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Built site for AMR: 2.0.0.9030@a4e2e25

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2023-07-10 14:52:49 +00:00
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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="">2.0.0.9028</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</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">
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</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.0.0.9028" id="amr-2009028">AMR 2.0.0.9028<a class="anchor" aria-label="anchor" href="#amr-2009028"></a></h2>
<h2 class="pkg-version" data-toc-text="2.0.0.9030" id="amr-2009030">AMR 2.0.0.9030<a class="anchor" aria-label="anchor" href="#amr-2009030"></a></h2>
<div class="section level3">
<h3 id="new-2-0-0-9028">New<a class="anchor" aria-label="anchor" href="#new-2-0-0-9028"></a></h3>
<h3 id="new-2-0-0-9030">New<a class="anchor" aria-label="anchor" href="#new-2-0-0-9030"></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</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 epidemiological cut-off (ECOFF) values. These ECOFFs can be used for MIC/disk interpretation using <code>as.sir(..., breakpoint_type = "ECOFF")</code>, which is an important new addition for veterinary microbiology.</li>
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<li>Added microbial codes for Gram-negative/positive anaerobic bacteria</li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-0-0-9028">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9028"></a></h3>
<h3 id="changed-2-0-0-9030">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9030"></a></h3>
<ul><li>Updated algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code> by giving more weight to fungi</li>
<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>When printing MO codes in a tibble, a mouse-hover now shows the full name of the microorganism</li>
<li>Plots for MIC and disk diffusion values:
<ul><li>Now have settable arguments for breakpoint type and PK/PD, like <code><a href="../reference/as.sir.html">as.sir()</a></code>
</li>
<li>Will now contain the name of the guideline table in the subtitle of the plot</li>
</ul></li>
<li>Fixed formatting for <code><a href="../reference/as.sir.html">sir_interpretation_history()</a></code>
</li>
<li>Fixed some WHONET codes for microorganisms and consequently a couple of entries in <code>clinical_breakpoints</code>
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</li>
<li>Fixed bug for indicating UTIs in <code><a href="../reference/as.sir.html">as.sir()</a></code>
</li>
<li>Greatly improved speed of <code><a href="../reference/as.sir.html">as.sir()</a></code>
</li>
</ul></div>
</div>
<div class="section level2">