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@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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">
@ -113,11 +113,11 @@ resistance() should be used to calculate resistance, susceptibility() should be
<dt id="arg-only-all-tested">only_all_tested<a class="anchor" aria-label="anchor" href="#arg-only-all-tested"></a></dt>
<dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antimicrobials, see section <em>Combination Therapy</em> below</p></dd>
<dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antimicrobials, see section <em>Combination Therapy</em> below.</p></dd>
<dt id="arg-ab-result">ab_result<a class="anchor" aria-label="anchor" href="#arg-ab-result"></a></dt>
<dd><p>Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R"</p></dd>
<dd><p>Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R".</p></dd>
<dt id="arg-confidence-level">confidence_level<a class="anchor" aria-label="anchor" href="#arg-confidence-level"></a></dt>
@ -129,15 +129,15 @@ resistance() should be used to calculate resistance, susceptibility() should be
<dt id="arg-collapse">collapse<a class="anchor" aria-label="anchor" href="#arg-collapse"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the output values should be 'collapsed', i.e. be merged together into one value, or a character value to use for collapsing</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the output values should be 'collapsed', i.e. be merged together into one value, or a character value to use for collapsing.</p></dd>
<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns with class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns with class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></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 column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dd><p>A column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code>.</p></dd>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
@ -145,7 +145,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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 all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - 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 all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code>.</p></dd>
</dl></div>
<div class="section level2">