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2023-06-22 13:20:36 +00:00
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15
reference/eucast_rules.html
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@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<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>
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@ -176,13 +176,14 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> version_breakpoints <span class="op">=</span> <span class="fl">12</span>,</span>
<span> version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,</span>
<span> version_resistant_phenotypes <span class="op">=</span> <span class="fl">1.2</span>,</span>
<span> ampc_cephalosporin_resistance <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> custom_rules <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="va">ab</span>, administration <span class="op">=</span> <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">12</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="va">ab</span>, administration <span class="op">=</span> <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">13</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
@ -221,11 +222,15 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt>version_breakpoints</dt>
<dd><p>the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "12.0", "11.0", or "10.0".</p></dd>
<dd><p>the version number to use for the EUCAST Clinical Breakpoints guideline. Can be "13.0", "12.0", "11.0", or "10.0".</p></dd>
<dt>version_expertrules</dt>
<dd><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2", or "3.1".</p></dd>
<dd><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".</p></dd>
<dt>version_resistant_phenotypes</dt>
<dd><p>the version number to use for the EUCAST Expected Resistant Phenotypes. Can be "1.2".</p></dd>
<dt>ampc_cephalosporin_resistance</dt>
@ -381,7 +386,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Tables' v12.0 (2022). This note will be shown once per session.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Tables' v13.0 (2023). This note will be shown once per session.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab name standard_dosage high_dosage </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>