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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9143@049baf0
This commit is contained in:
github-actions
@ -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="">1.8.2.9142</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</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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@ -201,30 +201,29 @@
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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] I R I R S R R I S S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I I S I S I I I I 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] -0.7745967 1.1618950 -0.7745967 1.1618950 -0.7745967 1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.1618950 -0.7745967 -0.7745967 -0.7745967</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN</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] 128 0.125 0.025 1 1 8 0.125 <=0.01 1 0.0625</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 256 16 0.025 8 0.001 128 0.001 0.005 0.025 0.025</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] 2.0067688 -0.4415318 -1.0100096 0.2929584 0.2929584 1.0274486</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4415318 -1.3336573 0.2929584 -0.6863619</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.4628662 0.8866012 -0.4563741 0.7425349 -1.1253971 1.3187999</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.1253971 -0.7908856 -0.4563741 -0.4563741</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] 2.0067688 -0.4415318 -1.0100096 0.2929584 0.2929584 1.0274486</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4415318 -1.3336573 0.2929584 -0.6863619</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.4628662 0.8866012 -0.4563741 0.7425349 -1.1253971 1.3187999</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.1253971 -0.7908856 -0.4563741 -0.4563741</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] 19 33 9 33 40 43 40 7 39 44</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 50 32 24 26 49 40 9 34 41 14</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] -0.8390265 0.1649368 -1.5561432 0.1649368 0.6669185 0.8820535</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.6669185 -1.6995665 0.5952068 0.9537652</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.311234687 0.007244391 -0.572306852 -0.427419042 1.238790782</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.586795633 -1.658965433 0.152132201 0.659239539 -1.296745906</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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@ -234,22 +233,22 @@
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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 R 20 1 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 17 >=16 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 22 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 18 >=16 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 25 8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 18 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 28 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 19 >=16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 21 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 18 8 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 21 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 24 0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 29 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 29 >=4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 31 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 24 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 20 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 23 0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 19 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 21 2 16</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] 0.210274980 -0.189659861 -0.361042252 0.008770745 0.395772293</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -0.660927881 0.080327628 0.590266790 0.025640147 -0.099422589</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.3578553 -0.2633009 0.2567155 0.7156924 0.4223198 0.1444269</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.6445214 -0.1375992 -0.5188196 0.3829419</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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@ -265,17 +264,17 @@
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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",</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 22 2 2 -0.361042252 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 17 >=16 <=0.25 -0.189659861 0.1713824</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J I 18 8 8 -0.099422589 0.2616197</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F I 18 1 4 -0.660927881 0.2998856</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D R 18 >=16 0.5 0.008770745 0.3698130</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I R 21 1 4 0.025640147 0.3866824</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 28 4 1 0.080327628 0.4413699</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 A R 20 1 >=16 0.210274980 0.5713172</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E S 25 8 8 0.395772293 0.7568145</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H R 19 >=16 8 0.590266790 0.9513090</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 29 0.5 1 0.2567155 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F R 24 0.5 2 0.1444269 0.1122886</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J S 21 2 16 0.3829419 0.1262264</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 E I 31 2 2 0.4223198 0.1656043</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 H S 23 0.5 8 -0.1375992 0.3943147</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 D I 29 >=4 4 0.7156924 0.4589769</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B S 24 0.5 4 -0.2633009 0.5200164</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 A I 21 2 1 -0.3578553 0.6145708</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 19 1 2 -0.5188196 0.7755351</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G I 20 1 1 -0.6445214 0.9012368</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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