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https://github.com/msberends/AMR.git
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cli-147-2091
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="">2.1.1.9051</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9052</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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@ -218,30 +218,30 @@
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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 I R S R R I I I I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R R S I I S I I R I</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 1.449138 1.449138 -0.621059</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-out co"><span class="r-pr">#></span> [1] 1.449138 1.449138 -0.621059 -0.621059 -0.621059 -0.621059 -0.621059</span>
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<span class="r-out co"><span class="r-pr">#></span> [8] -0.621059 1.449138 -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] 128 0.01 1 4 0.5 0.125 0.0625 0.01 0.25 256 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.002 0.5 0.125 128 0.25 0.5 256 0.125 0.125 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] 1.50474059 -1.18644827 0.12402228 0.51851322 -0.07322319 -0.46771414</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.66495961 -1.18644827 -0.27046866 1.70198606</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.6429088 -0.1673475 -0.5378223 1.3145519 -0.3525849 -0.1673475</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.4997893 -0.5378223 -0.5378223 1.1293145</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] 1.50474059 -1.18644827 0.12402228 0.51851322 -0.07322319 -0.46771414</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.66495961 -1.18644827 -0.27046866 1.70198606</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.6429088 -0.1673475 -0.5378223 1.3145519 -0.3525849 -0.1673475</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.4997893 -0.5378223 -0.5378223 1.1293145</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 25 20 10 7 42 36 37 21 50</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 40 45 43 14 42 40 37 15 42 11</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] 1.2084823 -0.3021206 -0.6305125 -1.2872964 -1.4843315 0.8144120</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.4203417 0.4860201 -0.5648341 1.3398391</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5182957 0.8832927 0.7372939 -1.3796886 0.6642945 0.5182957</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.2992975 -1.3066892 0.6642945 -1.5986868</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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@ -251,22 +251,22 @@
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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 17 2 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 28 2 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 19 2 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 31 4 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 25 1 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 1 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 24 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 30 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 29 2 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 21 4 4</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 17 <=0.5 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 26 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 18 4 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 22 <=0.5 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 30 <=0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 18 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 26 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 29 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 22 16 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 31 1 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">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] -0.13604780 0.41224903 -0.55390664 0.36116821 -0.57176848 -0.32254265</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.09348329 0.03500582 -0.05545497 0.73781418</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.12957466 -0.14083442 0.55230568 -0.36152662 -0.31478853 -0.33012168</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.17672648 0.13748045 -0.07163669 0.22282068</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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@ -282,17 +282,17 @@
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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 19 2 <=2 -0.55390664 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 E S 25 1 <=2 -0.57176848 0.01786185</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 F S 30 1 <=2 -0.32254265 0.23136399</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A R 17 2 <=2 -0.13604780 0.41785884</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I S 29 2 <=2 -0.05545497 0.49845167</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H I 30 1 4 0.03500582 0.58891246</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 24 1 8 0.09348329 0.64738993</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D I 31 4 <=2 0.36116821 0.91507485</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B R 28 2 <=2 0.41224903 0.96615567</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 21 4 4 0.73781418 1.29172082</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 18 4 >=8 0.55230568 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J S 31 1 4 0.22282068 0.3294850</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G I 26 8 2 0.17672648 0.3755792</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H S 29 8 1 0.13748045 0.4148252</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 A R 17 <=0.5 >=8 0.12957466 0.4227310</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I I 22 16 1 -0.07163669 0.6239424</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B I 26 <=0.5 4 -0.14083442 0.6931401</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 E I 30 <=0.5 1 -0.31478853 0.8670942</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 F S 18 4 2 -0.33012168 0.8824274</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D R 22 <=0.5 <=0.5 -0.36152662 0.9138323</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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