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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>, keep_operators <span class="op">=</span> <span class="st">"all"</span><span class="op">)</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="va">NA_mic_</span></span>
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<span></span>
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<span><span class="fu">limit_mic_range</span><span class="op">(</span><span class="va">x</span>, <span class="va">mic_range</span>, keep_operators <span class="op">=</span> <span class="st">"edges"</span>, as.mic <span class="op">=</span> <span class="cn">TRUE</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>keep_operators</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> specifying how to handle operators (such as <code>></code> and <code><=</code>) in the input. Accepts one of three values: <code>"all"</code> (or <code>TRUE</code>) to keep all operators, <code>"none"</code> (or <code>FALSE</code>) to remove all operators, or <code>"edges"</code> to keep operators only at both ends of the range.</p></dd>
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<dt>mic_range</dt>
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<dd><p>a manual range to limit the MIC values, e.g., <code>mic_range = c(0.001, 32)</code>. Use <code>NA</code> to set no limit on one side, e.g., <code>mic_range = c(NA, 32)</code>.</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 - the default is <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 a <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector. Bear 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 SIR values, use <code><a href="as.sir.html">as.sir()</a></code> on MIC values. It supports guidelines from EUCAST (2011-2023) and CLSI (2011-2023).</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" 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" tabindex="-1"></a>x</span>
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<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co">#> Class 'mic'</span></span>
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<span id="cb1-4"><a href="#cb1-4" 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" tabindex="-1"></a></span>
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<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="fu">is.factor</span>(x)</span>
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<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a><span class="co">#> [1] TRUE</span></span>
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<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a></span>
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<span id="cb1-9"><a href="#cb1-9" 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" tabindex="-1"></a><span class="co">#> [1] 32</span></span>
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<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a></span>
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<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a><span class="fu">median</span>(x)</span>
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<span id="cb1-13"><a href="#cb1-13" 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" 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" tabindex="-1"></a><span class="co">#> Class 'mic'</span></span>
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<span id="cb1-3"><a href="#cb1-3" 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" tabindex="-1"></a></span>
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<span id="cb1-5"><a href="#cb1-5" 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" 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" tabindex="-1"></a><span class="co">#> x hospital</span></span>
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<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a><span class="co">#> 1 16 A</span></span>
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<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a><span class="co">#> 5 64 A</span></span>
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<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a><span class="co">#> 6 >=128 A</span></span>
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<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a><span class="co">#> 8 32 A</span></span>
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<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a><span class="co">#> 9 32 A</span></span>
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<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a><span class="co">#> 10 16 A</span></span></code></pre><p></p></div>
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<p>All so-called <a href="https://rdrr.io/r/base/groupGeneric.html" class="external-link">group generic functions</a> are implemented for the MIC class (such as <code>!</code>, <code>!=</code>, <code><</code>, <code>>=</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">log2()</a></code>). Some functions of the <code>stats</code> package are also implemented (such as <code><a href="https://rdrr.io/r/stats/quantile.html" class="external-link">quantile()</a></code>, <code><a href="https://rdrr.io/r/stats/median.html" class="external-link">median()</a></code>, <code><a href="https://rdrr.io/r/stats/fivenum.html" class="external-link">fivenum()</a></code>). 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://rdatatable.gitlab.io/data.table/reference/fdroplevels.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>With <code>limit_mic_range()</code>, existing MIC ranges can be limited to a defined range of MIC values. This can be useful to better compare MIC distributions.</p>
|
||
<p>For <code>ggplot2</code>, use one of the <code><a href="plot.html">scale_*_mic()</a></code> functions to plot MIC values. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.</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.sir.html">as.sir()</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/SIR 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"># limit MICs using limit_mic_range()</span></span></span>
|
||
<span class="r-in"><span><span class="fu">limit_mic_range</span><span class="op">(</span><span class="va">mic_data</span>, mic_range <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">4</span>, <span class="fl">16</span><span class="op">)</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] >=16 <=4 <=4 <=4 8 <=4 8 >=16 >=16</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.sir.html">as.sir</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> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMX' (amoxicillin), EUCAST 2023...</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> pneumoniae - assuming body site 'Meningitis'.</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</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.sir.html">as.sir</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> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2023.</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMX' (amoxicillin), EUCAST 2023...</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> pneumoniae - assuming body site 'Meningitis'.</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</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-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-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-plt img"><img src="as.mic-4.png" alt="" width="700" height="433"></span>
|
||
</code></pre></div>
|
||
</div>
|
||
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|
||
</nav></aside></div>
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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|
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||
<div class="pkgdown-footer-right">
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<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: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
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