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<img src="../logo.svg" class="logo" alt=""><h1>Calculate Antimicrobial Resistance</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/proportion.R" class="external-link"><code>R/proportion.R</code></a>, <a href="https://github.com/msberends/AMR/blob/HEAD/R/sir_df.R" class="external-link"><code>R/sir_df.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/proportion.R" class="external-link"><code>R/proportion.R</code></a>, <a href="https://github.com/msberends/AMR/blob/main/R/sir_df.R" class="external-link"><code>R/sir_df.R</code></a></small>
<div class="d-none name"><code>proportion.Rd</code></div>
</div>
@ -220,59 +114,59 @@ resistance() should be used to calculate resistance, susceptibility() should be
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>...</dt>
<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with <code><a href="as.sir.html">as.sir()</a></code> if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See <em>Examples</em>.</p></dd>
<dt>minimum</dt>
<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>
<dt>as_percent</dt>
<dt id="arg-as-percent">as_percent<a class="anchor" aria-label="anchor" href="#arg-as-percent"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the output must be returned as a hundred fold with % sign (a character). A value of <code>0.123456</code> will then be returned as <code>"12.3%"</code>.</p></dd>
<dt>only_all_tested</dt>
<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 antibiotics, see section <em>Combination Therapy</em> below</p></dd>
<dt>ab_result</dt>
<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", "I", or "R"</p></dd>
<dt>confidence_level</dt>
<dt id="arg-confidence-level">confidence_level<a class="anchor" aria-label="anchor" href="#arg-confidence-level"></a></dt>
<dd><p>the confidence level for the returned confidence interval. For the calculation, the number of S or SI isolates, and R isolates are compared with the total number of available isolates with R, S, or I by using <code><a href="https://rdrr.io/r/stats/binom.test.html" class="external-link">binom.test()</a></code>, i.e., the Clopper-Pearson method.</p></dd>
<dt>side</dt>
<dt id="arg-side">side<a class="anchor" aria-label="anchor" href="#arg-side"></a></dt>
<dd><p>the side of the confidence interval to return. The default is <code>"both"</code> for a length 2 vector, but can also be (abbreviated as) <code>"min"</code>/<code>"left"</code>/<code>"lower"</code>/<code>"less"</code> or <code>"max"</code>/<code>"right"</code>/<code>"higher"</code>/<code>"greater"</code>.</p></dd>
<dt>collapse</dt>
<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>
<dt>data</dt>
<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>
<dt>translate_ab</dt>
<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="antibiotics.html">antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dt>language</dt>
<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 <a href="AMR-options.html">package option</a> <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>combine_SI</dt>
<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 and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code></p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>A <a href="https://rdrr.io/r/base/double.html" class="external-link">double</a> or, when <code>as_percent = TRUE</code>, a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>.</p>
<p>A <a href="https://rdrr.io/r/base/double.html" class="external-link">double</a> or, when <code>as_percent = TRUE</code>, a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>.</p>
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<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@ -284,7 +178,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<h2 id="combination-therapy">Combination Therapy<a class="anchor" aria-label="anchor" href="#combination-therapy"></a></h2>
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code>susceptibility()</code> works to calculate the %SI:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span>
@ -313,7 +207,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<h2 id="interpretation-of-sir">Interpretation of SIR<a class="anchor" aria-label="anchor" href="#interpretation-of-sir"></a></h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (<a href="https://www.eucast.org/newsiandr" class="external-link">https://www.eucast.org/newsiandr</a>):</p><ul><li><p><strong>S - Susceptible, standard dosing regimen</strong><br>
A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
@ -535,7 +429,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span><span class="co"># }</span></span></span>
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@ -549,9 +443,9 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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