P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-03-16 00:47:49 +01:00
Code Releases Activity

Built site for AMR@3.0.1.9026: 60e8f2b

Browse Source
This commit is contained in:
github-actions
2026-03-06 11:55:19 +00:00
parent acc807a02c
commit 599302f0bd
93 changed files with 185 additions and 147 deletions
Download Patch File Download Diff File Expand all files Collapse all files

16
news/index.html
View File

@@ -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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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="3.0.1.9023" id="amr-3019023">AMR 3.0.1.9023<a class="anchor" aria-label="anchor" href="#amr-3019023"></a></h2>
<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>
<div class="section level4">
<h4 id="new-3-0-1-9023">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9023"></a></h4>
<h4 id="new-3-0-1-9026">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9026"></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>
@@ -70,7 +70,6 @@
<li>Data set <code>esbl_isolates</code> to practise with AMR modelling</li>
<li>AMR selectors <code><a href="../reference/antimicrobial_selectors.html">peptides()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">phosphonics()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">spiropyrimidinetriones()</a></code>
</li>
<li>Antimicrobials in the <code>antimicrobials</code> data set: ceftibuten/avibactam (<code>CTA</code>), kasugamycin (<code>KAS</code>), ostreogrycin (<code>OST</code>), thiostrepton (<code>THS</code>), xeruborbactam (<code>XER</code>), zorbamycin (<code>ZOR</code>)</li>
<li>Support for Wildtype (WT) / Non-wildtype (NWT) in <code><a href="../reference/as.sir.html">as.sir()</a></code>, all plotting functions, and all susceptibility/resistance functions.
<ul><li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> gained an argument <code>as_wt_nwt</code>, which defaults to <code>TRUE</code> only when <code>breakpoint_type = "ECOFF"</code> (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li>
@@ -80,11 +79,12 @@
<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>)
<ul><li>
<code><a href="../reference/interpretive_rules.html">eucast_rules()</a></code> has become a wrapper around that function.</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>
</ul></div>
<div class="section level4">
<h4 id="fixes-3-0-1-9023">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9023"></a></h4>
<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>
<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>
@@ -94,7 +94,7 @@
<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>
</ul></div>
<div class="section level4">
<h4 id="updates-3-0-1-9023">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9023"></a></h4>
<h4 id="updates-3-0-1-9026">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9026"></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>
@@ -103,7 +103,7 @@
<code>antimicrobials$group</code> is now a <code>list</code> instead of a <code>character</code>, to contain any group the drug is in (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<li>
<code><a href="../reference/ab_property.html">ab_group()</a></code> gained an argument <code>all_groups</code> to return all groups the antimicrobial drug is in (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<li>Added taniborbactam (<code>TAN</code>) and cefepime/taniborbactam (<code>FTA</code>) to the <code>antimicrobials</code> data set</li>
<li>Added to the <code>antimicrobials</code> data set: cefepime/taniborbactam (<code>FTA</code>), ceftibuten/avibactam (<code>CTA</code>), kasugamycin (<code>KAS</code>), ostreogrycin (<code>OST</code>), taniborbactam (<code>TAN</code>), thiostrepton (<code>THS</code>), xeruborbactam (<code>XER</code>), and zorbamycin (<code>ZOR</code>)</li>
<li>Added explaining message to <code><a href="../reference/as.sir.html">as.sir()</a></code> when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
<li>Updated handling of capped MIC values (<code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, <code>&gt;=</code>) in <code><a href="../reference/as.sir.html">as.sir()</a></code> in the argument <code>capped_mic_handling</code>: (<a href="https://github.com/msberends/AMR/issues/243" class="external-link">#243</a>)
<ul><li>Introduced four clearly defined options: <code>"none"</code>, <code>"conservative"</code> (default), <code>"standard"</code>, and <code>"lenient"</code>