<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><metaname="description"content="Calculates a normalised mean for antimicrobial resistance between multiple observations, to help to identify similar isolates without comparing antibiograms by hand."><title>Calculate the Mean AMR Distance — mean_amr_distance • AMR (for R)</title><!-- favicons --><linkrel="icon"type="image/png"sizes="16x16"href="../favicon-16x16.png"><linkrel="icon"type="image/png"sizes="32x32"href="../favicon-32x32.png"><linkrel="apple-touch-icon"type="image/png"sizes="180x180"href="../apple-touch-icon.png"><linkrel="apple-touch-icon"type="image/png"sizes="120x120"href="../apple-touch-icon-120x120.png"><linkrel="apple-touch-icon"type="image/png"sizes="76x76"href="../apple-touch-icon-76x76.png"><linkrel="apple-touch-icon"type="image/png"sizes="60x60"href="../apple-touch-icon-60x60.png"><scriptsrc="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><linkhref="../deps/bootstrap-5.2.2/bootstrap.min.css"rel="stylesheet"><scriptsrc="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><linkhref="../deps/Fira_Code-0.4.5/font.css"rel="stylesheet"><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- bootstrap-toc --><scriptsrc="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js"integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- search --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js"integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js"integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js"integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww=="crossorigin="anonymous"></script><!-- pkgdown --><scriptsrc="../pkgdown.js"></script><linkhref="../extra.css"rel="stylesheet"><scriptsrc="../extra.js"></script><metaproperty="og:title"content="Calculate the Mean AMR Distance — mean_amr_distance"><metaproperty="og:description"content="Calculates a normalised mean for antimicrobial resistance between multiple observations, to help to identify similar isolates without comparing antibiograms by hand."><metaproperty="og:image"content="https://msberends.github.io/AMR/logo.svg"><metaname="twitter:card"content="summary_large_image"><metaname="twitter:creator"content="@msberends"><metaname="twitter:site"content="@msberends"><!-- mathjax
<p>Calculates a normalised mean for antimicrobial resistance between multiple observations, to help to identify similar isolates without comparing antibiograms by hand.</p>
<dd><p>a vector of class <ahref="as.sir.html">sir</a>, <ahref="as.mic.html">mic</a> or <ahref="as.disk.html">disk</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>
<dd><p>variables to select (supports <ahref="https://tidyselect.r-lib.org/reference/language.html"class="external-link">tidyselect language</a> such as <code>column1:column4</code> and <code>where(is.mic)</code>, and can thus also be <ahref="antibiotic_class_selectors.html">antibiotic selectors</a></p></dd>
<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 effectively <ahref="https://en.wikipedia.org/wiki/Standard_score"class="external-link">the Z-score</a>; a normalised numeric value to compare AMR test results which can help to identify similar isolates, without comparing antibiograms by hand.</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 thus calculated as <code>(log2(x) - mean(log2(x))) / sd(log2(x))</code>.</p>
<p>SIR values (see <code><ahref="as.sir.html">as.sir()</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>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_sir</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_disk</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 0 </span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 2</span> B_ENTRC_AVIM S S NA 0 </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>
<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>
