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Built site for AMR: 2.0.0.9015@5f9769a
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="">2.0.0.9014</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</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 +201,30 @@
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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] I I R I I I R S S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R R R I S R S I 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] -0.621059 -0.621059 1.449138 -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 1.449138</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] 0.01 8 0.025 2 0.125 0.005 128 0.01 2 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 4 128 0.5 0.025 0.002 32 128 16 0.5 128 </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] -1.0080431 0.9684558 -0.7371152 0.5585577 -0.2612383 -1.2129921</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.7882519 -1.0080431 0.5585577 0.3536087</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.07714511 0.97675198 -0.46261901 -1.24022626 -1.89583387 0.61690923</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.97675198 0.43698786 -0.46261901 0.97675198</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] -1.0080431 0.9684558 -0.7371152 0.5585577 -0.2612383 -1.2129921</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.7882519 -1.0080431 0.5585577 0.3536087</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.07714511 0.97675198 -0.46261901 -1.24022626 -1.89583387 0.61690923</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.97675198 0.43698786 -0.46261901 0.97675198</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] 10 50 31 17 26 49 37 45 28 13</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 9 46 37 23 13 47 10 23 6 38</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] -1.41392483 1.33156027 0.02745485 -0.93346493 -0.31573079 1.26292315</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.43927762 0.98837464 -0.17845653 -1.20801344</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.0287932 1.3209197 0.7493679 -0.1397127 -0.7747702 1.3844254</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9652875 -0.1397127 -1.2193105 0.8128737</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 +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 19 >=16 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 20 8 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 20 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 19 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 23 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 31 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 18 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 22 2 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 22 <=1 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 25 >=16 2</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 18 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 23 16 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 20 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 20 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 25 <=0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 22 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 26 1 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 22 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 31 2 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 19 8 0.25</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] -0.1865874 0.3129310 -0.1974612 -0.2212515 0.1561783 0.5594410</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.2653504 -0.4668135 -0.6252799 0.4034927</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.14918777 -0.03570087 0.13005928 0.13771386 -0.17506383 0.10002806</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.47691376 0.43333913 0.00264067 0.03308522</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 +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",</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 20 2 4 -0.1974612 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 A S 19 >=16 <=1 -0.1865874 0.01087383</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 D S 19 <=1 8 -0.2212515 0.02379027</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H I 22 2 <=1 -0.4668135 0.26935231</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 23 4 4 0.1561783 0.35363955</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I I 22 <=1 <=1 -0.6252799 0.42781873</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 18 2 4 0.2653504 0.46281164</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B R 20 8 <=1 0.3129310 0.51039218</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J I 25 >=16 2 0.4034927 0.60095395</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 F I 31 <=1 8 0.5594410 0.75690225</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 20 2 1 0.13005928 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 D I 20 8 2 0.13771386 0.007654579</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 F R 22 1 1 0.10002806 0.030031221</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J R 19 8 0.25 0.03308522 0.096974059</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I I 31 2 0.25 0.00264067 0.127418609</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 B I 23 16 0.25 -0.03570087 0.165760150</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 A I 18 4 2 -0.14918777 0.279247046</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 22 2 2 0.43333913 0.303279854</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E S 25 <=0.5 2 -0.17506383 0.305123107</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G I 26 1 0.25 -0.47691376 0.606973037</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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