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<img src="../logo.svg" class="logo" alt=""><h1>Mean AMR Distance</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/mean_amr_distance.R" class="external-link"><code>R/mean_amr_distance.R</code></a></small>
<div class="d-none name"><code>mean_amr_distance.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>This function calculates a normalised mean for antimicrobial resistance between multiple observations.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for default</span></span>
<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for mic</span></span>
<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for disk</span></span>
<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for rsi</span></span>
<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for data.frame</span></span>
<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">amr_distance_from_row</span><span class="op">(</span><span class="va">amr_distance</span>, <span class="va">row</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dd><p>a vector of class <a href="as.rsi.html">rsi</a>, <a href="as.rsi.html">rsi</a> or <a href="as.rsi.html">rsi</a>, or a <a href="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><a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">where(is.mic)</a></code>), and can thus also be <a href="antibiotic_class_selectors.html">antibiotic selectors</a></p></dd>
<dt>combine_SI</dt>
<dd><p>a <a href="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>
<dt>amr_distance</dt>
<dd><p>the outcome of <code>mean_amr_distance()</code></p></dd>
<dt>row</dt>
<dd><p>an index, such as a row number</p></dd>
</dl></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<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 <a href="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><a href="as.mic.html">as.mic()</a></code>) are transformed with <code><a href="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><a href="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><a href="https://rdrr.io/r/base/colSums.html" class="external-link">rowMeans()</a></code>), see <em>Examples</em>.</p>
<p>Use <code>amr_distance_from_row()</code> to subtract distances from the distance of one row, see <em>Examples</em>.</p>
</div>
<div class="section level2">
<h2 id="interpretation">Interpretation<a class="anchor" aria-label="anchor" href="#interpretation"></a></h2>
<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>
</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">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.002 0.5 0.005 0.005 1 0.005 32 0.0625 1 &gt;=64 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.1714935 0.2920876 -0.9286111 -0.9286111 0.4758210 -0.9286111</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.3944883 -0.2591128 0.4758210 1.5782217</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
<span class="r-in"><span> amox <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"amox"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> cipr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"cipr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> gent <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"gent"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 0.0625 4 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 4 8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 32 2 0.5 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 32 2 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 4 8 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 1 8 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 0.125 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &lt;=2 0.5 &gt;=16 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 32 1 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 1 4 1</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.69810970 0.10645099 -0.38692709 0.41316947 0.69213408 0.44073351</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.54222633 -0.51743382 0.45152367 0.04068523</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 0.0625 4 &lt;=0.5 -0.69810970</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 0.125 1 4 -0.54222633</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &lt;=2 0.5 &gt;=16 &lt;=0.5 -0.51743382</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 32 2 0.5 &lt;=0.5 -0.38692709</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 1 4 1 0.04068523</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 4 8 1 0.10645099</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 32 2 2 2 0.41316947</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 1 8 2 0.44073351</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 32 1 4 2 0.45152367</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 4 8 2 0.69213408</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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> amr_distance <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> check_id_C <span class="op">=</span> <span class="fu">amr_distance_from_row</span><span class="op">(</span><span class="va">amr_distance</span>, <span class="va">id</span> <span class="op">==</span> <span class="st">"C"</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">check_id_C</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">#&gt;</span> Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 32 2 0.5 &lt;=0.5 -0.38692709 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 H &lt;=2 0.5 &gt;=16 &lt;=0.5 -0.51743382 0.1305067</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 G 4 0.125 1 4 -0.54222633 0.1552992</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 A 16 0.0625 4 &lt;=0.5 -0.69810970 0.3111826</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 J 16 1 4 1 0.04068523 0.4276123</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 B 4 4 8 1 0.10645099 0.4933781</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 D 32 2 2 2 0.41316947 0.8000966</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 F 16 1 8 2 0.44073351 0.8276606</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 32 1 4 2 0.45152367 0.8384508</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 E 16 4 8 2 0.69213408 1.0790612</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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterococcus"</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_species</a></span><span class="op">(</span><span class="op">)</span> <span class="op">!=</span> <span class="st">""</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">TCY</span>, <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>d <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">d</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">#&gt;</span> Using column 'mo' as input for mo_genus()</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Using column 'mo' as input for mo_species()</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Calculating mean AMR distance based on columns "IPM", "MEM" and "TCY"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: mo [4]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo TCY IPM MEM d</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_ENTRC_AVIM S S NA <span style="color: #BB0000;">NaN</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_ENTRC_AVIM S S NA <span style="color: #BB0000;">NaN</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CSSL NA S NA <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_ENTRC_FACM S S NA -<span style="color: #BB0000;">2.66</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B_ENTRC_FACM S R R -<span style="color: #BB0000;">0.423</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_ENTRC_FACM S R R -<span style="color: #BB0000;">0.423</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 53 more rows</span></span>
</code></pre></div>
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<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>
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