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@@ -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="">3.0.1.9052</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9053</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">
@@ -49,11 +49,17 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9052" id="amr-3019052">AMR 3.0.1.9052<a class="anchor" aria-label="anchor" href="#amr-3019052"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9053" id="amr-3019053">AMR 3.0.1.9053<a class="anchor" aria-label="anchor" href="#amr-3019053"></a></h2>
<p>This will become release v3.1.0, intended for launch end of May.</p>
<div class="section level4">
<h4 id="new-3-0-1-9052">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9052"></a></h4>
<h4 id="new-3-0-1-9053">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9053"></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>
<li>Support for the <a href="https://future.futureverse.org" class="external-link"><code>future</code></a> package and its framework, as the previous implementation of parallel computing was slow
<ul><li>
<strong>Breaking change</strong>: <code><a href="../reference/as.sir.html">as.sir()</a></code> with <code>parallel = TRUE</code> now requires a non-sequential <code><a href="https://future.futureverse.org/reference/plan.html" class="external-link">future::plan()</a></code> to be active before the call — e.g., <code>future::plan(future::multisession)</code> — and throws an informative error if none is set.</li>
<li>New all-core usage setup: when the number of AB columns is smaller than the number of available cores, rows are now split into batches so all cores stay active (row-batch mode). Previously, a 6-column dataset on a 16-core machine would only use 6 cores; now all 16 are used, with each worker processing a smaller row slice (lower per-worker memory pressure and processing time)</li>
</ul></li>
<li>Integration with the <em>tidymodels</em> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
<ul><li>
<code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code> to transform <code>&lt;mic&gt;</code> columns with log2, and <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code> to convert <code>&lt;sir&gt;</code> columns to numeric</li>
<li>New <code>tidyselect</code> helpers:
@@ -86,9 +92,8 @@
<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-3-0-1-9052">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9052"></a></h4>
<ul><li>Fixed multiple bugs in the <code>parallel = TRUE</code> mode of <code><a href="../reference/as.sir.html">as.sir()</a></code> for data frames</li>
<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>
<h4 id="fixes-3-0-1-9053">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9053"></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>
<li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li>
@@ -104,12 +109,10 @@
<li>Fixed BRMO classification by including bacterial complexes (<a href="https://github.com/msberends/AMR/issues/275" class="external-link">#275</a>)</li>
<li>Fixed <code><a href="../reference/as.sir.html">as.sir()</a></code> for data frames silently deleting columns whose AB class was already <code>&lt;sir&gt;</code> when called a second time (re-running on already-converted data) (<a href="https://github.com/msberends/AMR/issues/278" class="external-link">#278</a>)</li>
<li>Fixed <code><a href="../reference/as.sir.html">as.sir()</a></code> for data frames incorrectly treating metadata columns (e.g. <code>patient</code>, <code>ward</code>) as antibiotic columns when their names coincidentally matched an antibiotic code; column content is now validated against AMR data patterns before inclusion</li>
<li>Improved parallel computing in <code><a href="../reference/as.sir.html">as.sir()</a></code>: when the number of AB columns is smaller than the number of available cores, rows are now split into batches so all cores stay active (row-batch mode). Previously, a 6-column dataset on a 16-core machine would only use 6 cores; now all 16 are used, with each worker processing a smaller row slice (lower per-worker memory pressure)</li>
<li>Fixed <code><a href="../reference/as.sir.html">as.sir()</a></code> ignoring <code>info = FALSE</code> for columns with no breakpoints (e.g. cefoxitin against <em>E. coli</em>): an operator-precedence bug (<code>&amp;&amp;</code>/<code>||</code>) caused the “Interpreting MIC values” intro message to fire unconditionally when <code>nrow(breakpoints) == 0</code>, regardless of <code>info</code>; the progress bar title was also not gated by <code>info</code>
</li>
<li>Fixed <code><a href="../reference/as.sir.html">as.sir()</a></code> ignoring <code>info = FALSE</code> for columns with no breakpoints (e.g. cefoxitin against <em>E. coli</em>)</li>
</ul></div>
<div class="section level4">
<h4 id="updates-3-0-1-9052">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9052"></a></h4>
<h4 id="updates-3-0-1-9053">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9053"></a></h4>
<ul><li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> with <code>reference_data</code>: custom guideline names now correctly classify values as R using EUCAST convention (<code>&gt; breakpoint_R</code> for MIC, <code>&lt; breakpoint_R</code> for disk); custom breakpoints with <code>host = NA</code> now serve as a host-agnostic fallback when no host-specific row matches (<a href="https://github.com/msberends/AMR/issues/239" class="external-link">#239</a>)</li>
<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>
@@ -134,7 +137,6 @@
</ul></li>
<li>
<code><a href="../reference/ab_property.html">ab_group()</a></code> now returns values consist with the AMR selectors (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<li>Added 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>
<div class="section level2">