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https://github.com/msberends/AMR.git
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Built site for AMR: 2.0.0.9013@9de19fd
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="">2.0.0.9012</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9013</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 +201,31 @@
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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] R R R I R R S I I I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R R S S I R S R S 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">sir</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.9486833 0.9486833 0.9486833 -0.9486833 0.9486833 0.9486833</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9486833 -0.9486833 -0.9486833 -0.9486833</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.9486833 0.9486833 -0.9486833 -0.9486833 -0.9486833 0.9486833</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9486833 0.9486833 -0.9486833 0.9486833</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] 0.002 64 0.002 1 4 <=0.001 4 <=0.001 >=128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.025 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.005 0.25 >=256 <=0.002 1 <=0.002 0.5 1 128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 4 </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] -0.9379400 1.2735605 -0.9379400 0.3869379 0.6824788 -1.0857105</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.6824788 -1.0857105 1.4213310 -0.3994858</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.07476790 -0.13959336 1.51738462 -1.29380847 0.19180224 -1.29380847</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.02610444 0.19180224 1.35168682 0.52319783</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] -0.9379400 1.2735605 -0.9379400 0.3869379 0.6824788 -1.0857105</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.6824788 -1.0857105 1.4213310 -0.3994858</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.07476790 -0.13959336 1.51738462 -1.29380847 0.19180224 -1.29380847</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.02610444 0.19180224 1.35168682 0.52319783</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] 48 44 10 38 45 41 41 29 7 18</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 22 44 8 29 39 44 15 49 11 24</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] 1.0456655 0.7826050 -1.4534093 0.3880142 0.8483701 0.5853096</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.5853096 -0.2038719 -1.6507046 -0.9272883</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.43795351 1.04435068 -1.38123800 0.03368873 0.70746337 1.04435068</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.90959576 1.38123800 -1.17910561 -0.30319859</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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@ -236,21 +236,21 @@
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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 R 20 <=1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 31 4 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 31 2 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 21 >=16 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 29 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 17 >=16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 26 2 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 30 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 19 >=16 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 25 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 20 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 23 0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 25 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 19 16 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 24 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 28 0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 31 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 22 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 21 0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 30 0.5 1</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",</span>
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<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.31240582 0.04314601 0.13961536 0.16220114 0.57419394 -0.13482592</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.09526481 0.05645479 0.08412615 -0.51724084</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.07375917 -0.63113176 -0.27390329 -0.21345353 0.03479741 -0.33098765</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.54821445 0.07224506 -0.75118940 0.61916787</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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@ -267,16 +267,16 @@
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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",</span>
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<span class="r-msg co"><span class="r-pr">#></span> and "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 I 31 2 >=16 0.13961536 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 D R 21 >=16 1 0.16220114 0.02258578</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I S 19 >=16 >=16 0.08412615 0.05548921</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H S 30 8 2 0.05645479 0.08316057</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B R 31 4 0.25 0.04314601 0.09646935</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G S 26 2 >=16 -0.09526481 0.23488017</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F I 17 >=16 8 -0.13482592 0.27444128</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 E R 29 4 8 0.57419394 0.43457858</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A R 20 <=1 4 -0.31240582 0.45202118</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 25 2 2 -0.51724084 0.65685620</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C I 25 0.5 1 -0.27390329 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F I 28 0.5 0.5 -0.33098765 0.05708436</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 D S 19 16 0.5 -0.21345353 0.06044977</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A S 20 2 2 -0.07375917 0.20014413</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 24 1 2 0.03479741 0.30870071</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H S 22 8 1 0.07224506 0.34614835</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B S 23 0.5 0.5 -0.63113176 0.35722847</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I S 21 0.5 0.5 -0.75118940 0.47728611</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J R 30 0.5 1 0.61916787 0.89307117</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G R 31 4 4 1.54821445 1.82211774</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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