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reference/bug_drug_combinations.html
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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="">2.1.1.9231</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</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">
@ -71,43 +71,43 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>a data set with antimicrobials columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
<dd><p>A data set with antimicrobials columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dd><p>Column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt id="arg-fun">FUN<a class="anchor" aria-label="anchor" href="#arg-fun"></a></dt>
<dd><p>the function to call on the <code>mo</code> column to transform the microorganism codes - the default is <code><a href="mo_property.html">mo_shortname()</a></code></p></dd>
<dd><p>The function to call on the <code>mo</code> column to transform the microorganism codes - the default is <code><a href="mo_property.html">mo_shortname()</a></code></p></dd>
<dt id="arg-include-n-rows">include_n_rows<a class="anchor" aria-label="anchor" href="#arg-include-n-rows"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if the total number of rows must be included in the output</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if the total number of rows must be included in the output</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>arguments passed on to <code>FUN</code></p></dd>
<dd><p>Arguments passed on to <code>FUN</code></p></dd>
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of length 1 containing column names of the <a href="antimicrobials.html">antimicrobials</a> data set</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of length 1 containing column names of the <a href="antimicrobials.html">antimicrobials</a> data set</p></dd>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the package option <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>Language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the package option <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt id="arg-minimum">minimum<a class="anchor" aria-label="anchor" href="#arg-minimum"></a></dt>
<dd><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see <em>Source</em>.</p></dd>
<dd><p>The minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see <em>Source</em>.</p></dd>
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether values S, SDD, and I should be summed, so resistance will be based on only R - the default is <code>TRUE</code></p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether values S, SDD, and I should be summed, so resistance will be based on only R - the default is <code>TRUE</code></p></dd>
<dt id="arg-add-ab-group">add_ab_group<a class="anchor" aria-label="anchor" href="#arg-add-ab-group"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate where the group of the antimicrobials must be included as a first column</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate where the group of the antimicrobials must be included as a first column</p></dd>
<dt id="arg-remove-intrinsic-resistant">remove_intrinsic_resistant<a class="anchor" aria-label="anchor" href="#arg-remove-intrinsic-resistant"></a></dt>