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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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</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">
@@ -49,9 +49,9 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9050" id="amr-3019050">AMR 3.0.1.9050<a class="anchor" aria-label="anchor" href="#amr-3019050"></a></h2>
<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>
<div class="section level4">
<h4 id="new-3-0-1-9050">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9050"></a></h4>
<h4 id="new-3-0-1-9052">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9052"></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>
<ul><li>
@@ -86,10 +86,8 @@
<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-3-0-1-9050">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9050"></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 (fixes <a href="https://github.com/msberends/AMR/issues/239" class="external-link">#239</a>)</li>
<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: (1) PSOCK workers (Windows / R &lt; 4.0) now correctly load the AMR package before processing, with a graceful fallback to sequential mode when the package cannot be loaded; (2) resolved stale-environment issue where the PSOCK path read a frozen copy of <code>AMR_env</code> instead of the live one, causing the wrong log entries to be captured; (3) fixed log-entry duplication in the fork-based path (<code>mclapply</code>) where pre-existing <code>sir_interpretation_history</code> rows were included in every worker’s captured log; (4) removed use of non-exported internal functions (<code>%pm&gt;%</code>, <code>pm_pull</code>, <code>as.sir.default</code>) from the worker closure, which made PSOCK workers fail; (5) suppressed per-column progress messages inside workers to prevent interleaved console output; (6) fixed a malformed Unicode escape <code>\u00a</code> (3 digits) in the “DONE” status message</li>
<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>
<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>
@@ -111,8 +109,10 @@
</li>
</ul></div>
<div class="section level4">
<h4 id="updates-3-0-1-9050">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9050"></a></h4>
<ul><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>
<h4 id="updates-3-0-1-9052">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9052"></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>
<li>
<code><a href="../reference/mdro.html">mdro()</a></code> now infers resistance for a <em>missing</em> base drug column from an <em>available</em> corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument <code>infer_from_combinations</code>, which defaults to <code>TRUE</code> (<a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a>). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).</li>
<li>