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Built site for AMR: 2.0.0.9021@766db4e
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="">2.0.0.9020</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9021</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 +218,31 @@
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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 I S I S I I R S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I I S R I R S R I 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] -0.4743416 -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 1.8973666 -0.4743416 1.8973666</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.621059 -0.621059 -0.621059 1.449138 -0.621059 1.449138 -0.621059</span>
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<span class="r-out co"><span class="r-pr">#></span> [8] 1.449138 -0.621059 -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] >=256 1 0.125 0.001 0.002 16 16 2 8 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 >=256 0.01 128 2 0.0625 0.25 >=256 <=0.005</span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 8 </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] 1.35903204 -0.01839609 -0.53493164 -1.73429005 -1.56211153 0.67031797</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.67031797 0.15378242 0.49813946 0.49813946</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.2688902 1.2713130 -1.2347441 1.1001793 0.0733772 -0.7822912</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4400238 1.2713130 -1.4058777 0.4156446</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] 1.35903204 -0.01839609 -0.53493164 -1.73429005 -1.56211153 0.67031797</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.67031797 0.15378242 0.49813946 0.49813946</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.2688902 1.2713130 -1.2347441 1.1001793 0.0733772 -0.7822912</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4400238 1.2713130 -1.4058777 0.4156446</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 49 14 39 45 24 24 8 41</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 48 34 46 9 17 8 45 43 48 23</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] 1.0096747 0.9453642 0.9453642 -1.3055030 0.3022593 0.6881223</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.6623981 -0.6623981 -1.6913659 0.4308803</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.9710659 0.1160393 0.8489193 -1.4107939 -0.9222073 -1.4718672</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.7878459 0.6656993 0.9710659 -0.5557673</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 +252,22 @@
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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 4 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 19 <=0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 27 4 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 30 >=8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 22 >=8 >=4</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 R 25 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 17 <=0.5 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 20 >=8 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 20 4 <=1</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 21 1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 22 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 30 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 19 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 28 4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 27 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 29 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 27 8 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 19 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 25 4 1</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] -0.19666410 -0.75540530 0.42065543 0.40679865 0.32292908 -0.05152683</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.21552084 -0.53867305 0.74027765 -0.56391237</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.05388613 0.61671804 -0.12926825 -0.45476979 0.55502550 -0.18356494</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.48848798 -0.05498737 0.35028931 -0.13404436</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 +283,17 @@
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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 S 27 4 >=4 0.42065543 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 D I 30 >=8 2 0.40679865 0.01385678</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E S 22 >=8 >=4 0.32292908 0.09772635</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G R 25 1 2 0.21552084 0.20513459</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I R 20 >=8 >=4 0.74027765 0.31962222</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 1 2 -0.05152683 0.47218226</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 A R 17 4 <=1 -0.19666410 0.61731953</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 17 <=0.5 >=4 -0.53867305 0.95932848</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J S 20 4 <=1 -0.56391237 0.98456780</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 B S 19 <=0.5 2 -0.75540530 1.17606073</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 1 2 -0.12926825 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J S 25 4 1 -0.13404436 0.004776111</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 F I 27 1 4 -0.18356494 0.054296697</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H I 27 8 <=0.25 -0.05498737 0.074280879</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D S 19 2 4 -0.45476979 0.325501539</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I R 19 4 4 0.35028931 0.479557557</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 29 4 8 0.48848798 0.617756223</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 E S 28 4 16 0.55502550 0.684293745</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B R 22 8 2 0.61671804 0.745986288</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A S 21 1 <=0.25 -1.05388613 0.924617881</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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