><a href="../reference/amr_course.html">amr_course()</a></code> to download and unpack course or webinar materials from GitHub in one call</li>
<li>Typed missing value constants <code>NA_ab_</code> and <code>NA_mo_</code>, for use in pipelines that need missing values of a specific class</li>
<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="fixes-3-0-1-9057">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9057"></a></h4>
<h4 id="fixed-3-0-1-9061">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9061"></a></h4>
<ul><li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> 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>); metadata columns (e.g. <code>patient</code>, <code>ward</code>) no longer misidentified as antibiotic columns; <code>info = FALSE</code> now suppresses all messages, including for columns without breakpoints</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>
<li>
<code>info = FALSE</code> now suppresses all messages, including for columns without breakpoints</li>
<li>Assumption of disk zones are now preferred over MIC values when input is only whole numbers (<a href="https://github.com/msberends/AMR/issues/291" class="external-link">#291</a>)</li>
</ul></li>
<li>
<code><a href="../reference/as.mic.html">as.mic()</a></code>: values in scientific notation (e.g. <code>1e-3</code>) now handled correctly</li>
<li>
<code><a href="../reference/as.ab.html">as.ab()</a></code>: codes containing “PH” or “TH” (e.g. <code>ETH</code>, <code>PHE</code>) no longer return <code>NA</code> when mixed with unrecognised input (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
<li>Combined MIC/SIR input values (e.g. <code>"&lt;= 0.002; S"</code> or <code>"S; 0.002"</code>) now parsed correctly (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li>
<li>
<code><a href="../reference/as.mo.html">as.mo()</a></code>:
<ul><li>Input of the form <code>"X complex"</code> now falls back to <code>"X"</code> when the complex is not a distinct taxon in the database, preventing <code>NA</code> results for valid clinical descriptions such as <code>"Proteus vulgaris complex"</code> (<a href="https://github.com/msberends/AMR/issues/287" class="external-link">#287</a>)</li>
<li>Abbreviated-genus input (e.g. <code>"S. apiospermum"</code>) now correctly ranks candidates whose species epithet exactly matches the input above more-prevalent organisms whose species does not match; fixes <code>"S. apiospermum"</code> resolving to <em>Staphylococcus</em> instead of <em>Scedosporium apiospermum</em> (<a href="https://github.com/msberends/AMR/issues/288" class="external-link">#288</a>)</li>
</ul></li>
<li>
<code>get_author_year()</code> in the microorganism reproduction script now strips <code>emend.</code> and everything after it, so <code>ref</code> reflects the combination authority rather than the emendation author (e.g. <em>Rhodococcus equi</em> now returns “Goodfellow et al., 1977” instead of “Nouioui et al., 2018”)</li>
<li>BRMO classification now includes bacterial complexes (<a href="https://github.com/msberends/AMR/issues/275" class="external-link">#275</a>)</li>
<li>Translation fixes for Italian CoNS/CoPS names (<a href="https://github.com/msberends/AMR/issues/256" class="external-link">#256</a>), Dutch antimicrobials, and <code><a href="../reference/proportion.html">sir_df()</a></code> foreign-language output (<a href="https://github.com/msberends/AMR/issues/272" class="external-link">#272</a>)</li>
<li>Fixed some EUCAST Expert Rules, mostly on <em>S. pneumoniae</em>
</li>
</ul></div>
<div class="section level4">
<h4 id="updates-3-0-1-9057">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9057"></a></h4>
<ul><li>
<h4 id="updated-3-0-1-9061">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9061"></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>
<li>
<code><a href="../reference/mo_property.html">mo_taxonomy()</a></code> and <code><a href="../reference/mo_property.html">mo_info()</a></code> gained <code>domain</code> for the list output</li>
<li>
<code><a href="../reference/antibiogram.html">antibiogram()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code> now also support parallel computing via the argument <code>parallel = TRUE</code> (<a href="https://github.com/msberends/AMR/issues/281" class="external-link">#281</a>)</li>
<li>
<code><a href="../reference/AMR-deprecated.html">custom_eucast_rules()</a></code> renamed to <code><a href="../reference/custom_interpretive_rules.html">custom_interpretive_rules()</a></code>; old name deprecated but still works (<a href="https://github.com/msberends/AMR/issues/268" class="external-link">#268</a>)</li>
<li>
<code><a href="../reference/mdro.html">mdro()</a></code> can now infer resistance from a drug+inhibitor combination when the base drug column is absent (e.g. piperacillin inferred from piperacillin/tazobactam); controlled via new <code>infer_from_combinations</code> argument (default <code>TRUE</code>) (<a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a>)</li>
<li>
<code><a href="../reference/antibiogram.html">wisca()</a></code> now more strictly follows Bielicki et al. (2016) by using <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Beta</mtext><mo stretchy="false" form="prefix">(</mo><mn>1</mn><mo>,</mo><mn>9999</mn><mo stretchy="false" form="postfix">)</mo></mrow><annotation encoding="application/x-tex">\text{Beta}(1, 9999)</annotation></semantics></math> for intrinsically resistant pairs, forcing near-zero susceptibility regardless of observed data (based on EUCAST Expected Resistant Phenotypes)</li>
<li>
<code><a href="../reference/proportion.html">susceptibility()</a></code> / <code><a href="../reference/proportion.html">resistance()</a></code>: new <code>guideline</code> argument (default EUCAST) to ensure the ‘I’ category is interpreted correctly per guideline</li>
<li>Capped MIC handling in <code><a href="../reference/as.sir.html">as.sir()</a></code> reworked into four clearly defined options: <code>"none"</code>, <code>"conservative"</code> (new default), <code>"standard"</code>, <code>"lenient"</code> (<a href="https://github.com/msberends/AMR/issues/243" class="external-link">#243</a>)</li>
<li>
<code><a href="../reference/as.mic.html">as.mic()</a></code> / <code><a href="../reference/as.mic.html">rescale_mic()</a></code>: new <code>round_to_next_log2</code> argument to round values up to the nearest log2 dilution level (<a href="https://github.com/msberends/AMR/issues/255" class="external-link">#255</a>)</li>
<li>
<code>antimicrobials$group</code> now a <code>list</code>, so drugs belonging to multiple groups are fully represented; use <code>ab_group(all_groups = TRUE)</code> to retrieve all groups for a drug (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<li>New antimicrobials added: cefepime/taniborbactam (<code>FTA</code>), ceftibuten/avibactam (<code>CTA</code>), clorobiocin (<code>CLB</code>), kasugamycin (<code>KAS</code>), ostreogrycin (<code>OST</code>), taniborbactam (<code>TAN</code>), thiostrepton (<code>THS</code>), xeruborbactam (<code>XER</code>), zorbamycin (<code>ZOR</code>)</li>
<li>Improved console messages with clickable links throughout, powered by <code>cli</code> (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li>
<code>antimicrobials$group</code> is now a <code>list</code>, so that drugs belonging to multiple groups are fully represented; use <code>ab_group(all_groups = TRUE)</code> to retrieve all groups for a drug (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<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>
</ul></div>
</div>
<div class="section level2">