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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9121@45a9697
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="">1.8.2.9120</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9121</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] S R I S S I S R S I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I R R R R R I I S 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] -0.4743416 1.8973666 -0.4743416 -0.4743416 -0.4743416 -0.4743416</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4743416 1.8973666 -0.4743416 -0.4743416</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] >=256 32 8 0.005 0.002 16 16 4 0.125 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 16 1 256 0.125 128 0.01 0.002 4 0.5 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] 1.3250871 0.7850408 0.4250100 -1.4910484 -1.7290159 0.6050254</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.6050254 0.2449945 -0.6550826 -0.1150363</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5666465 -0.1284197 1.2617128 -0.6497194 1.0879462 -1.2828998</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.6863733 0.2191134 -0.3021863 0.9141797</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] 1.3250871 0.7850408 0.4250100 -1.4910484 -1.7290159 0.6050254</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.6050254 0.2449945 -0.6550826 -0.1150363</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5666465 -0.1284197 1.2617128 -0.6497194 1.0879462 -1.2828998</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.6863733 0.2191134 -0.3021863 0.9141797</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] 50 49 21 41 42 7 13 6 10 29</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 15 35 11 14 42 16 45 41 41 47</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] 1.3154103 1.2587116 -0.3288526 0.8051218 0.8618206 -1.1226347</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7824423 -1.1793334 -0.9525385 0.1247372</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.0643966 0.2915226 -1.3355804 -1.1321925 0.7660944 -0.9966006</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.9694822 0.6982984 0.6982984 1.1050742</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 R 22 0.25 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 26 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 27 4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 30 0.25 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 17 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 30 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 19 0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 23 0.25 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 27 1 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 31 4 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 S 19 2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 23 0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 30 0.25 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 20 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 23 16 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 29 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 19 1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 28 0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 28 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 21 4 >=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" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.07399410 -0.03958601 0.56084503 0.09513514 -0.24454184 0.30038844</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.31486005 -0.91854813 0.11340013 0.37377319</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.65740570 -0.67731621 -0.39965959 0.52521431 0.54359791 0.52536651</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.78240570 0.12784483 0.09866131 0.69610233</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" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "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 27 4 16 0.56084503 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J I 31 4 2 0.37377319 0.1870718</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 F I 30 2 4 0.30038844 0.2604566</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 I R 27 1 <=0.5 0.11340013 0.4474449</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D R 30 0.25 1 0.09513514 0.4657099</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A R 22 0.25 8 0.07399410 0.4868509</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B I 26 2 2 -0.03958601 0.6004310</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 E S 17 2 8 -0.24454184 0.8053869</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 G S 19 0.5 16 -0.31486005 0.8757051</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H I 23 0.25 <=0.5 -0.91854813 1.4793932</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 30 0.25 0.5 -0.39965959 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 A S 19 2 0.5 -0.65740570 0.2577461</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 B I 23 0.5 0.5 -0.67731621 0.2776566</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G I 19 1 0.5 -0.78240570 0.3827461</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I I 28 2 2 0.09866131 0.4983209</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H R 28 0.5 0.5 0.12784483 0.5275044</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D R 20 8 4 0.52521431 0.9248739</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F S 29 8 4 0.52536651 0.9250261</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E S 23 16 >=16 0.54359791 0.9432575</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 21 4 >=16 0.69610233 1.0957619</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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