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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9131@db28301
This commit is contained in:
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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="">1.8.2.9126</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9131</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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@ -201,31 +201,30 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_sir</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">sir</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S S S R S I S R S S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R R I I I I R S S S</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</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 1.8973666 -0.4743416 -0.4743416</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4743416 1.8973666 -0.4743416 -0.4743416</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.449138 1.449138 -0.621059 -0.621059 -0.621059 -0.621059 1.449138</span>
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<span class="r-out co"><span class="r-pr">#></span> [8] -0.621059 -0.621059 -0.621059</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] 1 0.025 0.25 16 0.0625 <=0.001 0.5 0.01 32 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] >=128 32 0.25 2 0.5 0.002 0.025 64 8 64 </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] 0.23783965 -0.74097859 -0.13000382 0.97352658 -0.49784728 -1.59508466</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.05391792 -0.98410989 1.15744831 1.52529178</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.10682807 0.73345287 -0.57336033 -0.01329753 -0.38667273 -1.87378587</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.19352311 0.92014047 0.36007767 0.92014047</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] 0.23783965 -0.74097859 -0.13000382 0.97352658 -0.49784728 -1.59508466</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.05391792 -0.98410989 1.15744831 1.52529178</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.10682807 0.73345287 -0.57336033 -0.01329753 -0.38667273 -1.87378587</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.19352311 0.92014047 0.36007767 0.92014047</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] 14 25 22 37 32 46 42 49 34 49</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 40 43 7 33 17 6 43 34 8 46</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] -1.75679087 -0.83656708 -1.08753720 0.16731342 -0.25097012 0.92022379</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.58559696 1.17119391 -0.08365671 1.17119391</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.7494646 0.9322608 -1.2612940 0.3229400 -0.6519732 -1.3222261</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.9322608 0.3838721 -1.2003619 1.1150570</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>
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<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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@ -235,22 +234,22 @@
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<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>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 20 <=0.25 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 19 1 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 28 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 19 <=0.25 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 29 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 27 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 28 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 25 0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 19 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 22 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 29 <=2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 21 >=8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 31 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 19 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 21 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 31 <=2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 20 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 25 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 24 >=8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 20 >=8 2</span>
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<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>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.29224437 -0.04269298 -0.12726465 -0.81461826 0.24072419 -0.18648338</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.33589052 0.64003364 0.11169208 0.13496321</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.2859019 0.4406350 0.3166812 -0.7958139 -0.6894550 0.6117315</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7426344 0.3145374 0.9171062 -0.0868861</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
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@ -266,17 +265,17 @@
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C S 28 1 1 -0.12726465 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F S 27 1 1 -0.18648338 0.05921873</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 B S 19 1 16 -0.04269298 0.08457167</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A S 20 <=0.25 16 -0.29224437 0.16497972</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I I 19 4 8 0.11169208 0.23895672</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 J S 22 2 8 0.13496321 0.26222785</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E S 29 2 2 0.24072419 0.36798884</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 G I 28 8 1 0.33589052 0.46315517</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 D I 19 <=0.25 2 -0.81461826 0.68735362</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H R 25 0.5 4 0.64003364 0.76729829</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C R 31 4 1 0.3166812 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H R 25 4 2 0.3145374 0.002143877</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 B R 21 >=8 2 0.4406350 0.123953772</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F R 31 <=2 4 0.6117315 0.295050227</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J S 20 >=8 2 -0.0868861 0.403567331</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I R 24 >=8 4 0.9171062 0.600424979</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 A I 29 <=2 2 -0.2859019 0.602583175</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 E I 21 4 1 -0.6894550 1.006136186</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 G S 20 4 1 -0.7426344 1.059315640</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D S 19 4 1 -0.7958139 1.112495094</span>
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<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>
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<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
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<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>
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