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Built site for AMR: 2.0.0.9018@3018fb8
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="">2.0.0.9015</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9018</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] R R R I S R S I S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I R R I R I R R R 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] 0.9486833 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] -1.1618950 0.7745967 0.7745967 -1.1618950 0.7745967 -1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.7745967 0.7745967 0.7745967 -1.1618950</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] 4 128 0.5 0.025 0.002 32 128 16 0.5 128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.0625 4 128 0.0625 0.002 0.001 8 0.001 4 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] 0.07714511 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-out co"><span class="r-pr">#></span> [1] -0.3120147 0.6680004 1.4846796 -0.3120147 -1.1231053 -1.2864411</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8313362 -1.2864411 0.6680004 0.6680004</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] 0.07714511 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-out co"><span class="r-pr">#></span> [1] -0.3120147 0.6680004 1.4846796 -0.3120147 -1.1231053 -1.2864411</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8313362 -1.2864411 0.6680004 0.6680004</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] 9 46 37 23 13 47 10 23 6 38</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 10 15 33 50 37 6 50 7 27 42</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] -1.0287932 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-out co"><span class="r-pr">#></span> [1] -1.02416943 -0.73485604 0.30667220 1.29033776 0.53812292 -1.25562015</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.29033776 -1.19775747 -0.04050388 0.82743632</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 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-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 22 1 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 27 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 27 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 30 8 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 18 0.5 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 19 8 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 27 2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 21 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 30 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 19 4 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",</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] -0.14918777 -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-out co"><span class="r-pr">#></span> [1] 0.16915536 -0.32319888 0.10243586 1.05012543 -0.67969116 -0.02029945</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.10305622 0.26675770 -0.19285261 -0.47548846</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 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-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 27 8 2 0.10243586 0.0000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G S 27 2 >=4 0.10305622 0.0006203605</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A R 22 1 >=4 0.16915536 0.0667195016</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F I 19 8 >=4 -0.02029945 0.1227353089</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 H R 21 8 2 0.26675770 0.1643218437</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I S 30 4 1 -0.19285261 0.2952884682</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B R 27 0.5 1 -0.32319888 0.4256347323</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J S 19 4 2 -0.47548846 0.5779243144</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E S 18 0.5 >=4 -0.67969116 0.7821270147</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D R 30 8 >=4 1.05012543 0.9476895794</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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