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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9122@b6d2b13
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="">1.8.2.9121</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9122</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 R R R R R I I S S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I R R R S S S S 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] -0.9486833 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] -0.7745967 1.1618950 1.1618950 1.1618950 -0.7745967 -0.7745967</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7745967 -0.7745967 1.1618950 -0.7745967</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] 16 1 256 0.125 128 0.01 0.002 4 0.5 64 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.005 0.01 4 128 0.5 8 1 16 128 256 </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] 0.5666465 -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-out co"><span class="r-pr">#></span> [1] -1.68280513 -1.50019096 0.07829971 0.99137058 -0.46954282 0.26091388</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.28692864 0.44352805 0.99137058 1.17398475</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] 0.5666465 -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-out co"><span class="r-pr">#></span> [1] -1.68280513 -1.50019096 0.07829971 0.99137058 -0.46954282 0.26091388</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.28692864 0.44352805 0.99137058 1.17398475</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] 15 35 11 14 42 16 45 41 41 47</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 22 50 46 34 30 40 45 40 45 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] -1.0643966 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-out co"><span class="r-pr">#></span> [1] -2.05314598 1.25076709 0.77877951 -0.63718324 -1.10917082 0.07079814</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.66078261 0.07079814 0.66078261 0.30679193</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 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-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 23 1 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 26 2 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 22 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 20 4 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 19 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 20 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 23 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 27 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 28 >=8 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 30 4 <=0.5</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] -0.65740570 -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-out co"><span class="r-pr">#></span> [1] -0.34120857 0.06134898 0.25010555 -0.92421863 0.07471644 -0.31322538</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.11312833 -0.05183209 0.60088376 0.53030162</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 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-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 22 2 2 0.25010555 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G R 23 1 2 0.11312833 0.1369772</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E R 19 1 4 0.07471644 0.1753891</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B R 26 2 <=0.5 0.06134898 0.1887566</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J R 30 4 <=0.5 0.53030162 0.2801961</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H R 27 0.5 1 -0.05183209 0.3019376</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 I R 28 >=8 <=0.5 0.60088376 0.3507782</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F R 20 1 1 -0.31322538 0.5633309</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A R 23 1 <=0.5 -0.34120857 0.5913141</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D S 20 4 <=0.5 -0.92421863 1.1743242</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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