Built site for AMR@3.0.1.9030: e2102c0

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="">3.0.1.9026</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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="3.0.1.9026" id="amr-3019026">AMR 3.0.1.9026<a class="anchor" aria-label="anchor" href="#amr-3019026"></a></h2>
+<h2 class="pkg-version" data-toc-text="3.0.1.9030" id="amr-3019030">AMR 3.0.1.9030<a class="anchor" aria-label="anchor" href="#amr-3019030"></a></h2>
 <div class="section level4">
-<h4 id="new-3-0-1-9026">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9026"></a></h4>
+<h4 id="new-3-0-1-9030">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9030"></a></h4>
 <ul><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>
 <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>
@@ -84,17 +84,22 @@
 <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-3-0-1-9026">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9026"></a></h4>
-<ul><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>
+<h4 id="fixes-3-0-1-9030">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9030"></a></h4>
+<ul><li>
+<code><a href="../reference/mdro.html">mdro()</a></code>: when a base beta-lactam drug column is missing but a corresponding drug+inhibitor combination is present in the data and resistant (e.g., piperacillin/tazobactam = R while piperacillin is absent), the base drug is now correctly inferred as resistant. This ensures MDRO classification is not missed due to test-ordering differences in the laboratory. The reverse direction is also valid: susceptibility in a combination does not imply susceptibility in the base drug (the inhibitor may be responsible), so only resistance is propagated. Closes <a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a></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>
 <li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li>
 <li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where for numeric input the arguments <code>S</code>, <code>I</code>, and <code>R</code> would not be considered (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
 <li>Fixed some foreign translations of antimicrobial drugs</li>
 <li>Fixed a bug for printing column names to the console when using <code>mutate_at(vars(...), as.mic)</code> (<a href="https://github.com/msberends/AMR/issues/249" class="external-link">#249</a>)</li>
 <li>Fixed a bug to disregard <code>NI</code> for susceptibility proportion functions</li>
 <li>Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (<a href="https://github.com/msberends/AMR/issues/256" class="external-link">#256</a>)</li>
+<li>Fixed SIR and MIC coercion of combined values, e.g. <code>as.sir("&lt;= 0.002; S")</code> or <code>as.mic("S; 0.002")</code> (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li>
 </ul></div>
 <div class="section level4">
-<h4 id="updates-3-0-1-9026">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9026"></a></h4>
+<h4 id="updates-3-0-1-9030">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9030"></a></h4>
 <ul><li>
 <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> gained the argument <code>guideline</code>, which defaults to EUCAST, for interpreting the ‘I’ category correctly.</li>
 <li>

news/index.md

@@ -1,6 +1,6 @@
 # Changelog
 
-## AMR 3.0.1.9026
+## AMR 3.0.1.9030
 
 #### New
 
@@ -45,6 +45,24 @@
 
 #### Fixes
 
+- [`mdro()`](https://amr-for-r.org/reference/mdro.md): when a base
+  beta-lactam drug column is missing but a corresponding drug+inhibitor
+  combination is present in the data and resistant (e.g.,
+  piperacillin/tazobactam = R while piperacillin is absent), the base
+  drug is now correctly inferred as resistant. This ensures MDRO
+  classification is not missed due to test-ordering differences in the
+  laboratory. The reverse direction is also valid: susceptibility in a
+  combination does not imply susceptibility in the base drug (the
+  inhibitor may be responsible), so only resistance is propagated.
+  Closes [\#209](https://github.com/msberends/AMR/issues/209)
+- Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
+  where values that were purely numeric (e.g., `"1"`) and matched the
+  broad SIR-matching regex would be incorrectly stripped of all content
+  by the Unicode letter filter
+- Fixed a bug in [`as.mic()`](https://amr-for-r.org/reference/as.mic.md)
+  where MIC values in scientific notation (e.g., `"1e-3"`) were
+  incorrectly handled because the letter `e` was removed along with
+  other Unicode letters; scientific notation `e` is now preserved
 - Fixed a bug in [`as.ab()`](https://amr-for-r.org/reference/as.ab.md)
   where certain AB codes containing “PH” or “TH” (such as `ETH`, `MTH`,
   `PHE`, `PHN`, `STH`, `THA`, `THI1`) would incorrectly return `NA` when
@@ -64,6 +82,9 @@
 - Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo
   and CoPS to Stafilococco coagulasi-positivo
   ([\#256](https://github.com/msberends/AMR/issues/256))
+- Fixed SIR and MIC coercion of combined values,
+  e.g. `as.sir("<= 0.002; S")` or `as.mic("S; 0.002")`
+  ([\#252](https://github.com/msberends/AMR/issues/252))
 
 #### Updates