1
0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 00:23:03 +02:00

Built site for AMR@2.1.1.9250: 4a336d0

This commit is contained in:
github-actions
2025-04-21 13:45:25 +00:00
parent f12cfeeac0
commit 409fe1d197
79 changed files with 299 additions and 503 deletions

View File

@ -9,7 +9,7 @@ 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="">2.1.1.9249</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9250</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">
@ -130,7 +130,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt id="arg-overwrite">overwrite<a class="anchor" aria-label="anchor" href="#arg-overwrite"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether to overwrite non-<code>NA</code> values (default: <code>FALSE</code>). When <code>FALSE</code>, only <code>NA</code> values are modified. To ensure compliance with EUCAST guidelines, <strong>this should remain</strong> <code>FALSE</code>, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant.".</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether to overwrite non-<code>NA</code> values (default: <code>FALSE</code>). When <code>FALSE</code>, only non-SIR values are modified (i.e., any value that is not already S, I or R). To ensure compliance with EUCAST guidelines, <strong>this should remain</strong> <code>FALSE</code>, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant".</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
@ -275,22 +275,20 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<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> <span style="color: #0000BB;"> Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> Tables' v15.0 (2025). </span><span style="color: #BB0000;">This note will be shown once per session.</span></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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> TOB Tobramycin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> GEN Gentamicin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> CIP Ciprofloxacin 0.4 g x 2 iv 0.4 g x 3 iv</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab name standard_dosage high_dosage eucast_version</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 style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> TOB Tobramycin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> GEN Gentamicin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> CIP Ciprofloxacin 0.4 g x 2 iv 0.4 g x 3 iv 15</span>
<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>, version_breakpoints <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> Tables' v10.0 (2020). </span><span style="color: #BB0000;">This note will be shown once per session.</span></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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> TOB Tobramycin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> GEN Gentamicin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> CIP Ciprofloxacin 0.4 g x 2 iv 0.4 g x 3 iv</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab name standard_dosage high_dosage eucast_version</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 style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> TOB Tobramycin <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> GEN Gentamicin <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> CIP Ciprofloxacin <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>