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2022-10-19 09:58:58 +00:00
parent 205bfb053c
commit e2e3fa9184
91 changed files with 598 additions and 596 deletions
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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="">1.8.2.9022</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
@@ -201,7 +201,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt>only_rsi_columns</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>&lt;rsi&gt;</code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>rsi</code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
<dt>custom_rules</dt>
@@ -299,7 +299,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span><span class="co"># apply EUCAST rules: some results wil be changed</span></span></span>
<span class="r-in"><span><span class="va">b</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> class &lt;rsi&gt; . Transform them on beforehand, with e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> class 'rsi'. Transform them on beforehand, with e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - a %&gt;% as.rsi(CXM:AMX)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - a %&gt;% mutate_if(is.rsi.eligible, as.rsi)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - a %&gt;% mutate(across(where(is.rsi.eligible), as.rsi))</span>
@@ -317,7 +317,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span><span class="co"># containing all details about the transformations:</span></span></span>
<span class="r-in"><span><span class="va">c</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> class &lt;rsi&gt; . Transform them on beforehand, with e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> class 'rsi'. Transform them on beforehand, with e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - a %&gt;% as.rsi(CXM:AMX)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - a %&gt;% mutate_if(is.rsi.eligible, as.rsi)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - a %&gt;% mutate(across(where(is.rsi.eligible), as.rsi))</span>