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@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -152,7 +152,7 @@
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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 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>
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<dd><p>a vector of class <a href="as.rsi.html">rsi</a>, <a href="as.mic.html">mic</a> or <a href="as.disk.html">disk</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>
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<dt>...</dt>
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@ -173,10 +173,10 @@
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</dl></div>
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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>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>
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<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>
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<p>The mean AMR distance is effectively <a href="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>
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<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 thus calculated as <code>(log2(x) - mean(log2(x))) / sd(log2(x))</code>.</p>
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<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>
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<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>
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<p>For data sets, the mean AMR distance will be calculated per column, after which the mean per row will be returned, see <em>Examples</em>.</p>
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<p>Use <code>amr_distance_from_row()</code> to subtract distances from the distance of one row, see <em>Examples</em>.</p>
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</div>
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<div class="section level2">
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@ -188,104 +188,121 @@
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op"><-</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>
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<span class="r-in"><span><span class="va">x</span></span></span>
|
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">rsi</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_rsi</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="va">rsi</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S I S S R S S S I R</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">rsi</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.4743416 -0.4743416 -0.4743416 -0.4743416 1.8973666 -0.4743416</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4743416 -0.4743416 -0.4743416 1.8973666</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">mic</span> <span class="op"><-</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>
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<span class="r-in"><span><span class="va">mic</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.01 0.002 >=256 1 <=0.001 0.01 64 0.005 64 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] >=256 </span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.7233354 -1.0310806 1.2175417 0.1572324 -1.1636193 -0.7233354</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.9524644 -0.8558740 0.9524644 1.2175417</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] >=64 0.25 16 0.001 0.125 32 0.125 0.001 0.002 8 </span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.26281480 -0.01764874 0.94269891 -1.29263579 -0.17770669 1.10275686</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.17770669 -1.29263579 -1.13257785 0.78264097</span>
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<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
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<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.26281480 -0.01764874 0.94269891 -1.29263579 -0.17770669 1.10275686</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.17770669 -1.29263579 -1.13257785 0.78264097</span>
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||||
<span class="r-in"><span></span></span>
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||||
<span class="r-in"><span><span class="va">disk</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="va">disk</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] 17 29 32 37 48 40 28 37 40 49</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.9401430 -0.6951315 -0.3838786 0.1348763 1.2761369 0.4461291</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.7988824 0.1348763 0.4461291 1.3798878</span>
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||||
<span class="r-in"><span></span></span>
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||||
<span class="r-in"><span><span class="va">y</span> <span class="op"><-</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>
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||||
<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> amox <span class="op">=</span> <span class="fu"><a href="random.html">random_rsi</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_disk</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>
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||||
<span class="r-in"><span><span class="op">)</span></span></span>
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||||
<span class="r-in"><span><span class="va">y</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 8 1 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 32 >=4 1 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.25 4 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 16 >=4 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 >=4 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 16 1 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.5 1 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.25 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.5 1 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.125 >=8 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A R 23 >=16 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 24 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 24 8 0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 18 2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 17 4 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 22 8 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 29 2 0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 28 >=16 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 31 4 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 20 >=16 0.5</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">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "id" and "tobr"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.0410109 0.8951387 -0.4091718 0.5415853 -0.1399200 0.6721245</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.1964756 -0.6867320 -0.4492455 -0.2683146</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.76502575 -0.22559420 -0.39112580 0.14405101 -0.59747772 0.01884049</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.04569124 0.34391737 0.15560237 -0.25893050</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</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">#></span> ℹ Calculating mean AMR distance based on columns "gent" and "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">#></span> id amox cipr gent tobr amr_distance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.25 1 2 -0.6867320</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.5 1 0.5 -0.4492455</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.25 4 1 -0.4091718</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.125 >=8 0.5 -0.2683146</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.5 1 >=8 -0.1964756</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 >=4 1 2 -0.1399200</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 8 1 2 2 0.0410109</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 16 >=4 2 2 0.5415853</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 16 1 4 4 0.6721245</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 32 >=4 1 >=8 0.8951387</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 29 2 0.25 -1.2141339</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 24 8 0.25 -0.5147553</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 24 1 4 -0.1836920</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 17 4 1 -0.1743790</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 31 4 1 -0.1743790</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 18 2 4 0.1659973</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 20 >=16 0.5 0.1799668</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 22 8 2 0.5203431</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 28 >=16 1 0.5249996</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A R 23 >=16 2 0.8700324</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">%>%</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> amr_distance <span class="op">=</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-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">%>%</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">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C 4 0.25 4 1 -0.4091718 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 I 16 0.5 1 0.5 -0.4492455 0.0400737</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 J 8 0.125 >=8 0.5 -0.2683146 0.1408572</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 G 4 0.5 1 >=8 -0.1964756 0.2126962</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 >=4 1 2 -0.1399200 0.2692518</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 H 4 0.25 1 2 -0.6867320 0.2775602</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 A 8 1 2 2 0.0410109 0.4501827</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 D 16 >=4 2 2 0.5415853 0.9507571</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 F 16 1 4 4 0.6721245 1.0812963</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 B 32 >=4 1 >=8 0.8951387 1.3043105</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C S 24 8 0.25 -0.39112580 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 J S 20 >=16 0.5 -0.25893050 0.1321953</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 B I 24 1 4 -0.22559420 0.1655316</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 E S 17 4 1 -0.59747772 0.2063519</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 F S 22 8 2 0.01884049 0.4099663</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 G R 29 2 0.25 0.04569124 0.4368170</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 D R 18 2 4 0.14405101 0.5351768</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 I I 31 4 1 0.15560237 0.5467282</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 H S 28 >=16 1 0.34391737 0.7350432</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 A R 23 >=16 2 0.76502575 1.1561516</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">%>%</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">&</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">%>%</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">%>%</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">%>%</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">%>%</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="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>dist <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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">dist</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">#></span> ℹ Using column 'mo' as input for mo_genus()</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_species()</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "IPM", "MEM" and "TCY"</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "TCY", "IPM" and "MEM"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: mo [4]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo TCY IPM MEM d</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></span> mo TCY IPM MEM dist</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> B_ENTRC_AVIM S S NA 0 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B_ENTRC_AVIM S S NA 0 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></span> <span style="color: #949494;"># … with 53 more rows</span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
Reference in New Issue
Block a user