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reference/key_antimicrobials.html
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@@ -7,7 +7,7 @@
<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="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</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">
@@ -83,43 +83,43 @@
<dt id="arg-universal">universal<a class="anchor" aria-label="anchor" href="#arg-universal"></a></dt>
<dd><p>Names of <strong>broad-spectrum</strong> antimicrobial drugs, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antimicrobial drugs</p></dd>
<dd><p>Names of <strong>broad-spectrum</strong> antimicrobial drugs, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antimicrobial drugs.</p></dd>
<dt id="arg-gram-negative">gram_negative<a class="anchor" aria-label="anchor" href="#arg-gram-negative"></a></dt>
<dd><p>Names of antibiotic drugs for <strong>Gram-positives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antibiotic drugs</p></dd>
<dd><p>Names of antibiotic drugs for <strong>Gram-positives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antibiotic drugs.</p></dd>
<dt id="arg-gram-positive">gram_positive<a class="anchor" aria-label="anchor" href="#arg-gram-positive"></a></dt>
<dd><p>Names of antibiotic drugs for <strong>Gram-negatives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antibiotic drugs</p></dd>
<dd><p>Names of antibiotic drugs for <strong>Gram-negatives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antibiotic drugs.</p></dd>
<dt id="arg-antifungal">antifungal<a class="anchor" aria-label="anchor" href="#arg-antifungal"></a></dt>
<dd><p>Names of antifungal drugs for <strong>fungi</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antifungal drugs</p></dd>
<dd><p>Names of antifungal drugs for <strong>fungi</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antifungal drugs.</p></dd>
<dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns must be included that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <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 columns must be included that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>).</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Ignored, only in place to allow future extensions</p></dd>
<dd><p>Ignored, only in place to allow future extensions.</p></dd>
<dt id="arg-y-z">y, z<a class="anchor" aria-label="anchor" href="#arg-y-z"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vectors to compare</p></dd>
<dd><p><a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vectors to compare.</p></dd>
<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
<dd><p>Type to determine weighed isolates; can be <code>"keyantimicrobials"</code> or <code>"points"</code>, see <em>Details</em></p></dd>
<dd><p>Type to determine weighed isolates; can be <code>"keyantimicrobials"</code> or <code>"points"</code>, see <em>Details</em>.</p></dd>
<dt id="arg-ignore-i">ignore_I<a class="anchor" aria-label="anchor" href="#arg-ignore-i"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em></p></dd>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em>.</p></dd>
<dt id="arg-points-threshold">points_threshold<a class="anchor" aria-label="anchor" href="#arg-points-threshold"></a></dt>
<dd><p>Minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em></p></dd>
<dd><p>Minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em>.</p></dd>
</dl></div>
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