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Built site for AMR@2.1.1.9116: 175a677
This commit is contained in:
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@ -7,7 +7,7 @@
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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="">2.1.1.9112</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9116</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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@ -108,30 +108,30 @@
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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 S I I S I I R I I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I I S I I S S S R 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] 1.8973666 -0.4743416 -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] -0.4743416 -0.4743416 -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 -0.4743416 1.8973666 1.8973666</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] 0.002 0.5 0.125 128 0.25 0.5 256 0.125 0.125 64 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.001 256 0.25 0.5 32 0.002 8 0.125 0.002 0.125</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] -1.6429088 -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-out co"><span class="r-pr">#></span> [1] -1.2863106 1.6478483 0.0146555 0.1779748 1.1578905 -1.1229914</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8312519 -0.1486638 -1.1229914 -0.1486638</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] -1.6429088 -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-out co"><span class="r-pr">#></span> [1] -1.2863106 1.6478483 0.0146555 0.1779748 1.1578905 -1.1229914</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8312519 -0.1486638 -1.1229914 -0.1486638</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] 40 45 43 14 42 40 37 15 42 11</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 41 29 40 12 16 7 45 46 22 9</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] 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-out co"><span class="r-pr">#></span> [1] 0.9256143 0.1488750 0.8608860 -0.9515056 -0.6925925 -1.2751469</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.1845274 1.2492556 -0.3042229 -1.1456904</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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@ -141,22 +141,22 @@
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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 <=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-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 29 <=1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 30 4 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 26 16 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 18 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 29 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 31 16 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 31 <=1 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 21 16 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 31 16 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 21 <=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] 0.12957466 -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-out co"><span class="r-pr">#></span> [1] 0.04629994 -0.34117383 0.33391321 -0.69063550 -0.19222473 0.50618460</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.02978803 0.59753857 0.58783703 -0.87752733</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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@ -172,17 +172,17 @@
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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 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-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 26 16 16 0.33391321 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F R 31 16 <=2 0.50618460 0.1722714</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I I 31 16 16 0.58783703 0.2539238</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H R 21 16 16 0.59753857 0.2636254</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 A R 29 <=1 4 0.04629994 0.2876133</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G S 31 <=1 16 0.02978803 0.3041252</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E S 29 4 4 -0.19222473 0.5261379</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B I 30 4 <=2 -0.34117383 0.6750870</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 D I 18 2 8 -0.69063550 1.0245487</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 21 <=1 4 -0.87752733 1.2114405</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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