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<img src="../logo.svg" class="logo" alt=""><h1>Transform Input to Minimum Inhibitory Concentrations (MIC)</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/mic.R" class="external-link"><code>R/mic.R</code></a></small>
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<div class="d-none name"><code>as.mic.Rd</code></div>
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<div class="ref-description section level2">
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<p>This transforms vectors to a new class <code>mic</code>, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">as.mic</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
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<span></span>
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<span><span class="va">NA_mic_</span></span>
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<span></span>
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<span><span class="fu">is.mic</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># S3 method for mic</span></span>
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<span><span class="fu"><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels</a></span><span class="op">(</span><span class="va">x</span>, as.mic <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>x</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> or <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector</p></dd>
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<dt>na.rm</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether missing values should be removed</p></dd>
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<dt>as.mic</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the <code><mic></code> class should be kept, defaults to <code>FALSE</code></p></dd>
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<dt>...</dt>
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<dd><p>arguments passed on to methods</p></dd>
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</dl></div>
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<div class="section level2">
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<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
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<p>Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with additional class <code>mic</code>, that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> value.</p>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>To interpret MIC values as RSI values, use <code><a href="as.rsi.html">as.rsi()</a></code> on MIC values. It supports guidelines from EUCAST (2011-2022) and CLSI (2011-2022).</p>
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<p>This class for MIC values is a quite a special data type: formally it is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with valid MIC values as <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:</p>
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<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>x <span class="ot"><-</span> <span class="fu">random_mic</span>(<span class="dv">10</span>)</span>
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<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>x</span>
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<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#> Class <mic></span></span>
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<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] 16 1 8 8 64 >=128 0.0625 32 32 16</span></span>
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<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="fu">is.factor</span>(x)</span>
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<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] TRUE</span></span>
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<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a>x[<span class="dv">1</span>] <span class="sc">*</span> <span class="dv">2</span></span>
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<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] 32</span></span>
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<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="fu">median</span>(x)</span>
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<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] 26</span></span></code></pre><p></p></div>
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<p>This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> values in data analysis, e.g.:</p>
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<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>x[x <span class="sc">></span> <span class="dv">4</span>]</span>
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<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="co">#> Class <mic></span></span>
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<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] 16 8 8 64 >=128 32 32 16</span></span>
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<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>df <span class="ot"><-</span> <span class="fu">data.frame</span>(x, <span class="at">hospital =</span> <span class="st">"A"</span>)</span>
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<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="fu">subset</span>(df, x <span class="sc">></span> <span class="dv">4</span>) <span class="co"># or with dplyr: df %>% filter(x > 4)</span></span>
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<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="co">#> x hospital</span></span>
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<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="co">#> 1 16 A</span></span>
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<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="co">#> 5 64 A</span></span>
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<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="co">#> 6 >=128 A</span></span>
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<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="co">#> 8 32 A</span></span>
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<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="co">#> 9 32 A</span></span>
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<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="co">#> 10 16 A</span></span></code></pre><p></p></div>
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<p>The following <a href="https://rdrr.io/r/base/groupGeneric.html" class="external-link">generic functions</a> are implemented for the MIC class: <code>!</code>, <code>!=</code>, <code>%%</code>, <code>%/%</code>, <code>&</code>, <code>*</code>, <code>+</code>, <code>-</code>, <code>/</code>, <code><</code>, <code><=</code>, <code>==</code>, <code>></code>, <code>>=</code>, <code>^</code>, <code>|</code>, <code><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">acos()</a></code>, <code><a href="https://rdrr.io/r/base/Hyperbolic.html" class="external-link">acosh()</a></code>, <code><a href="https://rdrr.io/r/base/all.html" class="external-link">all()</a></code>, <code><a href="https://rdrr.io/r/base/any.html" class="external-link">any()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">asin()</a></code>, <code><a href="https://rdrr.io/r/base/Hyperbolic.html" class="external-link">asinh()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">atan()</a></code>, <code><a href="https://rdrr.io/r/base/Hyperbolic.html" class="external-link">atanh()</a></code>, <code><a href="https://rdrr.io/r/base/Round.html" class="external-link">ceiling()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">cos()</a></code>, <code><a href="https://rdrr.io/r/base/Hyperbolic.html" class="external-link">cosh()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">cospi()</a></code>, <code><a href="https://rdrr.io/r/base/cumsum.html" class="external-link">cummax()</a></code>, <code><a href="https://rdrr.io/r/base/cumsum.html" class="external-link">cummin()</a></code>, <code><a href="https://rdrr.io/r/base/cumsum.html" class="external-link">cumprod()</a></code>, <code><a href="https://rdrr.io/r/base/cumsum.html" class="external-link">cumsum()</a></code>, <code><a href="https://rdrr.io/r/base/Special.html" class="external-link">digamma()</a></code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp()</a></code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">expm1()</a></code>, <code><a href="https://rdrr.io/r/base/Round.html" class="external-link">floor()</a></code>, <code><a href="https://rdrr.io/r/base/Special.html" class="external-link">gamma()</a></code>, <code><a href="https://rdrr.io/r/base/Special.html" class="external-link">lgamma()</a></code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log()</a></code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log1p()</a></code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2()</a></code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log10()</a></code>, <code><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max()</a></code>, <code><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean()</a></code>, <code><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min()</a></code>, <code><a href="https://rdrr.io/r/base/prod.html" class="external-link">prod()</a></code>, <code><a href="https://rdrr.io/r/base/range.html" class="external-link">range()</a></code>, <code><a href="https://rdrr.io/r/base/Round.html" class="external-link">round()</a></code>, <code><a href="https://rdrr.io/r/base/sign.html" class="external-link">sign()</a></code>, <code><a href="https://rdrr.io/r/base/Round.html" class="external-link">signif()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">sin()</a></code>, <code><a href="https://rdrr.io/r/base/Hyperbolic.html" class="external-link">sinh()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">sinpi()</a></code>, <code><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt()</a></code>, <code><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">tan()</a></code>, <code><a href="https://rdrr.io/r/base/Hyperbolic.html" class="external-link">tanh()</a></code>, <code><a href="https://rdrr.io/r/base/Trig.html" class="external-link">tanpi()</a></code>, <code><a href="https://rdrr.io/r/base/Special.html" class="external-link">trigamma()</a></code> and <code><a href="https://rdrr.io/r/base/Round.html" class="external-link">trunc()</a></code>. Some functions of the <code>stats</code> package are also implemented: <code><a href="https://rdrr.io/r/stats/median.html" class="external-link">median()</a></code>, <code><a href="https://rdrr.io/r/stats/quantile.html" class="external-link">quantile()</a></code>, <code><a href="https://rdrr.io/r/stats/mad.html" class="external-link">mad()</a></code>, <code><a href="https://rdrr.io/r/stats/IQR.html" class="external-link">IQR()</a></code>, <code><a href="https://rdrr.io/r/stats/fivenum.html" class="external-link">fivenum()</a></code>. Also, <code><a href="https://rdrr.io/r/grDevices/boxplot.stats.html" class="external-link">boxplot.stats()</a></code> is supported. Since <code><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd()</a></code> and <code><a href="https://rdrr.io/r/stats/cor.html" class="external-link">var()</a></code> are non-generic functions, these could not be extended. Use <code><a href="https://rdrr.io/r/stats/mad.html" class="external-link">mad()</a></code> as an alternative, or use e.g. <code>sd(as.numeric(x))</code> where <code>x</code> is your vector of MIC values.</p>
|
||
<p>Using <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> or <code><a href="https://rdrr.io/r/base/numeric.html" class="external-link">as.numeric()</a></code> on MIC values will remove the operators and return a numeric vector. Do <strong>not</strong> use <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on MIC values as by the <span style="R">R</span> convention on <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a>s, it will return the index of the factor levels (which is often useless for regular users).</p>
|
||
<p>Use <code><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels()</a></code> to drop unused levels. At default, it will return a plain factor. Use <code>droplevels(..., as.mic = TRUE)</code> to maintain the <code><mic></code> class.</p>
|
||
<p><code>NA_mic_</code> is a missing value of the new <code><mic></code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||
<div class="dont-index"><p><code><a href="as.rsi.html">as.rsi()</a></code></p></div>
|
||
</div>
|
||
|
||
<div class="section level2">
|
||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">mic_data</span> <span class="op"><-</span> <span class="fu">as.mic</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">">=32"</span>, <span class="st">"1.0"</span>, <span class="st">"1"</span>, <span class="st">"1.00"</span>, <span class="fl">8</span>, <span class="st">"<=0.128"</span>, <span class="st">"8"</span>, <span class="st">"16"</span>, <span class="st">"16"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="va">mic_data</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] >=32 1 1 1 8 <=0.128 8 16 16 </span>
|
||
<span class="r-in"><span><span class="fu">is.mic</span><span class="op">(</span><span class="va">mic_data</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># this can also coerce combined MIC/RSI values:</span></span></span>
|
||
<span class="r-in"><span><span class="fu">as.mic</span><span class="op">(</span><span class="st">"<=0.002; S"</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] <=0.002</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># mathematical processing treats MICs as numeric values</span></span></span>
|
||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/fivenum.html" class="external-link">fivenum</a></span><span class="op">(</span><span class="va">mic_data</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.128 1.000 8.000 16.000 32.000</span>
|
||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/quantile.html" class="external-link">quantile</a></span><span class="op">(</span><span class="va">mic_data</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 0% 25% 50% 75% 100% </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 0.128 1.000 8.000 16.000 32.000 </span>
|
||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="va">mic_data</span> <span class="op"><</span> <span class="fl">512</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># interpret MIC values</span></span></span>
|
||
<span class="r-in"><span><span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu">as.mic</span><span class="op">(</span><span class="fl">2</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Streptococcus pneumoniae"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
|
||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMX' (amoxicillin) according to EUCAST</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
|
||
<span class="r-in"><span><span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu">as.mic</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.01</span>, <span class="fl">2</span>, <span class="fl">4</span>, <span class="fl">8</span><span class="op">)</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Streptococcus pneumoniae"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
|
||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMX' (amoxicillin) according to EUCAST</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] S R R R</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># plot MIC values, see ?plot</span></span></span>
|
||
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">mic_data</span><span class="op">)</span></span></span>
|
||
<span class="r-plt img"><img src="as.mic-1.png" alt="" width="700" height="433"></span>
|
||
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||
<span class="r-plt img"><img src="as.mic-2.png" alt="" width="700" height="433"></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> Loading required package: ggplot2</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||
<span class="r-plt img"><img src="as.mic-3.png" alt="" width="700" height="433"></span>
|
||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># Dutch</span></span></span>
|
||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||
<span class="r-plt img"><img src="as.mic-4.png" alt="" width="700" height="433"></span>
|
||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></span>
|
||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||
<span class="r-plt img"><img src="as.mic-5.png" alt="" width="700" height="433"></span>
|
||
</code></pre></div>
|
||
</div>
|
||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||
</nav></aside></div>
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown-footer-right">
|
||
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 200px;"></a></p>
|
||
</div>
|
||
|
||
</footer></div>
|
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|
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|
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