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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="">3.0.1.9033</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9034</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="3.0.1.9033" id="amr-3019033">AMR 3.0.1.9033<a class="anchor" aria-label="anchor" href="#amr-3019033"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9034" id="amr-3019034">AMR 3.0.1.9034<a class="anchor" aria-label="anchor" href="#amr-3019034"></a></h2>
<div class="section level4">
<h4 id="new-3-0-1-9033">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9033"></a></h4>
<h4 id="new-3-0-1-9034">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9034"></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>
@@ -76,15 +76,14 @@
<li>This transforms the output from S/R to WT/NWT</li>
<li>Functions such as <code><a href="../reference/proportion.html">susceptibility()</a></code> count WT as S and NWT as R</li>
</ul></li>
<li>
<code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, which allows future implementation of CLSI interpretive rules (<a href="https://github.com/msberends/AMR/issues/235" class="external-link">#235</a>)
<li>Function <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, which allows future implementation of CLSI interpretive rules (<a href="https://github.com/msberends/AMR/issues/235" class="external-link">#235</a>)
<ul><li>
<code><a href="../reference/interpretive_rules.html">eucast_rules()</a></code> has become a wrapper around that function</li>
</ul></li>
<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>
<li>Function <code><a href="../reference/amr_course.html">amr_course()</a></code>, which allows for automated download and unpacking of a GitHub repository for e.g. webinar use</li>
</ul></div>
<div class="section level4">
<h4 id="fixes-3-0-1-9033">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9033"></a></h4>
<h4 id="fixes-3-0-1-9034">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9034"></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>
@@ -97,7 +96,7 @@
<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-3-0-1-9033">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9033"></a></h4>
<h4 id="updates-3-0-1-9034">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9034"></a></h4>
<ul><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>
@@ -119,6 +118,7 @@
</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">

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# Changelog
## AMR 3.0.1.9033
## AMR 3.0.1.9034
#### New
@@ -35,14 +35,16 @@
- Functions such as
[`susceptibility()`](https://amr-for-r.org/reference/proportion.md)
count WT as S and NWT as R
- [`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md),
- Function
[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md),
which allows future implementation of CLSI interpretive rules
([\#235](https://github.com/msberends/AMR/issues/235))
- [`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
has become a wrapper around that function
- Two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R’s
`NA_character_` and `NA_integer_`, for use in pipelines that require
typed missing values
- Function
[`amr_course()`](https://amr-for-r.org/reference/amr_course.md), which
allows for automated download and unpacking of a GitHub repository for
e.g. webinar use
#### Fixes
@@ -126,6 +128,9 @@
- [`ab_group()`](https://amr-for-r.org/reference/ab_property.md) now
returns values consist with the AMR selectors
([\#246](https://github.com/msberends/AMR/issues/246))
- Added two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base
R’s `NA_character_` and `NA_integer_`, for use in pipelines that
require typed missing values
## AMR 3.0.1