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Built site for AMR: 2.0.0.9024@f065945

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2023-06-22 13:20:36 +00:00
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@ -10,7 +10,7 @@
<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="">2.0.0.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@ -159,10 +159,13 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.0.0.9023" id="amr-2009023">AMR 2.0.0.9023<a class="anchor" aria-label="anchor" href="#amr-2009023"></a></h2>
<h2 class="pkg-version" data-toc-text="2.0.0.9024" id="amr-2009024">AMR 2.0.0.9024<a class="anchor" aria-label="anchor" href="#amr-2009024"></a></h2>
<div class="section level3">
<h3 id="changed-2-0-0-9023">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9023"></a></h3>
<ul><li>Added oxygen tolerance from BacDive to over 25,000 bacteria in the <code>microorganisms</code> data set
<h3 id="new-2-0-0-9024">New<a class="anchor" aria-label="anchor" href="#new-2-0-0-9024"></a></h3>
<ul><li>Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to apply EUCAST Expert Rules.</li>
<li>The EUCAST dosage guideline of v13.0 has been added to the <code>dosage</code> data set</li>
<li>ECOFF: the <code>clinical_breakpoints</code> data set now contains the new column <code>ecoff</code>, in which the epidemiological cut-off (ECOFF) are available. These ECOFFs can be used for MIC/disk interpretation using <code>as.sir(..., ecoff = TRUE)</code>, which is an important new addition for veterinary microbiology.</li>
<li>Added oxygen tolerance from BacDive to over 25,000 bacteria in the <code>microorganisms</code> data set
<ul><li>Added <code><a href="../reference/mo_property.html">mo_oxygen_tolerance()</a></code> to retrieve the values</li>
<li>Added <code><a href="../reference/mo_property.html">mo_is_anaerobic()</a></code> to determine which genera/species are obligate anaerobic bacteria</li>
</ul></li>
@ -170,7 +173,10 @@
</li>
<li>Added SAS Transport files (file extension <code>.xpt</code>) to <a href="https://msberends.github.io/AMR/articles/datasets.html">our download page</a> to use in SAS software</li>
<li>Added microbial codes for Gram-negative/positive anaerobic bacteria</li>
<li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-0-0-9024">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9024"></a></h3>
<ul><li>
<code><a href="../reference/mo_property.html">mo_rank()</a></code> now returns <code>NA</code> for ‘unknown’ microorganisms (<code>B_ANAER</code>, <code>B_ANAER-NEG</code>, <code>B_ANAER-POS</code>, <code>B_GRAMN</code>, <code>B_GRAMP</code>, <code>F_FUNGUS</code>, <code>F_YEAST</code>, and <code>UNKNOWN</code>)</li>
<li>Fixed formatting for <code><a href="../reference/as.sir.html">sir_interpretation_history()</a></code>
</li>
@ -179,7 +185,11 @@
<li>Fixed a bug for <code><a href="../reference/as.mo.html">as.mo()</a></code> that led to coercion of <code>NA</code> values when using custom microorganism codes</li>
<li>Fixed usage of <code>icu_exclude</code> in <code>first_isolates()</code>
</li>
<li>Improved <code><a href="../reference/as.mo.html">as.mo()</a></code> algorithm for searching on only species names</li>
<li>Improved <code><a href="../reference/as.mo.html">as.mo()</a></code> algorithm:
<ul><li>Now allows searching on only species names</li>
<li>Fix for using the <code>keep_synonyms</code> argument when using MO codes as input</li>
<li>Fix for using the <code>minimum_matching_score</code> argument</li>
</ul></li>
<li>Updated the code table in <code>microorganisms.codes</code>
</li>
</ul></div>