P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 00:02:38 +02:00
Code Releases Activity

Built site for AMR@2.1.1.9221: 43660f2

Browse Source
This commit is contained in:
github-actions
2025-03-20 20:55:27 +00:00
parent fdab4a7cc4
commit 7b50a54fd5
80 changed files with 112 additions and 111 deletions
Download Patch File Download Diff File Expand all files Collapse all files

17
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="">2.1.1.9220</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9221</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">
@ -50,19 +50,19 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9220" id="amr-2119220">AMR 2.1.1.9220<a class="anchor" aria-label="anchor" href="#amr-2119220"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9221" id="amr-2119221">AMR 2.1.1.9221<a class="anchor" aria-label="anchor" href="#amr-2119221"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
<div class="section level5">
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9220">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9220"></a></h5>
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9221">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9221"></a></h5>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
</div>
<div class="section level3">
<h3 id="breaking-2-1-1-9220">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9220"></a></h3>
<h3 id="breaking-2-1-1-9221">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9221"></a></h3>
<ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li>
<li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over two years ago.</li>
</ul></div>
<div class="section level3">
<h3 id="new-2-1-1-9220">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9220"></a></h3>
<h3 id="new-2-1-1-9221">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9221"></a></h3>
<ul><li>
<strong>One Health implementation</strong>
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
@ -114,11 +114,12 @@
</ul></li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9220">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9220"></a></h3>
<h3 id="changed-2-1-1-9221">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9221"></a></h3>
<ul><li>SIR interpretation
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
<li>To get quantitative values, <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> on a <code>sir</code> object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become <code>NA</code>). Other functions using <code>sir</code> classes (e.g., <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code>) are updated to reflect the change to contain NI and SDD.</li>
<li>Combined MIC values (e.g., from CLSI) are now supported</li>
<li>The argument <code>conserve_capped_values</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code> has been replaced with <code>capped_mic_handling</code>, which allows greater flexibility in handling capped MIC values (<code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, <code>&gt;=</code>). The four available options (<code>"standard"</code>, <code>"strict"</code>, <code>"relaxed"</code>, <code>"inverse"</code>) provide full control over whether these values should be interpreted conservatively or ignored. Using <code>conserve_capped_values</code> is now deprecated and returns a warning.</li>
</ul></li>
<li>
@ -188,7 +189,7 @@
<li>Added console colours support of <code>sir</code> class for Positron</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9220">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9220"></a></h3>
<h3 id="other-2-1-1-9221">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9221"></a></h3>
<ul><li>Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way</li>
<li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
<li>Greatly improved <code>vctrs</code> integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/rowwise.html" class="external-link">rowwise()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/c_across.html" class="external-link">c_across()</a></code> are now supported for e.g. columns of class <code>mic</code>. Despite this, this <code>AMR</code> package is still zero-dependent on any other package, including <code>dplyr</code> and <code>vctrs</code>.</li>
@ -196,7 +197,7 @@
<li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
</ul></div>
<div class="section level3">
<h3 id="older-versions-2-1-1-9220">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9220"></a></h3>
<h3 id="older-versions-2-1-1-9221">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9221"></a></h3>
<p>This changelog only contains changes from AMR v3.0 (March 2025) and later.</p>
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>