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<dd><p>a vector of class <ahref="as.rsi.html">rsi</a>, <ahref="as.rsi.html">rsi</a> or <ahref="as.rsi.html">rsi</a>, or a <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a> containing columns of any of these classes</p></dd>
<dt>...</dt>
<dd><p>variables to select (supports tidy selection such as <code>column1:column4</code> and <code><ahref="https://tidyselect.r-lib.org/reference/language.html"class="external-link">where(is.mic)</a></code>), and can thus also be <ahref="antibiotic_class_selectors.html">antibiotic selectors</a></p></dd>
<dt>combine_SI</dt>
<dd><p>a <ahref="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 input only consists of S+I vs. R (susceptible vs. resistant), defaults to <code>TRUE</code></p></dd>
<p>The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand. For common numeric data this distance is equal to <ahref="https://en.wikipedia.org/wiki/Standard_score"class="external-link">Z scores</a> (the number of standard deviations from the mean).</p>
<p>MIC values (see <code><ahref="as.mic.html">as.mic()</a></code>) are transformed with <code><ahref="https://rdrr.io/r/base/Log.html"class="external-link">log2()</a></code> first; their distance is calculated as <code>(log2(x) - mean(log2(x))) / sd(log2(x))</code>.</p>
<p>R/SI values (see <code><ahref="as.rsi.html">as.rsi()</a></code>) are transformed using <code>"S"</code> = 1, <code>"I"</code> = 2, and <code>"R"</code> = 3. If <code>combine_SI</code> is <code>TRUE</code> (default), the <code>"I"</code> will be considered to be 1.</p>
<p>For data sets, the mean AMR distance will be calculated per variable, after which the mean of all columns will returned per row (using <code><ahref="https://rdrr.io/r/base/colSums.html"class="external-link">rowMeans()</a></code>), see <em>Examples</em>.</p>
<p>Isolates with distances less than 0.01 difference from each other should be considered similar. Differences lower than 0.025 should be considered suspicious.</p>
<spanclass="r-in"><span> id <spanclass="op">=</span><spanclass="va">LETTERS</span><spanclass="op">[</span><spanclass="fl">1</span><spanclass="op">:</span><spanclass="fl">10</span><spanclass="op">]</span>,</span></span>
<spanclass="r-in"><span> amox <spanclass="op">=</span><spanclass="fu"><ahref="random.html">random_mic</a></span><spanclass="op">(</span><spanclass="fl">10</span>, ab <spanclass="op">=</span><spanclass="st">"amox"</span>, mo <spanclass="op">=</span><spanclass="st">"Escherichia coli"</span><spanclass="op">)</span>,</span></span>
<spanclass="r-in"><span> cipr <spanclass="op">=</span><spanclass="fu"><ahref="random.html">random_mic</a></span><spanclass="op">(</span><spanclass="fl">10</span>, ab <spanclass="op">=</span><spanclass="st">"cipr"</span>, mo <spanclass="op">=</span><spanclass="st">"Escherichia coli"</span><spanclass="op">)</span>,</span></span>
<spanclass="r-in"><span> gent <spanclass="op">=</span><spanclass="fu"><ahref="random.html">random_mic</a></span><spanclass="op">(</span><spanclass="fl">10</span>, ab <spanclass="op">=</span><spanclass="st">"gent"</span>, mo <spanclass="op">=</span><spanclass="st">"Escherichia coli"</span><spanclass="op">)</span>,</span></span>
<spanclass="r-in"><span> tobr <spanclass="op">=</span><spanclass="fu"><ahref="random.html">random_mic</a></span><spanclass="op">(</span><spanclass="fl">10</span>, ab <spanclass="op">=</span><spanclass="st">"tobr"</span>, mo <spanclass="op">=</span><spanclass="st">"Escherichia coli"</span><spanclass="op">)</span></span></span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 1</span> B_ENTRC_AVIM S S NA <spanstyle="color: #BB0000;">NaN</span></span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 2</span> B_ENTRC_AVIM S S NA <spanstyle="color: #BB0000;">NaN</span></span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 3</span> B_ENTRC_CSSL NA S NA <spanstyle="color: #BB0000;">NA</span></span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 4</span> B_ENTRC_FACM S S NA -<spanstyle="color: #BB0000;">2.66</span></span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 5</span> B_ENTRC_FACM S R R -<spanstyle="color: #BB0000;">0.423</span></span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 6</span> B_ENTRC_FACM S R R -<spanstyle="color: #BB0000;">0.423</span></span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 7</span> B_ENTRC_FACM NA R R 0.224</span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 8</span> B_ENTRC_FACM NA R R 0.224</span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 9</span> B_ENTRC_FACM NA R R 0.224</span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;">10</span> B_ENTRC_FACM NA R R 0.224</span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #949494;"># … with 53 more rows</span></span>
</code></pre></div>
</div>
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<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <atarget="_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 <atarget="_blank"href="https://www.rug.nl"class="external-link">University of Groningen</a> and <atarget="_blank"href="https://www.umcg.nl"class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
