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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9140@551aaf6
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="">1.8.2.9139</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9140</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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@ -201,31 +201,31 @@
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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] S I I I S R R S S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I R S S S S I S 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] -0.621059 -0.621059 -0.621059 -0.621059 -0.621059 1.449138 1.449138</span>
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<span class="r-out co"><span class="r-pr">#></span> [8] -0.621059 -0.621059 1.449138</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.3162278 2.8460499 -0.3162278 -0.3162278 -0.3162278 -0.3162278</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.3162278 -0.3162278 -0.3162278 -0.3162278</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 4 0.025 0.0625 0.125 0.0625 0.5 <=0.001</span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.002 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 128 64 32 16 1 0.01 16 <=0.002 0.025 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.005 </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] 1.577512974 0.679329653 1.128421314 -0.515687110 -0.218853668</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.005692162 -0.218853668 0.454783823 -1.558445654 -1.333899824</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.15947366 0.99971247 0.83995127 0.68019008 0.04114529 -1.02028511</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.68019008 -1.39123912 -0.80909230 -1.18004631</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] 1.577512974 0.679329653 1.128421314 -0.515687110 -0.218853668</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.005692162 -0.218853668 0.454783823 -1.558445654 -1.333899824</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.15947366 0.99971247 0.83995127 0.68019008 0.04114529 -1.02028511</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.68019008 -1.39123912 -0.80909230 -1.18004631</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] 13 43 12 22 29 48 33 49 46 42</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 49 12 40 43 23 38 45 41 22 20</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] -1.4620469 0.6568616 -1.5326772 -0.8263743 -0.3319623 1.0100131</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.0494412 1.0806433 0.8687525 0.5862314</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.2292581 -1.6677196 0.5245879 0.7594780 -0.8064560 0.3679945</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.9160713 0.6028846 -0.8847527 -1.0413461</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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@ -235,22 +235,22 @@
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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 1 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 17 <=0.25 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 24 >=8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 30 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 25 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 30 <=0.25 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 31 0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 24 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 29 >=8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 23 <=0.25 <=0.5</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 24 <=1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 24 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 23 <=1 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 18 >=4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 30 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 29 <=1 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 31 >=4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 23 >=4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 27 2 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 29 2 2</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] -0.8596813 -0.5504918 0.4112103 0.5953262 -0.5447542 0.1262001</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.5139604 -0.1913348 0.9435300 -0.4439648</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.45266930 -0.27782465 -0.86367766 0.26800577 0.89315898 -0.49576332</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.89729364 0.39975640 -0.33288131 -0.03539855</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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@ -266,17 +266,17 @@
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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 24 >=8 1 0.4112103 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G R 31 0.5 4 0.5139604 0.1027501</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 D R 30 1 4 0.5953262 0.1841159</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F I 30 <=0.25 16 0.1262001 0.2850102</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I R 29 >=8 4 0.9435300 0.5323197</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H I 24 1 4 -0.1913348 0.6025451</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J R 23 <=0.25 <=0.5 -0.4439648 0.8551751</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 E S 25 0.5 1 -0.5447542 0.9559645</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B I 17 <=0.25 16 -0.5504918 0.9617021</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A S 19 1 <=0.5 -0.8596813 1.2708916</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 23 <=1 <=1 -0.86367766 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F S 29 <=1 <=1 -0.49576332 0.3679143</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A S 24 <=1 4 -0.45266930 0.4110084</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 I I 27 2 <=1 -0.33288131 0.5307963</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B S 24 <=1 8 -0.27782465 0.5858530</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 J S 29 2 2 -0.03539855 0.8282791</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D R 18 >=4 4 0.26800577 1.1316834</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 23 >=4 2 0.39975640 1.2634341</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E R 30 2 8 0.89315898 1.7568366</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G S 31 >=4 16 0.89729364 1.7609713</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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