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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>
<dd><p>a <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> or <ahref="https://rdrr.io/r/base/numeric.html"class="external-link">numeric</a> vector</p></dd>
<dt>na.rm</dt>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> indicating whether missing values should be removed</p></dd>
<dt>as.mic</dt>
<dd><p>a <ahref="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>
<p>Ordered <ahref="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 <ahref="https://rdrr.io/r/base/numeric.html"class="external-link">numeric</a> value.</p>
<p>To interpret MIC values as RSI values, use <code><ahref="as.rsi.html">as.rsi()</a></code> on MIC values. It supports guidelines from EUCAST (2011-2022) and CLSI (2011-2022).</p>
<p>This class for MIC values is a quite a special data type: formally it is an ordered <ahref="https://rdrr.io/r/base/factor.html"class="external-link">factor</a> with valid MIC values as <ahref="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>
<p>This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using <ahref="https://rdrr.io/r/base/numeric.html"class="external-link">numeric</a> values in data analysis, e.g.:</p>
<spanid="cb1-6"><ahref="#cb1-6"aria-hidden="true"tabindex="-1"></a><spanclass="fu">subset</span>(df, x <spanclass="sc">></span><spanclass="dv">4</span>) <spanclass="co"># or with dplyr: df %>% filter(x > 4)</span></span>
<spanid="cb1-7"><ahref="#cb1-7"aria-hidden="true"tabindex="-1"></a><spanclass="co">#> x hospital</span></span>
<p>Using <code><ahref="https://rdrr.io/r/base/double.html"class="external-link">as.double()</a></code> or <code><ahref="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><ahref="https://rdrr.io/r/base/integer.html"class="external-link">as.integer()</a></code> on MIC values as by the <spanstyle="R">R</span> convention on <ahref="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><ahref="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 <spanstyle="R">R</span>'s <code><ahref="https://rdrr.io/r/base/NA.html"class="external-link">NA_character_</a></code>.</p>
<spanclass="r-in"><span> mo <spanclass="op">=</span><spanclass="fu"><ahref="as.mo.html">as.mo</a></span><spanclass="op">(</span><spanclass="st">"Streptococcus pneumoniae"</span><spanclass="op">)</span>,</span></span>
<spanclass="r-in"><span> ab <spanclass="op">=</span><spanclass="st">"AMX"</span>,</span></span>
<spanclass="r-in"><span> mo <spanclass="op">=</span><spanclass="fu"><ahref="as.mo.html">as.mo</a></span><spanclass="op">(</span><spanclass="st">"Streptococcus pneumoniae"</span><spanclass="op">)</span>,</span></span>
<spanclass="r-in"><span> ab <spanclass="op">=</span><spanclass="st">"AMX"</span>,</span></span>
<spanclass="r-in"><span><spanclass="fu"><ahref="plot.html">plot</a></span><spanclass="op">(</span><spanclass="va">mic_data</span>, mo <spanclass="op">=</span><spanclass="st">"E. coli"</span>, ab <spanclass="op">=</span><spanclass="st">"cipro"</span><spanclass="op">)</span></span></span>
<spanclass="r-msg co"><spanclass="r-pr">#></span>ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
<spanclass="r-in"><span><spanclass="fu">autoplot</span><spanclass="op">(</span><spanclass="va">mic_data</span>, mo <spanclass="op">=</span><spanclass="st">"E. coli"</span>, ab <spanclass="op">=</span><spanclass="st">"cipro"</span><spanclass="op">)</span></span></span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in autoplot(mic_data, mo = "E. coli", ab = "cipro"):</span> could not find function "autoplot"</span>
<spanclass="r-in"><span><spanclass="fu">autoplot</span><spanclass="op">(</span><spanclass="va">mic_data</span>, mo <spanclass="op">=</span><spanclass="st">"E. coli"</span>, ab <spanclass="op">=</span><spanclass="st">"cipro"</span>, language <spanclass="op">=</span><spanclass="st">"nl"</span><spanclass="op">)</span><spanclass="co"># Dutch</span></span></span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "nl"):</span> could not find function "autoplot"</span>
<spanclass="r-in"><span><spanclass="fu">autoplot</span><spanclass="op">(</span><spanclass="va">mic_data</span>, mo <spanclass="op">=</span><spanclass="st">"E. coli"</span>, ab <spanclass="op">=</span><spanclass="st">"cipro"</span>, language <spanclass="op">=</span><spanclass="st">"uk"</span><spanclass="op">)</span><spanclass="co"># Ukrainian</span></span></span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "uk"):</span> could not find function "autoplot"</span>
</code></pre></div>
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<p></p><p><code>AMR</code> (for R). Developed at the <atarget="_blank"href="https://www.rug.nl"class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><atarget="_blank"href="https://www.certe.nl"class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <atarget="_blank"href="https://www.umcg.nl"class="external-link">University Medical Center Groningen</a>.</p>
